Data wrangling (tidyverse)

Murray Logan

9 March 2026

Motivating data

load(file = "../data/manipulationDatasets.RData")

dat.1

Treatment Plot Dose Time Resp1 Resp2
Control P1 H 1 8.12 3.06
Control P1 H 2 20.55 25.94
Control P1 H 3 27.49 29.85
Control P1 H 4 44.79 25.39
Control P1 M 1 20.99 20.31
Control P1 M 2 37.54 17.62
Control P1 M 3 61.46 98.44
Control P1 M 4 82.21 160.01
Control P1 L 1 31.73 21.22
Control P1 L 2 59.08 37.51
Control P1 L 3 94.54 119.22
Control P1 L 4 121.17 116.45
Control P2 H 1 8.14 23.93
Control P2 H 2 13.36 28.02
Control P2 H 3 33.37 37.17
Control P2 H 4 39.87 38.25
Control P2 M 1 19.95 19.73
Control P2 M 2 42.83 40.52
Control P2 M 3 62.46 4.81
Control P2 M 4 81.78 136.66
Control P2 L 1 32.76 30.70
Control P2 L 2 62.35 123.78
Control P2 L 3 90.22 113.87
Control P2 L 4 114.03 76.52
Exclusion P3 H 1 21.86 23.58
Exclusion P3 H 2 39.83 28.03
Exclusion P3 H 3 59.53 21.32
Exclusion P3 H 4 75.59 90.76
Exclusion P3 M 1 38.57 30.63
Exclusion P3 M 2 81.25 83.61
Exclusion P3 M 3 124.08 124.09
Exclusion P3 M 4 159.69 112.65
Exclusion P3 L 1 61.16 39.53
Exclusion P3 L 2 119.84 110.27
Exclusion P3 L 3 175.87 286.33
Exclusion P3 L 4 238.76 54.23
Exclusion P4 H 1 18.82 28.60
Exclusion P4 H 2 39.82 39.07
Exclusion P4 H 3 63.30 93.43
Exclusion P4 H 4 82.29 60.15
Exclusion P4 M 1 39.51 45.90
Exclusion P4 M 2 79.24 88.04
Exclusion P4 M 3 122.09 84.19
Exclusion P4 M 4 161.67 256.34
Exclusion P4 L 1 57.93 85.24
Exclusion P4 L 2 117.88 167.90
Exclusion P4 L 3 181.09 314.49
Exclusion P4 L 4 242.31 304.70

Data manipulation

  • base R syntax provides ways to manipulate and access a variety of data structures
  • code can be difficult to read and keep organised
  • exacerbated for grouped data
Treatment Plot Dose Time Resp1 Resp2
Control P1 H 1 8.12 3.06
Control P1 H 2 20.55 25.94
Control P1 H 3 27.49 29.85
Control P1 H 4 44.79 25.39
Control P1 M 1 20.99 20.31
Control P1 M 2 37.54 17.62
Control P1 M 3 61.46 98.44
Control P1 M 4 82.21 160.01
Control P1 L 1 31.73 21.22
Control P1 L 2 59.08 37.51
Control P1 L 3 94.54 119.22
Control P1 L 4 121.17 116.45
Control P2 H 1 8.14 23.93
Control P2 H 2 13.36 28.02
Control P2 H 3 33.37 37.17
Control P2 H 4 39.87 38.25
Control P2 M 1 19.95 19.73
Control P2 M 2 42.83 40.52
Control P2 M 3 62.46 4.81
Control P2 M 4 81.78 136.66
Control P2 L 1 32.76 30.70
Control P2 L 2 62.35 123.78
Control P2 L 3 90.22 113.87
Control P2 L 4 114.03 76.52
Exclusion P3 H 1 21.86 23.58
Exclusion P3 H 2 39.83 28.03
Exclusion P3 H 3 59.53 21.32
Exclusion P3 H 4 75.59 90.76
Exclusion P3 M 1 38.57 30.63
Exclusion P3 M 2 81.25 83.61
Exclusion P3 M 3 124.08 124.09
Exclusion P3 M 4 159.69 112.65
Exclusion P3 L 1 61.16 39.53
Exclusion P3 L 2 119.84 110.27
Exclusion P3 L 3 175.87 286.33
Exclusion P3 L 4 238.76 54.23
Exclusion P4 H 1 18.82 28.60
Exclusion P4 H 2 39.82 39.07
Exclusion P4 H 3 63.30 93.43
Exclusion P4 H 4 82.29 60.15
Exclusion P4 M 1 39.51 45.90
Exclusion P4 M 2 79.24 88.04
Exclusion P4 M 3 122.09 84.19
Exclusion P4 M 4 161.67 256.34
Exclusion P4 L 1 57.93 85.24
Exclusion P4 L 2 117.88 167.90
Exclusion P4 L 3 181.09 314.49
Exclusion P4 L 4 242.31 304.70

Base R

Specifying variables is cumbersome

data[,]

Single variable

dat.1$Resp1
dat.1[,'Var1']
dat.1[,5]

Multiple variables

dat.1[,c("Resp1", "Resp2")]
dat.1[,5:6]

Specific rows

dat.1[c(1:4, 13:16, 25:28, 37:40),]

Sorting

dat.1[order(dat.1$Dose), ]

Filtering

dat.1[dat.1$Dose == 'H', ]

Aggregating

tapply(dat.1$Resp1,dat.1$Dose, mean)

Data manipulation

  • enter the tidyverse ecosystem
  • a coherent set of manipulation focussed packages

Data manipulation

Data manipulation

Data manipulation

Manipulation functions (verbs)

Operating on a single dataset

  • operating on the rows
Function Action
dplyr::arrange() changing the order of rows
dplyr::filter() subset of rows based on column values
dplyr::slice() subset of rows based on position

Manipulation functions (verbs)

Operating on a single dataset

  • operating on the columns
Function Action
dplyr::select() subset of columns
dplyr::rename() change the name of columns
dplyr::pull() extract a single column as a vector
dplyr::distinct() unique combinations of column values
dplyr::mutate() adding columns and modifying column values
tidyr::unite() combine multiple columns together
tidyr::separate() separating a single column into multiple columns

Manipulation functions (verbs)

Operating on a single dataset

  • operating on the rows
Function Action
dplyr::summarise() aggregating (collapsing) to a single row
dplyr::count() count the number of unique combinations
dplyr::group_by() define groups of rows
  • reshaping (pivotting) the dataset
Function Action
tidyr::pivot_longer() lengthen data from wide format
tidyr::pivot_wider() widen data from long format

Manipulation functions (verbs)

Operating on two datasets

Function Action
dplyr::*_join() merge (join) two datasets together based on common fields

Data manipulation grammar

Piping

  • %>% (magrittr package)
  • |> (native pipe)
data |>
    select(...) |>
    group_by(...) |>
    summarise(...)


Any object can be passed (piped) to any function if that object is normally the function’s first argument

Manipulating data

  • re(arranging) data
  • subsetting data
  • summarising/aggregating data
  • joining datasets
Treatment Plot Dose Time Resp1 Resp2
Control P1 H 1 8.12 3.06
Control P1 H 2 20.55 25.94
Control P1 H 3 27.49 29.85
Control P1 H 4 44.79 25.39
Control P1 M 1 20.99 20.31
Control P1 M 2 37.54 17.62
Control P1 M 3 61.46 98.44
Control P1 M 4 82.21 160.01
Control P1 L 1 31.73 21.22
Control P1 L 2 59.08 37.51
Control P1 L 3 94.54 119.22
Control P1 L 4 121.17 116.45
Control P2 H 1 8.14 23.93
Control P2 H 2 13.36 28.02
Control P2 H 3 33.37 37.17
Control P2 H 4 39.87 38.25
Control P2 M 1 19.95 19.73
Control P2 M 2 42.83 40.52
Control P2 M 3 62.46 4.81
Control P2 M 4 81.78 136.66
Control P2 L 1 32.76 30.70
Control P2 L 2 62.35 123.78
Control P2 L 3 90.22 113.87
Control P2 L 4 114.03 76.52
Exclusion P3 H 1 21.86 23.58
Exclusion P3 H 2 39.83 28.03
Exclusion P3 H 3 59.53 21.32
Exclusion P3 H 4 75.59 90.76
Exclusion P3 M 1 38.57 30.63
Exclusion P3 M 2 81.25 83.61
Exclusion P3 M 3 124.08 124.09
Exclusion P3 M 4 159.69 112.65
Exclusion P3 L 1 61.16 39.53
Exclusion P3 L 2 119.84 110.27
Exclusion P3 L 3 175.87 286.33
Exclusion P3 L 4 238.76 54.23
Exclusion P4 H 1 18.82 28.60
Exclusion P4 H 2 39.82 39.07
Exclusion P4 H 3 63.30 93.43
Exclusion P4 H 4 82.29 60.15
Exclusion P4 M 1 39.51 45.90
Exclusion P4 M 2 79.24 88.04
Exclusion P4 M 3 122.09 84.19
Exclusion P4 M 4 161.67 256.34
Exclusion P4 L 1 57.93 85.24
Exclusion P4 L 2 117.88 167.90
Exclusion P4 L 3 181.09 314.49
Exclusion P4 L 4 242.31 304.70

Data manipulation packages

library(dplyr)
library(tidyr)
#OR to get the entire ecosystem
library(tidyverse)

Data files

head(dat.1)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
3   Control   P1    H    3 27.49 29.85
4   Control   P1    H    4 44.79 25.39
5   Control   P1    M    1 20.99 20.31
6   Control   P1    M    2 37.54 17.62
#OR
dat.1 |> head()
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
3   Control   P1    H    3 27.49 29.85
4   Control   P1    H    4 44.79 25.39
5   Control   P1    M    1 20.99 20.31
6   Control   P1    M    2 37.54 17.62

Data files

summary(dat.1)
     Treatment  Plot    Dose        Time          Resp1            Resp2       
 Control  :24   P1:12   H:16   Min.   :1.00   Min.   :  8.12   Min.   :  3.06  
 Exclusion:24   P2:12   L:16   1st Qu.:1.75   1st Qu.: 36.50   1st Qu.: 28.03  
                P3:12   M:16   Median :2.50   Median : 61.31   Median : 50.06  
                P4:12          Mean   :2.50   Mean   : 75.27   Mean   : 81.71  
                               3rd Qu.:3.25   3rd Qu.: 99.41   3rd Qu.:112.95  
                               Max.   :4.00   Max.   :242.31   Max.   :314.49

Data files

summary(dat.1)
     Treatment  Plot    Dose        Time          Resp1            Resp2       
 Control  :24   P1:12   H:16   Min.   :1.00   Min.   :  8.12   Min.   :  3.06  
 Exclusion:24   P2:12   L:16   1st Qu.:1.75   1st Qu.: 36.50   1st Qu.: 28.03  
                P3:12   M:16   Median :2.50   Median : 61.31   Median : 50.06  
                P4:12          Mean   :2.50   Mean   : 75.27   Mean   : 81.71  
                               3rd Qu.:3.25   3rd Qu.: 99.41   3rd Qu.:112.95  
                               Max.   :4.00   Max.   :242.31   Max.   :314.49  
dat.1 |> summary()
     Treatment  Plot    Dose        Time          Resp1            Resp2       
 Control  :24   P1:12   H:16   Min.   :1.00   Min.   :  8.12   Min.   :  3.06  
 Exclusion:24   P2:12   L:16   1st Qu.:1.75   1st Qu.: 36.50   1st Qu.: 28.03  
                P3:12   M:16   Median :2.50   Median : 61.31   Median : 50.06  
                P4:12          Mean   :2.50   Mean   : 75.27   Mean   : 81.71  
                               3rd Qu.:3.25   3rd Qu.: 99.41   3rd Qu.:112.95  
                               Max.   :4.00   Max.   :242.31   Max.   :314.49

Data files

str(dat.1)
'data.frame':   48 obs. of  6 variables:
 $ Treatment: Factor w/ 2 levels "Control","Exclusion": 1 1 1 1 1 1 1 1 1 1 ...
 $ Plot     : Factor w/ 4 levels "P1","P2","P3",..: 1 1 1 1 1 1 1 1 1 1 ...
 $ Dose     : Factor w/ 3 levels "H","L","M": 1 1 1 1 3 3 3 3 2 2 ...
 $ Time     : int  1 2 3 4 1 2 3 4 1 2 ...
 $ Resp1    : num  8.12 20.55 27.49 44.79 20.99 ...
 $ Resp2    : num  3.06 25.94 29.85 25.39 20.31 ...
 - attr(*, "out.attrs")=List of 2
  ..$ dim     : Named int [1:3] 4 3 4
  .. ..- attr(*, "names")= chr [1:3] "Time" "Dose" "Plot"
  ..$ dimnames:List of 3
  .. ..$ Time: chr [1:4] "Time=1" "Time=2" "Time=3" "Time=4"
  .. ..$ Dose: chr [1:3] "Dose=H" "Dose=M" "Dose=L"
  .. ..$ Plot: chr [1:4] "Plot=P1" "Plot=P2" "Plot=P3" "Plot=P4"

Dense summary

glimpse(dat.1)
Rows: 48
Columns: 6
$ Treatment <fct> Control, Control, Control, Control, Control, Control, Control, Control…
$ Plot      <fct> P1, P1, P1, P1, P1, P1, P1, P1, P1, P1, P1, P1, P2, P2, P2, P2, P2, P2…
$ Dose      <fct> H, H, H, H, M, M, M, M, L, L, L, L, H, H, H, H, M, M, M, M, L, L, L, L…
$ Time      <int> 1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4…
$ Resp1     <dbl> 8.12, 20.55, 27.49, 44.79, 20.99, 37.54, 61.46, 82.21, 31.73, 59.08, 9…
$ Resp2     <dbl> 3.06, 25.94, 29.85, 25.39, 20.31, 17.62, 98.44, 160.01, 21.22, 37.51, …

Dataframes and tibbles

Dataframes and tibbles

dat.1 |> as_tibble()
# A tibble: 48 × 6
   Treatment Plot  Dose   Time Resp1  Resp2
   <fct>     <fct> <fct> <int> <dbl>  <dbl>
 1 Control   P1    H         1  8.12   3.06
 2 Control   P1    H         2 20.6   25.9 
 3 Control   P1    H         3 27.5   29.8 
 4 Control   P1    H         4 44.8   25.4 
 5 Control   P1    M         1 21.0   20.3 
 6 Control   P1    M         2 37.5   17.6 
 7 Control   P1    M         3 61.5   98.4 
 8 Control   P1    M         4 82.2  160.  
 9 Control   P1    L         1 31.7   21.2 
10 Control   P1    L         2 59.1   37.5 
# ℹ 38 more rows

Tidyverse and tidy evaluation

Base R

Recall, specifying variables is cumbersome

data[,]

Single variable

dat.1$Resp1
dat.1[,'Var1']
dat.1[,5]

Multiple variables

dat.1[,c("Resp1", "Resp2")]
dat.1[,5:6]

Specific rows

dat.1[c(1:4, 13:16, 25:28, 37:40),]

Sorting

dat.1[order(dat.1$Dose), ]

Filtering

dat.1[dat.1$Dose == 'H', ]

Aggregating

tapply(dat.1$Resp1,dat.1$Dose,mean)

Tidy evaluation

  • data-masking - refer to variables directly
    • e.g. arrange(dat.1, Resp1)
    • e.g. filter(dat.1, Resp1 > 10)
    • applies to:
      • arrange()
      • filter()
      • count()
      • mutate()
      • summarise()
      • group_by()

Tidy evaluation

  • data-masking - refer to variables directly
  • tidy-selection - refer to variables by position, name or type
    • e.g. select(dat.1, Resp1)
    • e.g. select(dat.1, starts_with("Resp"))
    • e.g. select(dat.1, where(is.numeric))
    • applies it to:
      • select(), rename()
      • pull()
      • across()

Tidy evaluation

  • data-masking - refer to variables directly
  • tidy-selection - refer to variables by position, name or type
tidy-selection Examples
contains() 
select(dat.1, contains("esp"))
starts_with() 
select(dat.1, starts_with("Resp"))
ends_with() 
select(dat.1, ends_with("e"))
matches() 
select(dat.1, matches("^R.*[0-9]$"))
num_range() 
select(dat.1, num_range("Resp", 1:2))
where() 
select(dat.1, where(is.numeric))

Summary and vectorised functions

Summary and vectorised functions

  • take a vector and return a single value
    • e.g. mean()

  • take a vector and return a vector
    • e.g. log()

Sorting data


Sorting data (arrange)

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Sorting by Resp1

dat.1 |> arrange(Resp1)
   Treatment Plot Dose Time  Resp1  Resp2
1    Control   P1    H    1   8.12   3.06
2    Control   P2    H    1   8.14  23.93
3    Control   P2    H    2  13.36  28.02
4  Exclusion   P4    H    1  18.82  28.60
5    Control   P2    M    1  19.95  19.73
6    Control   P1    H    2  20.55  25.94
7    Control   P1    M    1  20.99  20.31
8  Exclusion   P3    H    1  21.86  23.58
9    Control   P1    H    3  27.49  29.85
10   Control   P1    L    1  31.73  21.22
11   Control   P2    L    1  32.76  30.70
12   Control   P2    H    3  33.37  37.17
13   Control   P1    M    2  37.54  17.62
14 Exclusion   P3    M    1  38.57  30.63
15 Exclusion   P4    M    1  39.51  45.90
16 Exclusion   P4    H    2  39.82  39.07
17 Exclusion   P3    H    2  39.83  28.03
18   Control   P2    H    4  39.87  38.25
19   Control   P2    M    2  42.83  40.52
20   Control   P1    H    4  44.79  25.39
21 Exclusion   P4    L    1  57.93  85.24
22   Control   P1    L    2  59.08  37.51
23 Exclusion   P3    H    3  59.53  21.32
24 Exclusion   P3    L    1  61.16  39.53
25   Control   P1    M    3  61.46  98.44
26   Control   P2    L    2  62.35 123.78
27   Control   P2    M    3  62.46   4.81
28 Exclusion   P4    H    3  63.30  93.43
29 Exclusion   P3    H    4  75.59  90.76
30 Exclusion   P4    M    2  79.24  88.04
31 Exclusion   P3    M    2  81.25  83.61
32   Control   P2    M    4  81.78 136.66
33   Control   P1    M    4  82.21 160.01
34 Exclusion   P4    H    4  82.29  60.15
35   Control   P2    L    3  90.22 113.87
36   Control   P1    L    3  94.54 119.22
37   Control   P2    L    4 114.03  76.52
38 Exclusion   P4    L    2 117.88 167.90
39 Exclusion   P3    L    2 119.84 110.27
40   Control   P1    L    4 121.17 116.45
41 Exclusion   P4    M    3 122.09  84.19
42 Exclusion   P3    M    3 124.08 124.09
43 Exclusion   P3    M    4 159.69 112.65
44 Exclusion   P4    M    4 161.67 256.34
45 Exclusion   P3    L    3 175.87 286.33
46 Exclusion   P4    L    3 181.09 314.49
47 Exclusion   P3    L    4 238.76  54.23
48 Exclusion   P4    L    4 242.31 304.70

Sorting data (arrange)

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Sorting by Resp1 (descending order)

dat.1 |> arrange(desc(Resp1))
   Treatment Plot Dose Time  Resp1  Resp2
1  Exclusion   P4    L    4 242.31 304.70
2  Exclusion   P3    L    4 238.76  54.23
3  Exclusion   P4    L    3 181.09 314.49
4  Exclusion   P3    L    3 175.87 286.33
5  Exclusion   P4    M    4 161.67 256.34
6  Exclusion   P3    M    4 159.69 112.65
7  Exclusion   P3    M    3 124.08 124.09
8  Exclusion   P4    M    3 122.09  84.19
9    Control   P1    L    4 121.17 116.45
10 Exclusion   P3    L    2 119.84 110.27
11 Exclusion   P4    L    2 117.88 167.90
12   Control   P2    L    4 114.03  76.52
13   Control   P1    L    3  94.54 119.22
14   Control   P2    L    3  90.22 113.87
15 Exclusion   P4    H    4  82.29  60.15
16   Control   P1    M    4  82.21 160.01
17   Control   P2    M    4  81.78 136.66
18 Exclusion   P3    M    2  81.25  83.61
19 Exclusion   P4    M    2  79.24  88.04
20 Exclusion   P3    H    4  75.59  90.76
21 Exclusion   P4    H    3  63.30  93.43
22   Control   P2    M    3  62.46   4.81
23   Control   P2    L    2  62.35 123.78
24   Control   P1    M    3  61.46  98.44
25 Exclusion   P3    L    1  61.16  39.53
26 Exclusion   P3    H    3  59.53  21.32
27   Control   P1    L    2  59.08  37.51
28 Exclusion   P4    L    1  57.93  85.24
29   Control   P1    H    4  44.79  25.39
30   Control   P2    M    2  42.83  40.52
31   Control   P2    H    4  39.87  38.25
32 Exclusion   P3    H    2  39.83  28.03
33 Exclusion   P4    H    2  39.82  39.07
34 Exclusion   P4    M    1  39.51  45.90
35 Exclusion   P3    M    1  38.57  30.63
36   Control   P1    M    2  37.54  17.62
37   Control   P2    H    3  33.37  37.17
38   Control   P2    L    1  32.76  30.70
39   Control   P1    L    1  31.73  21.22
40   Control   P1    H    3  27.49  29.85
41 Exclusion   P3    H    1  21.86  23.58
42   Control   P1    M    1  20.99  20.31
43   Control   P1    H    2  20.55  25.94
44   Control   P2    M    1  19.95  19.73
45 Exclusion   P4    H    1  18.82  28.60
46   Control   P2    H    2  13.36  28.02
47   Control   P2    H    1   8.14  23.93
48   Control   P1    H    1   8.12   3.06

Sorting data (arrange)

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Sorting by Dose and then Resp1

dat.1 |> arrange(Dose, Resp1)
   Treatment Plot Dose Time  Resp1  Resp2
1    Control   P1    H    1   8.12   3.06
2    Control   P2    H    1   8.14  23.93
3    Control   P2    H    2  13.36  28.02
4  Exclusion   P4    H    1  18.82  28.60
5    Control   P1    H    2  20.55  25.94
6  Exclusion   P3    H    1  21.86  23.58
7    Control   P1    H    3  27.49  29.85
8    Control   P2    H    3  33.37  37.17
9  Exclusion   P4    H    2  39.82  39.07
10 Exclusion   P3    H    2  39.83  28.03
11   Control   P2    H    4  39.87  38.25
12   Control   P1    H    4  44.79  25.39
13 Exclusion   P3    H    3  59.53  21.32
14 Exclusion   P4    H    3  63.30  93.43
15 Exclusion   P3    H    4  75.59  90.76
16 Exclusion   P4    H    4  82.29  60.15
17   Control   P1    L    1  31.73  21.22
18   Control   P2    L    1  32.76  30.70
19 Exclusion   P4    L    1  57.93  85.24
20   Control   P1    L    2  59.08  37.51
21 Exclusion   P3    L    1  61.16  39.53
22   Control   P2    L    2  62.35 123.78
23   Control   P2    L    3  90.22 113.87
24   Control   P1    L    3  94.54 119.22
25   Control   P2    L    4 114.03  76.52
26 Exclusion   P4    L    2 117.88 167.90
27 Exclusion   P3    L    2 119.84 110.27
28   Control   P1    L    4 121.17 116.45
29 Exclusion   P3    L    3 175.87 286.33
30 Exclusion   P4    L    3 181.09 314.49
31 Exclusion   P3    L    4 238.76  54.23
32 Exclusion   P4    L    4 242.31 304.70
33   Control   P2    M    1  19.95  19.73
34   Control   P1    M    1  20.99  20.31
35   Control   P1    M    2  37.54  17.62
36 Exclusion   P3    M    1  38.57  30.63
37 Exclusion   P4    M    1  39.51  45.90
38   Control   P2    M    2  42.83  40.52
39   Control   P1    M    3  61.46  98.44
40   Control   P2    M    3  62.46   4.81
41 Exclusion   P4    M    2  79.24  88.04
42 Exclusion   P3    M    2  81.25  83.61
43   Control   P2    M    4  81.78 136.66
44   Control   P1    M    4  82.21 160.01
45 Exclusion   P4    M    3 122.09  84.19
46 Exclusion   P3    M    3 124.08 124.09
47 Exclusion   P3    M    4 159.69 112.65
48 Exclusion   P4    M    4 161.67 256.34

Sorting data (arrange)

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Sort by the sum of Resp1 and Resp2

dat.1 |> arrange(Resp1 + Resp2)
   Treatment Plot Dose Time  Resp1  Resp2
1    Control   P1    H    1   8.12   3.06
2    Control   P2    H    1   8.14  23.93
3    Control   P2    M    1  19.95  19.73
4    Control   P1    M    1  20.99  20.31
5    Control   P2    H    2  13.36  28.02
6  Exclusion   P3    H    1  21.86  23.58
7    Control   P1    H    2  20.55  25.94
8  Exclusion   P4    H    1  18.82  28.60
9    Control   P1    L    1  31.73  21.22
10   Control   P1    M    2  37.54  17.62
11   Control   P1    H    3  27.49  29.85
12   Control   P2    L    1  32.76  30.70
13   Control   P2    M    3  62.46   4.81
14 Exclusion   P3    H    2  39.83  28.03
15 Exclusion   P3    M    1  38.57  30.63
16   Control   P1    H    4  44.79  25.39
17   Control   P2    H    3  33.37  37.17
18   Control   P2    H    4  39.87  38.25
19 Exclusion   P4    H    2  39.82  39.07
20 Exclusion   P3    H    3  59.53  21.32
21   Control   P2    M    2  42.83  40.52
22 Exclusion   P4    M    1  39.51  45.90
23   Control   P1    L    2  59.08  37.51
24 Exclusion   P3    L    1  61.16  39.53
25 Exclusion   P4    H    4  82.29  60.15
26 Exclusion   P4    L    1  57.93  85.24
27 Exclusion   P4    H    3  63.30  93.43
28   Control   P1    M    3  61.46  98.44
29 Exclusion   P3    M    2  81.25  83.61
30 Exclusion   P3    H    4  75.59  90.76
31 Exclusion   P4    M    2  79.24  88.04
32   Control   P2    L    2  62.35 123.78
33   Control   P2    L    4 114.03  76.52
34   Control   P2    L    3  90.22 113.87
35 Exclusion   P4    M    3 122.09  84.19
36   Control   P1    L    3  94.54 119.22
37   Control   P2    M    4  81.78 136.66
38 Exclusion   P3    L    2 119.84 110.27
39   Control   P1    L    4 121.17 116.45
40   Control   P1    M    4  82.21 160.01
41 Exclusion   P3    M    3 124.08 124.09
42 Exclusion   P3    M    4 159.69 112.65
43 Exclusion   P4    L    2 117.88 167.90
44 Exclusion   P3    L    4 238.76  54.23
45 Exclusion   P4    M    4 161.67 256.34
46 Exclusion   P3    L    3 175.87 286.33
47 Exclusion   P4    L    3 181.09 314.49
48 Exclusion   P4    L    4 242.31 304.70

Your turn

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
  • sort by Treatment and then Time

Your turn

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
  • sort by Treatment and then Time
dat.1 |> arrange(Treatment, Time)
   Treatment Plot Dose Time  Resp1  Resp2
1    Control   P1    H    1   8.12   3.06
2    Control   P1    M    1  20.99  20.31
3    Control   P1    L    1  31.73  21.22
4    Control   P2    H    1   8.14  23.93
5    Control   P2    M    1  19.95  19.73
6    Control   P2    L    1  32.76  30.70
7    Control   P1    H    2  20.55  25.94
8    Control   P1    M    2  37.54  17.62
9    Control   P1    L    2  59.08  37.51
10   Control   P2    H    2  13.36  28.02
11   Control   P2    M    2  42.83  40.52
12   Control   P2    L    2  62.35 123.78
13   Control   P1    H    3  27.49  29.85
14   Control   P1    M    3  61.46  98.44
15   Control   P1    L    3  94.54 119.22
16   Control   P2    H    3  33.37  37.17
17   Control   P2    M    3  62.46   4.81
18   Control   P2    L    3  90.22 113.87
19   Control   P1    H    4  44.79  25.39
20   Control   P1    M    4  82.21 160.01
21   Control   P1    L    4 121.17 116.45
22   Control   P2    H    4  39.87  38.25
23   Control   P2    M    4  81.78 136.66
24   Control   P2    L    4 114.03  76.52
25 Exclusion   P3    H    1  21.86  23.58
26 Exclusion   P3    M    1  38.57  30.63
27 Exclusion   P3    L    1  61.16  39.53
28 Exclusion   P4    H    1  18.82  28.60
29 Exclusion   P4    M    1  39.51  45.90
30 Exclusion   P4    L    1  57.93  85.24
31 Exclusion   P3    H    2  39.83  28.03
32 Exclusion   P3    M    2  81.25  83.61
33 Exclusion   P3    L    2 119.84 110.27
34 Exclusion   P4    H    2  39.82  39.07
35 Exclusion   P4    M    2  79.24  88.04
36 Exclusion   P4    L    2 117.88 167.90
37 Exclusion   P3    H    3  59.53  21.32
38 Exclusion   P3    M    3 124.08 124.09
39 Exclusion   P3    L    3 175.87 286.33
40 Exclusion   P4    H    3  63.30  93.43
41 Exclusion   P4    M    3 122.09  84.19
42 Exclusion   P4    L    3 181.09 314.49
43 Exclusion   P3    H    4  75.59  90.76
44 Exclusion   P3    M    4 159.69 112.65
45 Exclusion   P3    L    4 238.76  54.23
46 Exclusion   P4    H    4  82.29  60.15
47 Exclusion   P4    M    4 161.67 256.34
48 Exclusion   P4    L    4 242.31 304.70

Your turn

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
  • sort by Treatment and then the mean of Resp1 and Resp2

Your turn

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
  • sort by Treatment and then the mean of Resp1 and Resp2
dat.1 |> arrange(Treatment, mean(c(Resp1, Resp2)))
   Treatment Plot Dose Time  Resp1  Resp2
1    Control   P1    H    1   8.12   3.06
2    Control   P1    H    2  20.55  25.94
3    Control   P1    H    3  27.49  29.85
4    Control   P1    H    4  44.79  25.39
5    Control   P1    M    1  20.99  20.31
6    Control   P1    M    2  37.54  17.62
7    Control   P1    M    3  61.46  98.44
8    Control   P1    M    4  82.21 160.01
9    Control   P1    L    1  31.73  21.22
10   Control   P1    L    2  59.08  37.51
11   Control   P1    L    3  94.54 119.22
12   Control   P1    L    4 121.17 116.45
13   Control   P2    H    1   8.14  23.93
14   Control   P2    H    2  13.36  28.02
15   Control   P2    H    3  33.37  37.17
16   Control   P2    H    4  39.87  38.25
17   Control   P2    M    1  19.95  19.73
18   Control   P2    M    2  42.83  40.52
19   Control   P2    M    3  62.46   4.81
20   Control   P2    M    4  81.78 136.66
21   Control   P2    L    1  32.76  30.70
22   Control   P2    L    2  62.35 123.78
23   Control   P2    L    3  90.22 113.87
24   Control   P2    L    4 114.03  76.52
25 Exclusion   P3    H    1  21.86  23.58
26 Exclusion   P3    H    2  39.83  28.03
27 Exclusion   P3    H    3  59.53  21.32
28 Exclusion   P3    H    4  75.59  90.76
29 Exclusion   P3    M    1  38.57  30.63
30 Exclusion   P3    M    2  81.25  83.61
31 Exclusion   P3    M    3 124.08 124.09
32 Exclusion   P3    M    4 159.69 112.65
33 Exclusion   P3    L    1  61.16  39.53
34 Exclusion   P3    L    2 119.84 110.27
35 Exclusion   P3    L    3 175.87 286.33
36 Exclusion   P3    L    4 238.76  54.23
37 Exclusion   P4    H    1  18.82  28.60
38 Exclusion   P4    H    2  39.82  39.07
39 Exclusion   P4    H    3  63.30  93.43
40 Exclusion   P4    H    4  82.29  60.15
41 Exclusion   P4    M    1  39.51  45.90
42 Exclusion   P4    M    2  79.24  88.04
43 Exclusion   P4    M    3 122.09  84.19
44 Exclusion   P4    M    4 161.67 256.34
45 Exclusion   P4    L    1  57.93  85.24
46 Exclusion   P4    L    2 117.88 167.90
47 Exclusion   P4    L    3 181.09 314.49
48 Exclusion   P4    L    4 242.31 304.70

Subset columns


Selecting columns (select)

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> select(Treatment, Plot, Dose, Time, Resp1)
   Treatment Plot Dose Time  Resp1
1    Control   P1    H    1   8.12
2    Control   P1    H    2  20.55
3    Control   P1    H    3  27.49
4    Control   P1    H    4  44.79
5    Control   P1    M    1  20.99
6    Control   P1    M    2  37.54
7    Control   P1    M    3  61.46
8    Control   P1    M    4  82.21
9    Control   P1    L    1  31.73
10   Control   P1    L    2  59.08
11   Control   P1    L    3  94.54
12   Control   P1    L    4 121.17
13   Control   P2    H    1   8.14
14   Control   P2    H    2  13.36
15   Control   P2    H    3  33.37
16   Control   P2    H    4  39.87
17   Control   P2    M    1  19.95
18   Control   P2    M    2  42.83
19   Control   P2    M    3  62.46
20   Control   P2    M    4  81.78
21   Control   P2    L    1  32.76
22   Control   P2    L    2  62.35
23   Control   P2    L    3  90.22
24   Control   P2    L    4 114.03
25 Exclusion   P3    H    1  21.86
26 Exclusion   P3    H    2  39.83
27 Exclusion   P3    H    3  59.53
28 Exclusion   P3    H    4  75.59
29 Exclusion   P3    M    1  38.57
30 Exclusion   P3    M    2  81.25
31 Exclusion   P3    M    3 124.08
32 Exclusion   P3    M    4 159.69
33 Exclusion   P3    L    1  61.16
34 Exclusion   P3    L    2 119.84
35 Exclusion   P3    L    3 175.87
36 Exclusion   P3    L    4 238.76
37 Exclusion   P4    H    1  18.82
38 Exclusion   P4    H    2  39.82
39 Exclusion   P4    H    3  63.30
40 Exclusion   P4    H    4  82.29
41 Exclusion   P4    M    1  39.51
42 Exclusion   P4    M    2  79.24
43 Exclusion   P4    M    3 122.09
44 Exclusion   P4    M    4 161.67
45 Exclusion   P4    L    1  57.93
46 Exclusion   P4    L    2 117.88
47 Exclusion   P4    L    3 181.09
48 Exclusion   P4    L    4 242.31

Selecting columns (select)

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> select(-Resp2)
   Treatment Plot Dose Time  Resp1
1    Control   P1    H    1   8.12
2    Control   P1    H    2  20.55
3    Control   P1    H    3  27.49
4    Control   P1    H    4  44.79
5    Control   P1    M    1  20.99
6    Control   P1    M    2  37.54
7    Control   P1    M    3  61.46
8    Control   P1    M    4  82.21
9    Control   P1    L    1  31.73
10   Control   P1    L    2  59.08
11   Control   P1    L    3  94.54
12   Control   P1    L    4 121.17
13   Control   P2    H    1   8.14
14   Control   P2    H    2  13.36
15   Control   P2    H    3  33.37
16   Control   P2    H    4  39.87
17   Control   P2    M    1  19.95
18   Control   P2    M    2  42.83
19   Control   P2    M    3  62.46
20   Control   P2    M    4  81.78
21   Control   P2    L    1  32.76
22   Control   P2    L    2  62.35
23   Control   P2    L    3  90.22
24   Control   P2    L    4 114.03
25 Exclusion   P3    H    1  21.86
26 Exclusion   P3    H    2  39.83
27 Exclusion   P3    H    3  59.53
28 Exclusion   P3    H    4  75.59
29 Exclusion   P3    M    1  38.57
30 Exclusion   P3    M    2  81.25
31 Exclusion   P3    M    3 124.08
32 Exclusion   P3    M    4 159.69
33 Exclusion   P3    L    1  61.16
34 Exclusion   P3    L    2 119.84
35 Exclusion   P3    L    3 175.87
36 Exclusion   P3    L    4 238.76
37 Exclusion   P4    H    1  18.82
38 Exclusion   P4    H    2  39.82
39 Exclusion   P4    H    3  63.30
40 Exclusion   P4    H    4  82.29
41 Exclusion   P4    M    1  39.51
42 Exclusion   P4    M    2  79.24
43 Exclusion   P4    M    3 122.09
44 Exclusion   P4    M    4 161.67
45 Exclusion   P4    L    1  57.93
46 Exclusion   P4    L    2 117.88
47 Exclusion   P4    L    3 181.09
48 Exclusion   P4    L    4 242.31

Selecting columns (select)

Selection helper functions

Helper function description Ignore case
contains() Var names containing “string” TRUE
starts_with() Var names starting with “string” TRUE
ends_with() Var names ending with “string” TRUE
matches() Var names matched with regexp TRUE
num_range() Var names starting with “string” followed by “numbers” TRUE
everything() Select all variables - useful in combination with others
all_of() Checks that all nominated variables are present
any_of() Acts on those nominated variables that do exist
where() Acts on those variables for which a function returns TRUE
if_any() Combine multiple filter selects
if_all() Combine multiple filter selects

must evaluate to TRUE/FALSE

Selecting columns (select)

Selection helper functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> select(contains("R"))
   Treatment  Resp1  Resp2
1    Control   8.12   3.06
2    Control  20.55  25.94
3    Control  27.49  29.85
4    Control  44.79  25.39
5    Control  20.99  20.31
6    Control  37.54  17.62
7    Control  61.46  98.44
8    Control  82.21 160.01
9    Control  31.73  21.22
10   Control  59.08  37.51
11   Control  94.54 119.22
12   Control 121.17 116.45
13   Control   8.14  23.93
14   Control  13.36  28.02
15   Control  33.37  37.17
16   Control  39.87  38.25
17   Control  19.95  19.73
18   Control  42.83  40.52
19   Control  62.46   4.81
20   Control  81.78 136.66
21   Control  32.76  30.70
22   Control  62.35 123.78
23   Control  90.22 113.87
24   Control 114.03  76.52
25 Exclusion  21.86  23.58
26 Exclusion  39.83  28.03
27 Exclusion  59.53  21.32
28 Exclusion  75.59  90.76
29 Exclusion  38.57  30.63
30 Exclusion  81.25  83.61
31 Exclusion 124.08 124.09
32 Exclusion 159.69 112.65
33 Exclusion  61.16  39.53
34 Exclusion 119.84 110.27
35 Exclusion 175.87 286.33
36 Exclusion 238.76  54.23
37 Exclusion  18.82  28.60
38 Exclusion  39.82  39.07
39 Exclusion  63.30  93.43
40 Exclusion  82.29  60.15
41 Exclusion  39.51  45.90
42 Exclusion  79.24  88.04
43 Exclusion 122.09  84.19
44 Exclusion 161.67 256.34
45 Exclusion  57.93  85.24
46 Exclusion 117.88 167.90
47 Exclusion 181.09 314.49
48 Exclusion 242.31 304.70

Selecting columns (select)

Selection helper functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> select(starts_with("R"))
    Resp1  Resp2
1    8.12   3.06
2   20.55  25.94
3   27.49  29.85
4   44.79  25.39
5   20.99  20.31
6   37.54  17.62
7   61.46  98.44
8   82.21 160.01
9   31.73  21.22
10  59.08  37.51
11  94.54 119.22
12 121.17 116.45
13   8.14  23.93
14  13.36  28.02
15  33.37  37.17
16  39.87  38.25
17  19.95  19.73
18  42.83  40.52
19  62.46   4.81
20  81.78 136.66
21  32.76  30.70
22  62.35 123.78
23  90.22 113.87
24 114.03  76.52
25  21.86  23.58
26  39.83  28.03
27  59.53  21.32
28  75.59  90.76
29  38.57  30.63
30  81.25  83.61
31 124.08 124.09
32 159.69 112.65
33  61.16  39.53
34 119.84 110.27
35 175.87 286.33
36 238.76  54.23
37  18.82  28.60
38  39.82  39.07
39  63.30  93.43
40  82.29  60.15
41  39.51  45.90
42  79.24  88.04
43 122.09  84.19
44 161.67 256.34
45  57.93  85.24
46 117.88 167.90
47 181.09 314.49
48 242.31 304.70

Selecting columns (select)

Selection helper functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> select(ends_with("e"))
   Dose Time
1     H    1
2     H    2
3     H    3
4     H    4
5     M    1
6     M    2
7     M    3
8     M    4
9     L    1
10    L    2
11    L    3
12    L    4
13    H    1
14    H    2
15    H    3
16    H    4
17    M    1
18    M    2
19    M    3
20    M    4
21    L    1
22    L    2
23    L    3
24    L    4
25    H    1
26    H    2
27    H    3
28    H    4
29    M    1
30    M    2
31    M    3
32    M    4
33    L    1
34    L    2
35    L    3
36    L    4
37    H    1
38    H    2
39    H    3
40    H    4
41    M    1
42    M    2
43    M    3
44    M    4
45    L    1
46    L    2
47    L    3
48    L    4

Selecting columns (select)

Selection helper functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> select(matches("^.{4}$"))
   Plot Dose Time
1    P1    H    1
2    P1    H    2
3    P1    H    3
4    P1    H    4
5    P1    M    1
6    P1    M    2
7    P1    M    3
8    P1    M    4
9    P1    L    1
10   P1    L    2
11   P1    L    3
12   P1    L    4
13   P2    H    1
14   P2    H    2
15   P2    H    3
16   P2    H    4
17   P2    M    1
18   P2    M    2
19   P2    M    3
20   P2    M    4
21   P2    L    1
22   P2    L    2
23   P2    L    3
24   P2    L    4
25   P3    H    1
26   P3    H    2
27   P3    H    3
28   P3    H    4
29   P3    M    1
30   P3    M    2
31   P3    M    3
32   P3    M    4
33   P3    L    1
34   P3    L    2
35   P3    L    3
36   P3    L    4
37   P4    H    1
38   P4    H    2
39   P4    H    3
40   P4    H    4
41   P4    M    1
42   P4    M    2
43   P4    M    3
44   P4    M    4
45   P4    L    1
46   P4    L    2
47   P4    L    3
48   P4    L    4

Regular expressions (regexp)

Selecting columns (select)

Selection helper functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> select(Treatment:Time)
   Treatment Plot Dose Time
1    Control   P1    H    1
2    Control   P1    H    2
3    Control   P1    H    3
4    Control   P1    H    4
5    Control   P1    M    1
6    Control   P1    M    2
7    Control   P1    M    3
8    Control   P1    M    4
9    Control   P1    L    1
10   Control   P1    L    2
11   Control   P1    L    3
12   Control   P1    L    4
13   Control   P2    H    1
14   Control   P2    H    2
15   Control   P2    H    3
16   Control   P2    H    4
17   Control   P2    M    1
18   Control   P2    M    2
19   Control   P2    M    3
20   Control   P2    M    4
21   Control   P2    L    1
22   Control   P2    L    2
23   Control   P2    L    3
24   Control   P2    L    4
25 Exclusion   P3    H    1
26 Exclusion   P3    H    2
27 Exclusion   P3    H    3
28 Exclusion   P3    H    4
29 Exclusion   P3    M    1
30 Exclusion   P3    M    2
31 Exclusion   P3    M    3
32 Exclusion   P3    M    4
33 Exclusion   P3    L    1
34 Exclusion   P3    L    2
35 Exclusion   P3    L    3
36 Exclusion   P3    L    4
37 Exclusion   P4    H    1
38 Exclusion   P4    H    2
39 Exclusion   P4    H    3
40 Exclusion   P4    H    4
41 Exclusion   P4    M    1
42 Exclusion   P4    M    2
43 Exclusion   P4    M    3
44 Exclusion   P4    M    4
45 Exclusion   P4    L    1
46 Exclusion   P4    L    2
47 Exclusion   P4    L    3
48 Exclusion   P4    L    4

Selecting columns (select)

Selection helper functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> select(num_range('Resp', 1:2), everything())
    Resp1  Resp2 Treatment Plot Dose Time
1    8.12   3.06   Control   P1    H    1
2   20.55  25.94   Control   P1    H    2
3   27.49  29.85   Control   P1    H    3
4   44.79  25.39   Control   P1    H    4
5   20.99  20.31   Control   P1    M    1
6   37.54  17.62   Control   P1    M    2
7   61.46  98.44   Control   P1    M    3
8   82.21 160.01   Control   P1    M    4
9   31.73  21.22   Control   P1    L    1
10  59.08  37.51   Control   P1    L    2
11  94.54 119.22   Control   P1    L    3
12 121.17 116.45   Control   P1    L    4
13   8.14  23.93   Control   P2    H    1
14  13.36  28.02   Control   P2    H    2
15  33.37  37.17   Control   P2    H    3
16  39.87  38.25   Control   P2    H    4
17  19.95  19.73   Control   P2    M    1
18  42.83  40.52   Control   P2    M    2
19  62.46   4.81   Control   P2    M    3
20  81.78 136.66   Control   P2    M    4
21  32.76  30.70   Control   P2    L    1
22  62.35 123.78   Control   P2    L    2
23  90.22 113.87   Control   P2    L    3
24 114.03  76.52   Control   P2    L    4
25  21.86  23.58 Exclusion   P3    H    1
26  39.83  28.03 Exclusion   P3    H    2
27  59.53  21.32 Exclusion   P3    H    3
28  75.59  90.76 Exclusion   P3    H    4
29  38.57  30.63 Exclusion   P3    M    1
30  81.25  83.61 Exclusion   P3    M    2
31 124.08 124.09 Exclusion   P3    M    3
32 159.69 112.65 Exclusion   P3    M    4
33  61.16  39.53 Exclusion   P3    L    1
34 119.84 110.27 Exclusion   P3    L    2
35 175.87 286.33 Exclusion   P3    L    3
36 238.76  54.23 Exclusion   P3    L    4
37  18.82  28.60 Exclusion   P4    H    1
38  39.82  39.07 Exclusion   P4    H    2
39  63.30  93.43 Exclusion   P4    H    3
40  82.29  60.15 Exclusion   P4    H    4
41  39.51  45.90 Exclusion   P4    M    1
42  79.24  88.04 Exclusion   P4    M    2
43 122.09  84.19 Exclusion   P4    M    3
44 161.67 256.34 Exclusion   P4    M    4
45  57.93  85.24 Exclusion   P4    L    1
46 117.88 167.90 Exclusion   P4    L    2
47 181.09 314.49 Exclusion   P4    L    3
48 242.31 304.70 Exclusion   P4    L    4

Selecting columns (select)

Selection helper functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Exclude a set of variables (that may not exist)

vars <- c("Plot", "fish")
dat.1 |> select(-any_of(vars))
   Treatment Dose Time  Resp1  Resp2
1    Control    H    1   8.12   3.06
2    Control    H    2  20.55  25.94
3    Control    H    3  27.49  29.85
4    Control    H    4  44.79  25.39
5    Control    M    1  20.99  20.31
6    Control    M    2  37.54  17.62
7    Control    M    3  61.46  98.44
8    Control    M    4  82.21 160.01
9    Control    L    1  31.73  21.22
10   Control    L    2  59.08  37.51
11   Control    L    3  94.54 119.22
12   Control    L    4 121.17 116.45
13   Control    H    1   8.14  23.93
14   Control    H    2  13.36  28.02
15   Control    H    3  33.37  37.17
16   Control    H    4  39.87  38.25
17   Control    M    1  19.95  19.73
18   Control    M    2  42.83  40.52
19   Control    M    3  62.46   4.81
20   Control    M    4  81.78 136.66
21   Control    L    1  32.76  30.70
22   Control    L    2  62.35 123.78
23   Control    L    3  90.22 113.87
24   Control    L    4 114.03  76.52
25 Exclusion    H    1  21.86  23.58
26 Exclusion    H    2  39.83  28.03
27 Exclusion    H    3  59.53  21.32
28 Exclusion    H    4  75.59  90.76
29 Exclusion    M    1  38.57  30.63
30 Exclusion    M    2  81.25  83.61
31 Exclusion    M    3 124.08 124.09
32 Exclusion    M    4 159.69 112.65
33 Exclusion    L    1  61.16  39.53
34 Exclusion    L    2 119.84 110.27
35 Exclusion    L    3 175.87 286.33
36 Exclusion    L    4 238.76  54.23
37 Exclusion    H    1  18.82  28.60
38 Exclusion    H    2  39.82  39.07
39 Exclusion    H    3  63.30  93.43
40 Exclusion    H    4  82.29  60.15
41 Exclusion    M    1  39.51  45.90
42 Exclusion    M    2  79.24  88.04
43 Exclusion    M    3 122.09  84.19
44 Exclusion    M    4 161.67 256.34
45 Exclusion    L    1  57.93  85.24
46 Exclusion    L    2 117.88 167.90
47 Exclusion    L    3 181.09 314.49
48 Exclusion    L    4 242.31 304.70

Selecting columns (select)

Selection helper functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Select numeric variables

dat.1 |> select(where(is.numeric))
   Time  Resp1  Resp2
1     1   8.12   3.06
2     2  20.55  25.94
3     3  27.49  29.85
4     4  44.79  25.39
5     1  20.99  20.31
6     2  37.54  17.62
7     3  61.46  98.44
8     4  82.21 160.01
9     1  31.73  21.22
10    2  59.08  37.51
11    3  94.54 119.22
12    4 121.17 116.45
13    1   8.14  23.93
14    2  13.36  28.02
15    3  33.37  37.17
16    4  39.87  38.25
17    1  19.95  19.73
18    2  42.83  40.52
19    3  62.46   4.81
20    4  81.78 136.66
21    1  32.76  30.70
22    2  62.35 123.78
23    3  90.22 113.87
24    4 114.03  76.52
25    1  21.86  23.58
26    2  39.83  28.03
27    3  59.53  21.32
28    4  75.59  90.76
29    1  38.57  30.63
30    2  81.25  83.61
31    3 124.08 124.09
32    4 159.69 112.65
33    1  61.16  39.53
34    2 119.84 110.27
35    3 175.87 286.33
36    4 238.76  54.23
37    1  18.82  28.60
38    2  39.82  39.07
39    3  63.30  93.43
40    4  82.29  60.15
41    1  39.51  45.90
42    2  79.24  88.04
43    3 122.09  84.19
44    4 161.67 256.34
45    1  57.93  85.24
46    2 117.88 167.90
47    3 181.09 314.49
48    4 242.31 304.70

Your turn

nasa |> head(2)
  time y x   lat      long       date cloudhigh cloudlow cloudmid ozone pressure surftemp
1    1 1 1 -21.2 -113.8000 1995-01-01       0.5     31.0      2.0   260     1000    297.4
2    1 1 2 -21.2 -111.2957 1995-01-01       1.5     31.5      2.5   260     1000    297.4
  temperature  id day month year
1       296.9 1-1   0     1 1995
2       296.5 2-1   0     1 1995

Select lat, long, and cloud.. columns

Your turn

nasa |> head(2)
  time y x   lat      long       date cloudhigh cloudlow cloudmid ozone pressure surftemp
1    1 1 1 -21.2 -113.8000 1995-01-01       0.5     31.0      2.0   260     1000    297.4
2    1 1 2 -21.2 -111.2957 1995-01-01       1.5     31.5      2.5   260     1000    297.4
  temperature  id day month year
1       296.9 1-1   0     1 1995
2       296.5 2-1   0     1 1995
nasa |> select(lat, long, starts_with("cloud")) |> head()
    lat      long cloudhigh cloudlow cloudmid
1 -21.2 -113.8000       0.5     31.0      2.0
2 -21.2 -111.2957       1.5     31.5      2.5
3 -21.2 -108.7913       1.5     32.5      3.5
4 -21.2 -106.2870       1.0     39.0      4.0
5 -21.2 -103.7826       0.5     48.0      4.5
6 -21.2 -101.2783       0.0     50.0      2.5

Your turn

tikus[1:10, c(1:3, 76:77)]
    time rep Psammocora contigua Millepora intrincata Heliopora coerulea
V1    81   1                   0                   24                461
V2    81   2                   0                    0                271
V3    81   3                   0                    0                221
V4    81   4                   0                    0                154
V5    81   5                   0                    0                  0
V6    81   6                   0                    0                  0
V7    81   7                   0                    0                  0
V8    81   8                   0                    0                  0
V9    81   9                   0                    0                  0
V10   81  10                   0                    0                  0

Select rep, time and only Species that DONT contain pora

Your turn

Select rep, time and only Species that DONT contain pora

tikas |> dplyr::select(-contains("pora"))
## OR if we wanted to alter the order...
tikas |> dplyr::select(rep, time, everything(), -contains("pora"))

Select awkward names

dplyr::select(tikus, `Pocillopora damicornis`)
    Pocillopora damicornis
V1                      79
V2                      51
V3                      42
V4                      15
V5                       9
V6                      72
V7                       0
V8                      16
V9                       0
V10                     16
V11                      0
V12                      0
V13                      0
V14                      0
V15                      0
V16                      0
V17                      0
V18                      0
V19                      0
V20                      0
V21                      0
V22                      0
V23                      0
V24                      0
V25                      0
V26                      0
V27                      0
V28                      0
V29                      0
V30                      0
V31                      0
V32                      0
V33                      0
V34                      0
V35                      0
V36                      0
V37                      0
V38                      0
V39                      0
V40                      0
V41                     18
V42                      0
V43                      0
V44                      0
V45                      0
V46                      0
V47                      0
V48                      0
V49                      0
V50                      0
V51                      0
V52                      0
V53                      0
V54                      0
V55                      0
V56                      0
V57                     10
V58                      0
V59                     30
V60                      0

Selecting a single variable

dat.1 |> pull(Resp1)
 [1]   8.12  20.55  27.49  44.79  20.99  37.54  61.46  82.21  31.73  59.08  94.54 121.17
[13]   8.14  13.36  33.37  39.87  19.95  42.83  62.46  81.78  32.76  62.35  90.22 114.03
[25]  21.86  39.83  59.53  75.59  38.57  81.25 124.08 159.69  61.16 119.84 175.87 238.76
[37]  18.82  39.82  63.30  82.29  39.51  79.24 122.09 161.67  57.93 117.88 181.09 242.31

Re-naming columns (vectors)

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> rename(Exposure = Treatment, Richness = Resp1)
    Exposure Plot Dose Time Richness  Resp2
1    Control   P1    H    1     8.12   3.06
2    Control   P1    H    2    20.55  25.94
3    Control   P1    H    3    27.49  29.85
4    Control   P1    H    4    44.79  25.39
5    Control   P1    M    1    20.99  20.31
6    Control   P1    M    2    37.54  17.62
7    Control   P1    M    3    61.46  98.44
8    Control   P1    M    4    82.21 160.01
9    Control   P1    L    1    31.73  21.22
10   Control   P1    L    2    59.08  37.51
11   Control   P1    L    3    94.54 119.22
12   Control   P1    L    4   121.17 116.45
13   Control   P2    H    1     8.14  23.93
14   Control   P2    H    2    13.36  28.02
15   Control   P2    H    3    33.37  37.17
16   Control   P2    H    4    39.87  38.25
17   Control   P2    M    1    19.95  19.73
18   Control   P2    M    2    42.83  40.52
19   Control   P2    M    3    62.46   4.81
20   Control   P2    M    4    81.78 136.66
21   Control   P2    L    1    32.76  30.70
22   Control   P2    L    2    62.35 123.78
23   Control   P2    L    3    90.22 113.87
24   Control   P2    L    4   114.03  76.52
25 Exclusion   P3    H    1    21.86  23.58
26 Exclusion   P3    H    2    39.83  28.03
27 Exclusion   P3    H    3    59.53  21.32
28 Exclusion   P3    H    4    75.59  90.76
29 Exclusion   P3    M    1    38.57  30.63
30 Exclusion   P3    M    2    81.25  83.61
31 Exclusion   P3    M    3   124.08 124.09
32 Exclusion   P3    M    4   159.69 112.65
33 Exclusion   P3    L    1    61.16  39.53
34 Exclusion   P3    L    2   119.84 110.27
35 Exclusion   P3    L    3   175.87 286.33
36 Exclusion   P3    L    4   238.76  54.23
37 Exclusion   P4    H    1    18.82  28.60
38 Exclusion   P4    H    2    39.82  39.07
39 Exclusion   P4    H    3    63.30  93.43
40 Exclusion   P4    H    4    82.29  60.15
41 Exclusion   P4    M    1    39.51  45.90
42 Exclusion   P4    M    2    79.24  88.04
43 Exclusion   P4    M    3   122.09  84.19
44 Exclusion   P4    M    4   161.67 256.34
45 Exclusion   P4    L    1    57.93  85.24
46 Exclusion   P4    L    2   117.88 167.90
47 Exclusion   P4    L    3   181.09 314.49
48 Exclusion   P4    L    4   242.31 304.70

Filtering


Filtering

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> filter(Dose == "H")
   Treatment Plot Dose Time Resp1 Resp2
1    Control   P1    H    1  8.12  3.06
2    Control   P1    H    2 20.55 25.94
3    Control   P1    H    3 27.49 29.85
4    Control   P1    H    4 44.79 25.39
5    Control   P2    H    1  8.14 23.93
6    Control   P2    H    2 13.36 28.02
7    Control   P2    H    3 33.37 37.17
8    Control   P2    H    4 39.87 38.25
9  Exclusion   P3    H    1 21.86 23.58
10 Exclusion   P3    H    2 39.83 28.03
11 Exclusion   P3    H    3 59.53 21.32
12 Exclusion   P3    H    4 75.59 90.76
13 Exclusion   P4    H    1 18.82 28.60
14 Exclusion   P4    H    2 39.82 39.07
15 Exclusion   P4    H    3 63.30 93.43
16 Exclusion   P4    H    4 82.29 60.15

Filtering

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> filter(Dose %in% c("H","M"))
   Treatment Plot Dose Time  Resp1  Resp2
1    Control   P1    H    1   8.12   3.06
2    Control   P1    H    2  20.55  25.94
3    Control   P1    H    3  27.49  29.85
4    Control   P1    H    4  44.79  25.39
5    Control   P1    M    1  20.99  20.31
6    Control   P1    M    2  37.54  17.62
7    Control   P1    M    3  61.46  98.44
8    Control   P1    M    4  82.21 160.01
9    Control   P2    H    1   8.14  23.93
10   Control   P2    H    2  13.36  28.02
11   Control   P2    H    3  33.37  37.17
12   Control   P2    H    4  39.87  38.25
13   Control   P2    M    1  19.95  19.73
14   Control   P2    M    2  42.83  40.52
15   Control   P2    M    3  62.46   4.81
16   Control   P2    M    4  81.78 136.66
17 Exclusion   P3    H    1  21.86  23.58
18 Exclusion   P3    H    2  39.83  28.03
19 Exclusion   P3    H    3  59.53  21.32
20 Exclusion   P3    H    4  75.59  90.76
21 Exclusion   P3    M    1  38.57  30.63
22 Exclusion   P3    M    2  81.25  83.61
23 Exclusion   P3    M    3 124.08 124.09
24 Exclusion   P3    M    4 159.69 112.65
25 Exclusion   P4    H    1  18.82  28.60
26 Exclusion   P4    H    2  39.82  39.07
27 Exclusion   P4    H    3  63.30  93.43
28 Exclusion   P4    H    4  82.29  60.15
29 Exclusion   P4    M    1  39.51  45.90
30 Exclusion   P4    M    2  79.24  88.04
31 Exclusion   P4    M    3 122.09  84.19
32 Exclusion   P4    M    4 161.67 256.34

Filtering

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> filter(Dose == "H" & Resp1 < 25)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
3   Control   P2    H    1  8.14 23.93
4   Control   P2    H    2 13.36 28.02
5 Exclusion   P3    H    1 21.86 23.58
6 Exclusion   P4    H    1 18.82 28.60
dat.1 |> filter(Dose == "H" | Resp1 < 25)
   Treatment Plot Dose Time Resp1 Resp2
1    Control   P1    H    1  8.12  3.06
2    Control   P1    H    2 20.55 25.94
3    Control   P1    H    3 27.49 29.85
4    Control   P1    H    4 44.79 25.39
5    Control   P1    M    1 20.99 20.31
6    Control   P2    H    1  8.14 23.93
7    Control   P2    H    2 13.36 28.02
8    Control   P2    H    3 33.37 37.17
9    Control   P2    H    4 39.87 38.25
10   Control   P2    M    1 19.95 19.73
11 Exclusion   P3    H    1 21.86 23.58
12 Exclusion   P3    H    2 39.83 28.03
13 Exclusion   P3    H    3 59.53 21.32
14 Exclusion   P3    H    4 75.59 90.76
15 Exclusion   P4    H    1 18.82 28.60
16 Exclusion   P4    H    2 39.82 39.07
17 Exclusion   P4    H    3 63.30 93.43
18 Exclusion   P4    H    4 82.29 60.15

Filtering

Selection helper functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Select rows based on the value of all/any “Resp” variables

dat.1 |> filter(if_all(starts_with("Resp"), ~ . < 10))
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
dat.1 |> filter(if_any(starts_with("Resp"), ~ . < 10))
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P2    H    1  8.14 23.93
3   Control   P2    M    3 62.46  4.81

Your turn

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Keep only those rows with Resp1 less than 40 and Time greater than 1 or Dose is equal to L

Your turn

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Keep only those rows with Resp1 less than 40 and Time greater than 1 or Dose is equal to L

dat.1 |> filter(Resp1 < 40 & (Time > 1 |  Dose == "L"))
   Treatment Plot Dose Time Resp1 Resp2
1    Control   P1    H    2 20.55 25.94
2    Control   P1    H    3 27.49 29.85
3    Control   P1    M    2 37.54 17.62
4    Control   P1    L    1 31.73 21.22
5    Control   P2    H    2 13.36 28.02
6    Control   P2    H    3 33.37 37.17
7    Control   P2    H    4 39.87 38.25
8    Control   P2    L    1 32.76 30.70
9  Exclusion   P3    H    2 39.83 28.03
10 Exclusion   P4    H    2 39.82 39.07

Your turn

options(width = 80)
glimpse(nasa)
Rows: 41,472
Columns: 17
$ time        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1…
$ y           <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1…
$ x           <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,…
$ lat         <dbl> -21.20000, -21.20000, -21.20000, -21.20000, -21.20000, -21…
$ long        <dbl> -113.80000, -111.29565, -108.79130, -106.28696, -103.78261…
$ date        <dttm> 1995-01-01, 1995-01-01, 1995-01-01, 1995-01-01, 1995-01-0…
$ cloudhigh   <dbl> 0.5, 1.5, 1.5, 1.0, 0.5, 0.0, 0.0, 0.0, 0.5, 1.0, 1.0, 1.0…
$ cloudlow    <dbl> 31.0, 31.5, 32.5, 39.0, 48.0, 50.0, 51.0, 52.5, 54.0, 56.0…
$ cloudmid    <dbl> 2.0, 2.5, 3.5, 4.0, 4.5, 2.5, 4.5, 5.0, 8.5, 11.5, 11.5, 1…
$ ozone       <int> 260, 260, 260, 258, 258, 258, 256, 258, 256, 258, 258, 254…
$ pressure    <int> 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000…
$ surftemp    <dbl> 297.4, 297.4, 297.4, 296.9, 296.5, 296.5, 295.5, 295.5, 29…
$ temperature <dbl> 296.9, 296.5, 296.0, 296.5, 295.5, 295.0, 295.5, 295.0, 29…
$ id          <chr> "1-1", "2-1", "3-1", "4-1", "5-1", "6-1", "7-1", "8-1", "9…
$ day         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ month       <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1…
$ year        <dbl> 1995, 1995, 1995, 1995, 1995, 1995, 1995, 1995, 1995, 1995…



Filter to the largest ozone value for the second month of the last year

Your turn

Filter to the largest ozone value for the second month of the last year

nasa |> filter(year == max(year) & month == 2) |>
    arrange(-ozone) |> head(5)
nasa |> filter(year == max(year) & month == 2) |>
    arrange(-ozone) |> slice(1:5)
##OR
nasa |> filter(year == max(year) & month == 2) |>
    top_n(5, ozone)

Your turn

Filter to all ozone values between 320 and 325 in the first month of the last year

glimpse(nasa)
Rows: 41,472
Columns: 17
$ time        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1…
$ y           <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1…
$ x           <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,…
$ lat         <dbl> -21.20000, -21.20000, -21.20000, -21.20000, -21.20000, -21…
$ long        <dbl> -113.80000, -111.29565, -108.79130, -106.28696, -103.78261…
$ date        <dttm> 1995-01-01, 1995-01-01, 1995-01-01, 1995-01-01, 1995-01-0…
$ cloudhigh   <dbl> 0.5, 1.5, 1.5, 1.0, 0.5, 0.0, 0.0, 0.0, 0.5, 1.0, 1.0, 1.0…
$ cloudlow    <dbl> 31.0, 31.5, 32.5, 39.0, 48.0, 50.0, 51.0, 52.5, 54.0, 56.0…
$ cloudmid    <dbl> 2.0, 2.5, 3.5, 4.0, 4.5, 2.5, 4.5, 5.0, 8.5, 11.5, 11.5, 1…
$ ozone       <int> 260, 260, 260, 258, 258, 258, 256, 258, 256, 258, 258, 254…
$ pressure    <int> 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000…
$ surftemp    <dbl> 297.4, 297.4, 297.4, 296.9, 296.5, 296.5, 295.5, 295.5, 29…
$ temperature <dbl> 296.9, 296.5, 296.0, 296.5, 295.5, 295.0, 295.5, 295.0, 29…
$ id          <chr> "1-1", "2-1", "3-1", "4-1", "5-1", "6-1", "7-1", "8-1", "9…
$ day         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ month       <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1…
$ year        <dbl> 1995, 1995, 1995, 1995, 1995, 1995, 1995, 1995, 1995, 1995…

Your turn

Filter to all ozone values between 320 and 325 in the first month of the last year

nasa |> filter(ozone > 320 & ozone < 325, month == first(month),
       year == last(year))
##OR
nasa |> filter(between(ozone, 320, 325), month == first(month),
       year == last(year))

Slicing

Filtering by row number

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> slice(1:4)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
3   Control   P1    H    3 27.49 29.85
4   Control   P1    H    4 44.79 25.39
dat.1 |> slice(c(1:4, 7))
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
3   Control   P1    H    3 27.49 29.85
4   Control   P1    H    4 44.79 25.39
5   Control   P1    M    3 61.46 98.44

Sampling

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> sample_n(10, replace = TRUE)
   Treatment Plot Dose Time  Resp1  Resp2
1    Control   P1    M    4  82.21 160.01
2  Exclusion   P4    M    2  79.24  88.04
3  Exclusion   P4    H    3  63.30  93.43
4    Control   P1    M    3  61.46  98.44
5  Exclusion   P3    H    3  59.53  21.32
6  Exclusion   P4    M    3 122.09  84.19
7    Control   P1    L    1  31.73  21.22
8    Control   P2    M    4  81.78 136.66
9  Exclusion   P3    L    2 119.84 110.27
10 Exclusion   P4    H    1  18.82  28.60

Sampling

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> sample_frac(0.5, replace = TRUE)
   Treatment Plot Dose Time  Resp1  Resp2
1  Exclusion   P3    M    1  38.57  30.63
2    Control   P1    L    3  94.54 119.22
3    Control   P1    H    2  20.55  25.94
4    Control   P1    H    3  27.49  29.85
5  Exclusion   P4    L    3 181.09 314.49
6  Exclusion   P4    H    2  39.82  39.07
7  Exclusion   P4    M    1  39.51  45.90
8    Control   P2    H    3  33.37  37.17
9  Exclusion   P3    H    4  75.59  90.76
10   Control   P1    M    1  20.99  20.31
11 Exclusion   P3    H    4  75.59  90.76
12   Control   P2    H    2  13.36  28.02
13 Exclusion   P4    H    1  18.82  28.60
14 Exclusion   P4    M    3 122.09  84.19
15 Exclusion   P4    M    3 122.09  84.19
16   Control   P2    M    1  19.95  19.73
17   Control   P1    H    1   8.12   3.06
18 Exclusion   P3    H    2  39.83  28.03
19 Exclusion   P4    L    1  57.93  85.24
20 Exclusion   P3    L    1  61.16  39.53
21   Control   P2    M    3  62.46   4.81
22 Exclusion   P3    H    2  39.83  28.03
23   Control   P2    L    3  90.22 113.87
24   Control   P1    H    4  44.79  25.39

Effects of filtering

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
#examine the levels of the Cond factor
str(dat.1$Dose)
 Factor w/ 3 levels "H","L","M": 1 1 1 1 3 3 3 3 2 2 ...
str(dat.1$Plot)
 Factor w/ 4 levels "P1","P2","P3",..: 1 1 1 1 1 1 1 1 1 1 ...
levels(dat.1$Plot)
[1] "P1" "P2" "P3" "P4"
levels(dat.1$Treatment)
[1] "Control"   "Exclusion"

Effects of filtering

#subset the dataset to just Plot = "P1"
dat.3 <- dat.1 |> filter(Plot == "P1", Time == 1)
#examine subset data
dat.3
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    M    1 20.99 20.31
3   Control   P1    L    1 31.73 21.22
#examine the levels of the Cond factor
levels(dat.3$Dose)
[1] "H" "L" "M"
levels(dat.3$Plot)
[1] "P1" "P2" "P3" "P4"
levels(dat.3$Treatment)
[1] "Control"   "Exclusion"

Effects of filtering

Correction - all factors

#subset the dataset to just Dose H
dat.3 <-  dat.1 |> filter(Plot == "P1")
#drop the unused factor levels from all factors
dat.3 <- dat.3 |> droplevels()
#examine the levels of each factor
levels(dat.3$Dose)
[1] "H" "L" "M"
levels(dat.3$Plot)
[1] "P1"
levels(dat.3$Treatment)
[1] "Control"

Adding / modifying columns

Mutate

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> mutate(Sum = Resp1 + Resp2)
   Treatment Plot Dose Time  Resp1  Resp2    Sum
1    Control   P1    H    1   8.12   3.06  11.18
2    Control   P1    H    2  20.55  25.94  46.49
3    Control   P1    H    3  27.49  29.85  57.34
4    Control   P1    H    4  44.79  25.39  70.18
5    Control   P1    M    1  20.99  20.31  41.30
6    Control   P1    M    2  37.54  17.62  55.16
7    Control   P1    M    3  61.46  98.44 159.90
8    Control   P1    M    4  82.21 160.01 242.22
9    Control   P1    L    1  31.73  21.22  52.95
10   Control   P1    L    2  59.08  37.51  96.59
11   Control   P1    L    3  94.54 119.22 213.76
12   Control   P1    L    4 121.17 116.45 237.62
13   Control   P2    H    1   8.14  23.93  32.07
14   Control   P2    H    2  13.36  28.02  41.38
15   Control   P2    H    3  33.37  37.17  70.54
16   Control   P2    H    4  39.87  38.25  78.12
17   Control   P2    M    1  19.95  19.73  39.68
18   Control   P2    M    2  42.83  40.52  83.35
19   Control   P2    M    3  62.46   4.81  67.27
20   Control   P2    M    4  81.78 136.66 218.44
21   Control   P2    L    1  32.76  30.70  63.46
22   Control   P2    L    2  62.35 123.78 186.13
23   Control   P2    L    3  90.22 113.87 204.09
24   Control   P2    L    4 114.03  76.52 190.55
25 Exclusion   P3    H    1  21.86  23.58  45.44
26 Exclusion   P3    H    2  39.83  28.03  67.86
27 Exclusion   P3    H    3  59.53  21.32  80.85
28 Exclusion   P3    H    4  75.59  90.76 166.35
29 Exclusion   P3    M    1  38.57  30.63  69.20
30 Exclusion   P3    M    2  81.25  83.61 164.86
31 Exclusion   P3    M    3 124.08 124.09 248.17
32 Exclusion   P3    M    4 159.69 112.65 272.34
33 Exclusion   P3    L    1  61.16  39.53 100.69
34 Exclusion   P3    L    2 119.84 110.27 230.11
35 Exclusion   P3    L    3 175.87 286.33 462.20
36 Exclusion   P3    L    4 238.76  54.23 292.99
37 Exclusion   P4    H    1  18.82  28.60  47.42
38 Exclusion   P4    H    2  39.82  39.07  78.89
39 Exclusion   P4    H    3  63.30  93.43 156.73
40 Exclusion   P4    H    4  82.29  60.15 142.44
41 Exclusion   P4    M    1  39.51  45.90  85.41
42 Exclusion   P4    M    2  79.24  88.04 167.28
43 Exclusion   P4    M    3 122.09  84.19 206.28
44 Exclusion   P4    M    4 161.67 256.34 418.01
45 Exclusion   P4    L    1  57.93  85.24 143.17
46 Exclusion   P4    L    2 117.88 167.90 285.78
47 Exclusion   P4    L    3 181.09 314.49 495.58
48 Exclusion   P4    L    4 242.31 304.70 547.01

Mutate

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Transformations

dat.1 |> mutate(logResp1 = log(Resp1))
   Treatment Plot Dose Time  Resp1  Resp2 logResp1
1    Control   P1    H    1   8.12   3.06 2.094330
2    Control   P1    H    2  20.55  25.94 3.022861
3    Control   P1    H    3  27.49  29.85 3.313822
4    Control   P1    H    4  44.79  25.39 3.801985
5    Control   P1    M    1  20.99  20.31 3.044046
6    Control   P1    M    2  37.54  17.62 3.625407
7    Control   P1    M    3  61.46  98.44 4.118387
8    Control   P1    M    4  82.21 160.01 4.409277
9    Control   P1    L    1  31.73  21.22 3.457263
10   Control   P1    L    2  59.08  37.51 4.078892
11   Control   P1    L    3  94.54 119.22 4.549023
12   Control   P1    L    4 121.17 116.45 4.797195
13   Control   P2    H    1   8.14  23.93 2.096790
14   Control   P2    H    2  13.36  28.02 2.592265
15   Control   P2    H    3  33.37  37.17 3.507657
16   Control   P2    H    4  39.87  38.25 3.685624
17   Control   P2    M    1  19.95  19.73 2.993229
18   Control   P2    M    2  42.83  40.52 3.757239
19   Control   P2    M    3  62.46   4.81 4.134526
20   Control   P2    M    4  81.78 136.66 4.404033
21   Control   P2    L    1  32.76  30.70 3.489208
22   Control   P2    L    2  62.35 123.78 4.132764
23   Control   P2    L    3  90.22 113.87 4.502251
24   Control   P2    L    4 114.03  76.52 4.736462
25 Exclusion   P3    H    1  21.86  23.58 3.084658
26 Exclusion   P3    H    2  39.83  28.03 3.684620
27 Exclusion   P3    H    3  59.53  21.32 4.086480
28 Exclusion   P3    H    4  75.59  90.76 4.325324
29 Exclusion   P3    M    1  38.57  30.63 3.652475
30 Exclusion   P3    M    2  81.25  83.61 4.397531
31 Exclusion   P3    M    3 124.08 124.09 4.820927
32 Exclusion   P3    M    4 159.69 112.65 5.073234
33 Exclusion   P3    L    1  61.16  39.53 4.113493
34 Exclusion   P3    L    2 119.84 110.27 4.786158
35 Exclusion   P3    L    3 175.87 286.33 5.169745
36 Exclusion   P3    L    4 238.76  54.23 5.475459
37 Exclusion   P4    H    1  18.82  28.60 2.934920
38 Exclusion   P4    H    2  39.82  39.07 3.684369
39 Exclusion   P4    H    3  63.30  93.43 4.147885
40 Exclusion   P4    H    4  82.29  60.15 4.410250
41 Exclusion   P4    M    1  39.51  45.90 3.676554
42 Exclusion   P4    M    2  79.24  88.04 4.372481
43 Exclusion   P4    M    3 122.09  84.19 4.804758
44 Exclusion   P4    M    4 161.67 256.34 5.085557
45 Exclusion   P4    L    1  57.93  85.24 4.059235
46 Exclusion   P4    L    2 117.88 167.90 4.769667
47 Exclusion   P4    L    3 181.09 314.49 5.198994
48 Exclusion   P4    L    4 242.31 304.70 5.490218

Mutate

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Transformations

dat.1 |> mutate(logResp1 = log(Resp1),
                 logResp2 = log(Resp2))
   Treatment Plot Dose Time  Resp1  Resp2 logResp1 logResp2
1    Control   P1    H    1   8.12   3.06 2.094330 1.118415
2    Control   P1    H    2  20.55  25.94 3.022861 3.255786
3    Control   P1    H    3  27.49  29.85 3.313822 3.396185
4    Control   P1    H    4  44.79  25.39 3.801985 3.234355
5    Control   P1    M    1  20.99  20.31 3.044046 3.011113
6    Control   P1    M    2  37.54  17.62 3.625407 2.869035
7    Control   P1    M    3  61.46  98.44 4.118387 4.589447
8    Control   P1    M    4  82.21 160.01 4.409277 5.075236
9    Control   P1    L    1  31.73  21.22 3.457263 3.054944
10   Control   P1    L    2  59.08  37.51 4.078892 3.624608
11   Control   P1    L    3  94.54 119.22 4.549023 4.780971
12   Control   P1    L    4 121.17 116.45 4.797195 4.757462
13   Control   P2    H    1   8.14  23.93 2.096790 3.175133
14   Control   P2    H    2  13.36  28.02 2.592265 3.332919
15   Control   P2    H    3  33.37  37.17 3.507657 3.615502
16   Control   P2    H    4  39.87  38.25 3.685624 3.644144
17   Control   P2    M    1  19.95  19.73 2.993229 2.982140
18   Control   P2    M    2  42.83  40.52 3.757239 3.701796
19   Control   P2    M    3  62.46   4.81 4.134526 1.570697
20   Control   P2    M    4  81.78 136.66 4.404033 4.917496
21   Control   P2    L    1  32.76  30.70 3.489208 3.424263
22   Control   P2    L    2  62.35 123.78 4.132764 4.818506
23   Control   P2    L    3  90.22 113.87 4.502251 4.735057
24   Control   P2    L    4 114.03  76.52 4.736462 4.337552
25 Exclusion   P3    H    1  21.86  23.58 3.084658 3.160399
26 Exclusion   P3    H    2  39.83  28.03 3.684620 3.333275
27 Exclusion   P3    H    3  59.53  21.32 4.086480 3.059646
28 Exclusion   P3    H    4  75.59  90.76 4.325324 4.508219
29 Exclusion   P3    M    1  38.57  30.63 3.652475 3.421980
30 Exclusion   P3    M    2  81.25  83.61 4.397531 4.426163
31 Exclusion   P3    M    3 124.08 124.09 4.820927 4.821007
32 Exclusion   P3    M    4 159.69 112.65 5.073234 4.724286
33 Exclusion   P3    L    1  61.16  39.53 4.113493 3.677060
34 Exclusion   P3    L    2 119.84 110.27 4.786158 4.702932
35 Exclusion   P3    L    3 175.87 286.33 5.169745 5.657145
36 Exclusion   P3    L    4 238.76  54.23 5.475459 3.993234
37 Exclusion   P4    H    1  18.82  28.60 2.934920 3.353407
38 Exclusion   P4    H    2  39.82  39.07 3.684369 3.665355
39 Exclusion   P4    H    3  63.30  93.43 4.147885 4.537212
40 Exclusion   P4    H    4  82.29  60.15 4.410250 4.096841
41 Exclusion   P4    M    1  39.51  45.90 3.676554 3.826465
42 Exclusion   P4    M    2  79.24  88.04 4.372481 4.477791
43 Exclusion   P4    M    3 122.09  84.19 4.804758 4.433076
44 Exclusion   P4    M    4 161.67 256.34 5.085557 5.546505
45 Exclusion   P4    L    1  57.93  85.24 4.059235 4.445471
46 Exclusion   P4    L    2 117.88 167.90 4.769667 5.123369
47 Exclusion   P4    L    3 181.09 314.49 5.198994 5.750952
48 Exclusion   P4    L    4 242.31 304.70 5.490218 5.719328

Mutate

Select helper functions

Helper function Description
across() Use selection helper functions semantics 
across(.cols, .fns, .names)
  • .cols - tidy select (Selection helper function)
  • .fn - a function to apply (or list of functions)
  • .names - a glue specification determining the format of the new variable names

Mutate

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Transformations - multiple variables

dat.1 |> mutate(across(c(Resp1, Resp2),
                        log))
   Treatment Plot Dose Time    Resp1    Resp2
1    Control   P1    H    1 2.094330 1.118415
2    Control   P1    H    2 3.022861 3.255786
3    Control   P1    H    3 3.313822 3.396185
4    Control   P1    H    4 3.801985 3.234355
5    Control   P1    M    1 3.044046 3.011113
6    Control   P1    M    2 3.625407 2.869035
7    Control   P1    M    3 4.118387 4.589447
8    Control   P1    M    4 4.409277 5.075236
9    Control   P1    L    1 3.457263 3.054944
10   Control   P1    L    2 4.078892 3.624608
11   Control   P1    L    3 4.549023 4.780971
12   Control   P1    L    4 4.797195 4.757462
13   Control   P2    H    1 2.096790 3.175133
14   Control   P2    H    2 2.592265 3.332919
15   Control   P2    H    3 3.507657 3.615502
16   Control   P2    H    4 3.685624 3.644144
17   Control   P2    M    1 2.993229 2.982140
18   Control   P2    M    2 3.757239 3.701796
19   Control   P2    M    3 4.134526 1.570697
20   Control   P2    M    4 4.404033 4.917496
21   Control   P2    L    1 3.489208 3.424263
22   Control   P2    L    2 4.132764 4.818506
23   Control   P2    L    3 4.502251 4.735057
24   Control   P2    L    4 4.736462 4.337552
25 Exclusion   P3    H    1 3.084658 3.160399
26 Exclusion   P3    H    2 3.684620 3.333275
27 Exclusion   P3    H    3 4.086480 3.059646
28 Exclusion   P3    H    4 4.325324 4.508219
29 Exclusion   P3    M    1 3.652475 3.421980
30 Exclusion   P3    M    2 4.397531 4.426163
31 Exclusion   P3    M    3 4.820927 4.821007
32 Exclusion   P3    M    4 5.073234 4.724286
33 Exclusion   P3    L    1 4.113493 3.677060
34 Exclusion   P3    L    2 4.786158 4.702932
35 Exclusion   P3    L    3 5.169745 5.657145
36 Exclusion   P3    L    4 5.475459 3.993234
37 Exclusion   P4    H    1 2.934920 3.353407
38 Exclusion   P4    H    2 3.684369 3.665355
39 Exclusion   P4    H    3 4.147885 4.537212
40 Exclusion   P4    H    4 4.410250 4.096841
41 Exclusion   P4    M    1 3.676554 3.826465
42 Exclusion   P4    M    2 4.372481 4.477791
43 Exclusion   P4    M    3 4.804758 4.433076
44 Exclusion   P4    M    4 5.085557 5.546505
45 Exclusion   P4    L    1 4.059235 4.445471
46 Exclusion   P4    L    2 4.769667 5.123369
47 Exclusion   P4    L    3 5.198994 5.750952
48 Exclusion   P4    L    4 5.490218 5.719328

Mutate

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Transformations - multiple variables

dat.1 |> mutate(across(c(Resp1, Resp2),
                        log,
                        .names = "l{.col}"))
   Treatment Plot Dose Time  Resp1  Resp2   lResp1   lResp2
1    Control   P1    H    1   8.12   3.06 2.094330 1.118415
2    Control   P1    H    2  20.55  25.94 3.022861 3.255786
3    Control   P1    H    3  27.49  29.85 3.313822 3.396185
4    Control   P1    H    4  44.79  25.39 3.801985 3.234355
5    Control   P1    M    1  20.99  20.31 3.044046 3.011113
6    Control   P1    M    2  37.54  17.62 3.625407 2.869035
7    Control   P1    M    3  61.46  98.44 4.118387 4.589447
8    Control   P1    M    4  82.21 160.01 4.409277 5.075236
9    Control   P1    L    1  31.73  21.22 3.457263 3.054944
10   Control   P1    L    2  59.08  37.51 4.078892 3.624608
11   Control   P1    L    3  94.54 119.22 4.549023 4.780971
12   Control   P1    L    4 121.17 116.45 4.797195 4.757462
13   Control   P2    H    1   8.14  23.93 2.096790 3.175133
14   Control   P2    H    2  13.36  28.02 2.592265 3.332919
15   Control   P2    H    3  33.37  37.17 3.507657 3.615502
16   Control   P2    H    4  39.87  38.25 3.685624 3.644144
17   Control   P2    M    1  19.95  19.73 2.993229 2.982140
18   Control   P2    M    2  42.83  40.52 3.757239 3.701796
19   Control   P2    M    3  62.46   4.81 4.134526 1.570697
20   Control   P2    M    4  81.78 136.66 4.404033 4.917496
21   Control   P2    L    1  32.76  30.70 3.489208 3.424263
22   Control   P2    L    2  62.35 123.78 4.132764 4.818506
23   Control   P2    L    3  90.22 113.87 4.502251 4.735057
24   Control   P2    L    4 114.03  76.52 4.736462 4.337552
25 Exclusion   P3    H    1  21.86  23.58 3.084658 3.160399
26 Exclusion   P3    H    2  39.83  28.03 3.684620 3.333275
27 Exclusion   P3    H    3  59.53  21.32 4.086480 3.059646
28 Exclusion   P3    H    4  75.59  90.76 4.325324 4.508219
29 Exclusion   P3    M    1  38.57  30.63 3.652475 3.421980
30 Exclusion   P3    M    2  81.25  83.61 4.397531 4.426163
31 Exclusion   P3    M    3 124.08 124.09 4.820927 4.821007
32 Exclusion   P3    M    4 159.69 112.65 5.073234 4.724286
33 Exclusion   P3    L    1  61.16  39.53 4.113493 3.677060
34 Exclusion   P3    L    2 119.84 110.27 4.786158 4.702932
35 Exclusion   P3    L    3 175.87 286.33 5.169745 5.657145
36 Exclusion   P3    L    4 238.76  54.23 5.475459 3.993234
37 Exclusion   P4    H    1  18.82  28.60 2.934920 3.353407
38 Exclusion   P4    H    2  39.82  39.07 3.684369 3.665355
39 Exclusion   P4    H    3  63.30  93.43 4.147885 4.537212
40 Exclusion   P4    H    4  82.29  60.15 4.410250 4.096841
41 Exclusion   P4    M    1  39.51  45.90 3.676554 3.826465
42 Exclusion   P4    M    2  79.24  88.04 4.372481 4.477791
43 Exclusion   P4    M    3 122.09  84.19 4.804758 4.433076
44 Exclusion   P4    M    4 161.67 256.34 5.085557 5.546505
45 Exclusion   P4    L    1  57.93  85.24 4.059235 4.445471
46 Exclusion   P4    L    2 117.88 167.90 4.769667 5.123369
47 Exclusion   P4    L    3 181.09 314.49 5.198994 5.750952
48 Exclusion   P4    L    4 242.31 304.70 5.490218 5.719328

Mutate

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Transformations - all numeric variables

dat.1 |> mutate(across(where(is.numeric),
                        log,
                        .names = "l{.col}"))
   Treatment Plot Dose Time  Resp1  Resp2     lTime   lResp1   lResp2
1    Control   P1    H    1   8.12   3.06 0.0000000 2.094330 1.118415
2    Control   P1    H    2  20.55  25.94 0.6931472 3.022861 3.255786
3    Control   P1    H    3  27.49  29.85 1.0986123 3.313822 3.396185
4    Control   P1    H    4  44.79  25.39 1.3862944 3.801985 3.234355
5    Control   P1    M    1  20.99  20.31 0.0000000 3.044046 3.011113
6    Control   P1    M    2  37.54  17.62 0.6931472 3.625407 2.869035
7    Control   P1    M    3  61.46  98.44 1.0986123 4.118387 4.589447
8    Control   P1    M    4  82.21 160.01 1.3862944 4.409277 5.075236
9    Control   P1    L    1  31.73  21.22 0.0000000 3.457263 3.054944
10   Control   P1    L    2  59.08  37.51 0.6931472 4.078892 3.624608
11   Control   P1    L    3  94.54 119.22 1.0986123 4.549023 4.780971
12   Control   P1    L    4 121.17 116.45 1.3862944 4.797195 4.757462
13   Control   P2    H    1   8.14  23.93 0.0000000 2.096790 3.175133
14   Control   P2    H    2  13.36  28.02 0.6931472 2.592265 3.332919
15   Control   P2    H    3  33.37  37.17 1.0986123 3.507657 3.615502
16   Control   P2    H    4  39.87  38.25 1.3862944 3.685624 3.644144
17   Control   P2    M    1  19.95  19.73 0.0000000 2.993229 2.982140
18   Control   P2    M    2  42.83  40.52 0.6931472 3.757239 3.701796
19   Control   P2    M    3  62.46   4.81 1.0986123 4.134526 1.570697
20   Control   P2    M    4  81.78 136.66 1.3862944 4.404033 4.917496
21   Control   P2    L    1  32.76  30.70 0.0000000 3.489208 3.424263
22   Control   P2    L    2  62.35 123.78 0.6931472 4.132764 4.818506
23   Control   P2    L    3  90.22 113.87 1.0986123 4.502251 4.735057
24   Control   P2    L    4 114.03  76.52 1.3862944 4.736462 4.337552
25 Exclusion   P3    H    1  21.86  23.58 0.0000000 3.084658 3.160399
26 Exclusion   P3    H    2  39.83  28.03 0.6931472 3.684620 3.333275
27 Exclusion   P3    H    3  59.53  21.32 1.0986123 4.086480 3.059646
28 Exclusion   P3    H    4  75.59  90.76 1.3862944 4.325324 4.508219
29 Exclusion   P3    M    1  38.57  30.63 0.0000000 3.652475 3.421980
30 Exclusion   P3    M    2  81.25  83.61 0.6931472 4.397531 4.426163
31 Exclusion   P3    M    3 124.08 124.09 1.0986123 4.820927 4.821007
32 Exclusion   P3    M    4 159.69 112.65 1.3862944 5.073234 4.724286
33 Exclusion   P3    L    1  61.16  39.53 0.0000000 4.113493 3.677060
34 Exclusion   P3    L    2 119.84 110.27 0.6931472 4.786158 4.702932
35 Exclusion   P3    L    3 175.87 286.33 1.0986123 5.169745 5.657145
36 Exclusion   P3    L    4 238.76  54.23 1.3862944 5.475459 3.993234
37 Exclusion   P4    H    1  18.82  28.60 0.0000000 2.934920 3.353407
38 Exclusion   P4    H    2  39.82  39.07 0.6931472 3.684369 3.665355
39 Exclusion   P4    H    3  63.30  93.43 1.0986123 4.147885 4.537212
40 Exclusion   P4    H    4  82.29  60.15 1.3862944 4.410250 4.096841
41 Exclusion   P4    M    1  39.51  45.90 0.0000000 3.676554 3.826465
42 Exclusion   P4    M    2  79.24  88.04 0.6931472 4.372481 4.477791
43 Exclusion   P4    M    3 122.09  84.19 1.0986123 4.804758 4.433076
44 Exclusion   P4    M    4 161.67 256.34 1.3862944 5.085557 5.546505
45 Exclusion   P4    L    1  57.93  85.24 0.0000000 4.059235 4.445471
46 Exclusion   P4    L    2 117.88 167.90 0.6931472 4.769667 5.123369
47 Exclusion   P4    L    3 181.09 314.49 1.0986123 5.198994 5.750952
48 Exclusion   P4    L    4 242.31 304.70 1.3862944 5.490218 5.719328

Mutate

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Transformations - all “Resp#” variables

dat.1 |> mutate(across(num_range("Resp", 1:2),
                        log,
                        .names = "l{.col}"))
   Treatment Plot Dose Time  Resp1  Resp2   lResp1   lResp2
1    Control   P1    H    1   8.12   3.06 2.094330 1.118415
2    Control   P1    H    2  20.55  25.94 3.022861 3.255786
3    Control   P1    H    3  27.49  29.85 3.313822 3.396185
4    Control   P1    H    4  44.79  25.39 3.801985 3.234355
5    Control   P1    M    1  20.99  20.31 3.044046 3.011113
6    Control   P1    M    2  37.54  17.62 3.625407 2.869035
7    Control   P1    M    3  61.46  98.44 4.118387 4.589447
8    Control   P1    M    4  82.21 160.01 4.409277 5.075236
9    Control   P1    L    1  31.73  21.22 3.457263 3.054944
10   Control   P1    L    2  59.08  37.51 4.078892 3.624608
11   Control   P1    L    3  94.54 119.22 4.549023 4.780971
12   Control   P1    L    4 121.17 116.45 4.797195 4.757462
13   Control   P2    H    1   8.14  23.93 2.096790 3.175133
14   Control   P2    H    2  13.36  28.02 2.592265 3.332919
15   Control   P2    H    3  33.37  37.17 3.507657 3.615502
16   Control   P2    H    4  39.87  38.25 3.685624 3.644144
17   Control   P2    M    1  19.95  19.73 2.993229 2.982140
18   Control   P2    M    2  42.83  40.52 3.757239 3.701796
19   Control   P2    M    3  62.46   4.81 4.134526 1.570697
20   Control   P2    M    4  81.78 136.66 4.404033 4.917496
21   Control   P2    L    1  32.76  30.70 3.489208 3.424263
22   Control   P2    L    2  62.35 123.78 4.132764 4.818506
23   Control   P2    L    3  90.22 113.87 4.502251 4.735057
24   Control   P2    L    4 114.03  76.52 4.736462 4.337552
25 Exclusion   P3    H    1  21.86  23.58 3.084658 3.160399
26 Exclusion   P3    H    2  39.83  28.03 3.684620 3.333275
27 Exclusion   P3    H    3  59.53  21.32 4.086480 3.059646
28 Exclusion   P3    H    4  75.59  90.76 4.325324 4.508219
29 Exclusion   P3    M    1  38.57  30.63 3.652475 3.421980
30 Exclusion   P3    M    2  81.25  83.61 4.397531 4.426163
31 Exclusion   P3    M    3 124.08 124.09 4.820927 4.821007
32 Exclusion   P3    M    4 159.69 112.65 5.073234 4.724286
33 Exclusion   P3    L    1  61.16  39.53 4.113493 3.677060
34 Exclusion   P3    L    2 119.84 110.27 4.786158 4.702932
35 Exclusion   P3    L    3 175.87 286.33 5.169745 5.657145
36 Exclusion   P3    L    4 238.76  54.23 5.475459 3.993234
37 Exclusion   P4    H    1  18.82  28.60 2.934920 3.353407
38 Exclusion   P4    H    2  39.82  39.07 3.684369 3.665355
39 Exclusion   P4    H    3  63.30  93.43 4.147885 4.537212
40 Exclusion   P4    H    4  82.29  60.15 4.410250 4.096841
41 Exclusion   P4    M    1  39.51  45.90 3.676554 3.826465
42 Exclusion   P4    M    2  79.24  88.04 4.372481 4.477791
43 Exclusion   P4    M    3 122.09  84.19 4.804758 4.433076
44 Exclusion   P4    M    4 161.67 256.34 5.085557 5.546505
45 Exclusion   P4    L    1  57.93  85.24 4.059235 4.445471
46 Exclusion   P4    L    2 117.88 167.90 4.769667 5.123369
47 Exclusion   P4    L    3 181.09 314.49 5.198994 5.750952
48 Exclusion   P4    L    4 242.31 304.70 5.490218 5.719328

Mutate

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Transformations - multiple variables and functions

dat.1 |> mutate(across(c(Resp1, Resp2),
                        list(l=log, s=sqrt),
                        .names = "{.fn}.{.col}"))
   Treatment Plot Dose Time  Resp1  Resp2  l.Resp1   s.Resp1  l.Resp2   s.Resp2
1    Control   P1    H    1   8.12   3.06 2.094330  2.849561 1.118415  1.749286
2    Control   P1    H    2  20.55  25.94 3.022861  4.533211 3.255786  5.093133
3    Control   P1    H    3  27.49  29.85 3.313822  5.243091 3.396185  5.463515
4    Control   P1    H    4  44.79  25.39 3.801985  6.692533 3.234355  5.038849
5    Control   P1    M    1  20.99  20.31 3.044046  4.581484 3.011113  4.506662
6    Control   P1    M    2  37.54  17.62 3.625407  6.126989 2.869035  4.197618
7    Control   P1    M    3  61.46  98.44 4.118387  7.839643 4.589447  9.921693
8    Control   P1    M    4  82.21 160.01 4.409277  9.066973 5.075236 12.649506
9    Control   P1    L    1  31.73  21.22 3.457263  5.632939 3.054944  4.606517
10   Control   P1    L    2  59.08  37.51 4.078892  7.686352 3.624608  6.124541
11   Control   P1    L    3  94.54 119.22 4.549023  9.723168 4.780971 10.918791
12   Control   P1    L    4 121.17 116.45 4.797195 11.007725 4.757462 10.791200
13   Control   P2    H    1   8.14  23.93 2.096790  2.853069 3.175133  4.891830
14   Control   P2    H    2  13.36  28.02 2.592265  3.655133 3.332919  5.293392
15   Control   P2    H    3  33.37  37.17 3.507657  5.776677 3.615502  6.096720
16   Control   P2    H    4  39.87  38.25 3.685624  6.314270 3.644144  6.184658
17   Control   P2    M    1  19.95  19.73 2.993229  4.466542 2.982140  4.441846
18   Control   P2    M    2  42.83  40.52 3.757239  6.544463 3.701796  6.365532
19   Control   P2    M    3  62.46   4.81 4.134526  7.903164 1.570697  2.193171
20   Control   P2    M    4  81.78 136.66 4.404033  9.043230 4.917496 11.690167
21   Control   P2    L    1  32.76  30.70 3.489208  5.723635 3.424263  5.540758
22   Control   P2    L    2  62.35 123.78 4.132764  7.896202 4.818506 11.125646
23   Control   P2    L    3  90.22 113.87 4.502251  9.498421 4.735057 10.670989
24   Control   P2    L    4 114.03  76.52 4.736462 10.678483 4.337552  8.747571
25 Exclusion   P3    H    1  21.86  23.58 3.084658  4.675468 3.160399  4.855924
26 Exclusion   P3    H    2  39.83  28.03 3.684620  6.311101 3.333275  5.294337
27 Exclusion   P3    H    3  59.53  21.32 4.086480  7.715569 3.059646  4.617359
28 Exclusion   P3    H    4  75.59  90.76 4.325324  8.694251 4.508219  9.526804
29 Exclusion   P3    M    1  38.57  30.63 3.652475  6.210475 3.421980  5.534438
30 Exclusion   P3    M    2  81.25  83.61 4.397531  9.013878 4.426163  9.143850
31 Exclusion   P3    M    3 124.08 124.09 4.820927 11.139120 4.821007 11.139569
32 Exclusion   P3    M    4 159.69 112.65 5.073234 12.636851 4.724286 10.613670
33 Exclusion   P3    L    1  61.16  39.53 4.113493  7.820486 3.677060  6.287289
34 Exclusion   P3    L    2 119.84 110.27 4.786158 10.947146 4.702932 10.500952
35 Exclusion   P3    L    3 175.87 286.33 5.169745 13.261599 5.657145 16.921288
36 Exclusion   P3    L    4 238.76  54.23 5.475459 15.451861 3.993234  7.364102
37 Exclusion   P4    H    1  18.82  28.60 2.934920  4.338202 3.353407  5.347897
38 Exclusion   P4    H    2  39.82  39.07 3.684369  6.310309 3.665355  6.250600
39 Exclusion   P4    H    3  63.30  93.43 4.147885  7.956130 4.537212  9.665920
40 Exclusion   P4    H    4  82.29  60.15 4.410250  9.071384 4.096841  7.755643
41 Exclusion   P4    M    1  39.51  45.90 3.676554  6.285698 3.826465  6.774954
42 Exclusion   P4    M    2  79.24  88.04 4.372481  8.901685 4.477791  9.382963
43 Exclusion   P4    M    3 122.09  84.19 4.804758 11.049434 4.433076  9.175511
44 Exclusion   P4    M    4 161.67 256.34 5.085557 12.714952 5.546505 16.010621
45 Exclusion   P4    L    1  57.93  85.24 4.059235  7.611176 4.445471  9.232551
46 Exclusion   P4    L    2 117.88 167.90 4.769667 10.857256 5.123369 12.957623
47 Exclusion   P4    L    3 181.09 314.49 5.198994 13.456968 5.750952 17.733866
48 Exclusion   P4    L    4 242.31 304.70 5.490218 15.566310 5.719328 17.455658

Mutate

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Centering

dat.1 |> mutate(MeanResp1 = mean(Resp1),
                 cResp1 = Resp1 - MeanResp1)
## OR if just want the centered variable..
#dat.1 |> mutate(cResp1=Resp1-mean(Resp1))
   Treatment Plot Dose Time  Resp1  Resp2 MeanResp1      cResp1
1    Control   P1    H    1   8.12   3.06  75.26604 -67.1460417
2    Control   P1    H    2  20.55  25.94  75.26604 -54.7160417
3    Control   P1    H    3  27.49  29.85  75.26604 -47.7760417
4    Control   P1    H    4  44.79  25.39  75.26604 -30.4760417
5    Control   P1    M    1  20.99  20.31  75.26604 -54.2760417
6    Control   P1    M    2  37.54  17.62  75.26604 -37.7260417
7    Control   P1    M    3  61.46  98.44  75.26604 -13.8060417
8    Control   P1    M    4  82.21 160.01  75.26604   6.9439583
9    Control   P1    L    1  31.73  21.22  75.26604 -43.5360417
10   Control   P1    L    2  59.08  37.51  75.26604 -16.1860417
11   Control   P1    L    3  94.54 119.22  75.26604  19.2739583
12   Control   P1    L    4 121.17 116.45  75.26604  45.9039583
13   Control   P2    H    1   8.14  23.93  75.26604 -67.1260417
14   Control   P2    H    2  13.36  28.02  75.26604 -61.9060417
15   Control   P2    H    3  33.37  37.17  75.26604 -41.8960417
16   Control   P2    H    4  39.87  38.25  75.26604 -35.3960417
17   Control   P2    M    1  19.95  19.73  75.26604 -55.3160417
18   Control   P2    M    2  42.83  40.52  75.26604 -32.4360417
19   Control   P2    M    3  62.46   4.81  75.26604 -12.8060417
20   Control   P2    M    4  81.78 136.66  75.26604   6.5139583
21   Control   P2    L    1  32.76  30.70  75.26604 -42.5060417
22   Control   P2    L    2  62.35 123.78  75.26604 -12.9160417
23   Control   P2    L    3  90.22 113.87  75.26604  14.9539583
24   Control   P2    L    4 114.03  76.52  75.26604  38.7639583
25 Exclusion   P3    H    1  21.86  23.58  75.26604 -53.4060417
26 Exclusion   P3    H    2  39.83  28.03  75.26604 -35.4360417
27 Exclusion   P3    H    3  59.53  21.32  75.26604 -15.7360417
28 Exclusion   P3    H    4  75.59  90.76  75.26604   0.3239583
29 Exclusion   P3    M    1  38.57  30.63  75.26604 -36.6960417
30 Exclusion   P3    M    2  81.25  83.61  75.26604   5.9839583
31 Exclusion   P3    M    3 124.08 124.09  75.26604  48.8139583
32 Exclusion   P3    M    4 159.69 112.65  75.26604  84.4239583
33 Exclusion   P3    L    1  61.16  39.53  75.26604 -14.1060417
34 Exclusion   P3    L    2 119.84 110.27  75.26604  44.5739583
35 Exclusion   P3    L    3 175.87 286.33  75.26604 100.6039583
36 Exclusion   P3    L    4 238.76  54.23  75.26604 163.4939583
37 Exclusion   P4    H    1  18.82  28.60  75.26604 -56.4460417
38 Exclusion   P4    H    2  39.82  39.07  75.26604 -35.4460417
39 Exclusion   P4    H    3  63.30  93.43  75.26604 -11.9660417
40 Exclusion   P4    H    4  82.29  60.15  75.26604   7.0239583
41 Exclusion   P4    M    1  39.51  45.90  75.26604 -35.7560417
42 Exclusion   P4    M    2  79.24  88.04  75.26604   3.9739583
43 Exclusion   P4    M    3 122.09  84.19  75.26604  46.8239583
44 Exclusion   P4    M    4 161.67 256.34  75.26604  86.4039583
45 Exclusion   P4    L    1  57.93  85.24  75.26604 -17.3360417
46 Exclusion   P4    L    2 117.88 167.90  75.26604  42.6139583
47 Exclusion   P4    L    3 181.09 314.49  75.26604 105.8239583
48 Exclusion   P4    L    4 242.31 304.70  75.26604 167.0439583

Mutate

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Row counter

dat.1 |> mutate(N = 1:n())
   Treatment Plot Dose Time  Resp1  Resp2  N
1    Control   P1    H    1   8.12   3.06  1
2    Control   P1    H    2  20.55  25.94  2
3    Control   P1    H    3  27.49  29.85  3
4    Control   P1    H    4  44.79  25.39  4
5    Control   P1    M    1  20.99  20.31  5
6    Control   P1    M    2  37.54  17.62  6
7    Control   P1    M    3  61.46  98.44  7
8    Control   P1    M    4  82.21 160.01  8
9    Control   P1    L    1  31.73  21.22  9
10   Control   P1    L    2  59.08  37.51 10
11   Control   P1    L    3  94.54 119.22 11
12   Control   P1    L    4 121.17 116.45 12
13   Control   P2    H    1   8.14  23.93 13
14   Control   P2    H    2  13.36  28.02 14
15   Control   P2    H    3  33.37  37.17 15
16   Control   P2    H    4  39.87  38.25 16
17   Control   P2    M    1  19.95  19.73 17
18   Control   P2    M    2  42.83  40.52 18
19   Control   P2    M    3  62.46   4.81 19
20   Control   P2    M    4  81.78 136.66 20
21   Control   P2    L    1  32.76  30.70 21
22   Control   P2    L    2  62.35 123.78 22
23   Control   P2    L    3  90.22 113.87 23
24   Control   P2    L    4 114.03  76.52 24
25 Exclusion   P3    H    1  21.86  23.58 25
26 Exclusion   P3    H    2  39.83  28.03 26
27 Exclusion   P3    H    3  59.53  21.32 27
28 Exclusion   P3    H    4  75.59  90.76 28
29 Exclusion   P3    M    1  38.57  30.63 29
30 Exclusion   P3    M    2  81.25  83.61 30
31 Exclusion   P3    M    3 124.08 124.09 31
32 Exclusion   P3    M    4 159.69 112.65 32
33 Exclusion   P3    L    1  61.16  39.53 33
34 Exclusion   P3    L    2 119.84 110.27 34
35 Exclusion   P3    L    3 175.87 286.33 35
36 Exclusion   P3    L    4 238.76  54.23 36
37 Exclusion   P4    H    1  18.82  28.60 37
38 Exclusion   P4    H    2  39.82  39.07 38
39 Exclusion   P4    H    3  63.30  93.43 39
40 Exclusion   P4    H    4  82.29  60.15 40
41 Exclusion   P4    M    1  39.51  45.90 41
42 Exclusion   P4    M    2  79.24  88.04 42
43 Exclusion   P4    M    3 122.09  84.19 43
44 Exclusion   P4    M    4 161.67 256.34 44
45 Exclusion   P4    L    1  57.93  85.24 45
46 Exclusion   P4    L    2 117.88 167.90 46
47 Exclusion   P4    L    3 181.09 314.49 47
48 Exclusion   P4    L    4 242.31 304.70 48

Mutate

dat.1 |> head(2) |> as_tibble()
# A tibble: 2 × 6
  Treatment Plot  Dose   Time Resp1 Resp2
  <fct>     <fct> <fct> <int> <dbl> <dbl>
1 Control   P1    H         1  8.12  3.06
2 Control   P1    H         2 20.6  25.9

Changing vector types (classes)

dat.1 |> mutate(Time = factor(Time)) |> as_tibble()
# A tibble: 48 × 6
   Treatment Plot  Dose  Time  Resp1  Resp2
   <fct>     <fct> <fct> <fct> <dbl>  <dbl>
 1 Control   P1    H     1      8.12   3.06
 2 Control   P1    H     2     20.6   25.9 
 3 Control   P1    H     3     27.5   29.8 
 4 Control   P1    H     4     44.8   25.4 
 5 Control   P1    M     1     21.0   20.3 
 6 Control   P1    M     2     37.5   17.6 
 7 Control   P1    M     3     61.5   98.4 
 8 Control   P1    M     4     82.2  160.  
 9 Control   P1    L     1     31.7   21.2 
10 Control   P1    L     2     59.1   37.5 
# ℹ 38 more rows

Mutate

dat.1 |> head(2) |> as_tibble()
# A tibble: 2 × 6
  Treatment Plot  Dose   Time Resp1 Resp2
  <fct>     <fct> <fct> <int> <dbl> <dbl>
1 Control   P1    H         1  8.12  3.06
2 Control   P1    H         2 20.6  25.9

Changing factor labels

dat.1 |> mutate(Dose = fct_recode(Dose, High = 'H',  Medium = 'M')) |>
  as_tibble()
# A tibble: 48 × 6
   Treatment Plot  Dose    Time Resp1  Resp2
   <fct>     <fct> <fct>  <int> <dbl>  <dbl>
 1 Control   P1    High       1  8.12   3.06
 2 Control   P1    High       2 20.6   25.9 
 3 Control   P1    High       3 27.5   29.8 
 4 Control   P1    High       4 44.8   25.4 
 5 Control   P1    Medium     1 21.0   20.3 
 6 Control   P1    Medium     2 37.5   17.6 
 7 Control   P1    Medium     3 61.5   98.4 
 8 Control   P1    Medium     4 82.2  160.  
 9 Control   P1    L          1 31.7   21.2 
10 Control   P1    L          2 59.1   37.5 
# ℹ 38 more rows

Mutate

dat.1 |> head(2) |> as_tibble()
# A tibble: 2 × 6
  Treatment Plot  Dose   Time Resp1 Resp2
  <fct>     <fct> <fct> <int> <dbl> <dbl>
1 Control   P1    H         1  8.12  3.06
2 Control   P1    H         2 20.6  25.9

Changing factor levels

dat.1 |> pull(Dose)
 [1] H H H H M M M M L L L L H H H H M M M M L L L L H H H H M M M M L L L L H H H H M M M M L L L L
Levels: H L M
dat.1 |>
    mutate(Dose = fct_relevel(Dose, c("L", "M", "H"))) |>
    as_tibble() |>
    pull(Dose)
 [1] H H H H M M M M L L L L H H H H M M M M L L L L H H H H M M M M L L L L H H H H M M M M L L L L
Levels: L M H

Mutate

dat.1 |> head(2) |> as_tibble()
# A tibble: 2 × 6
  Treatment Plot  Dose   Time Resp1 Resp2
  <fct>     <fct> <fct> <int> <dbl> <dbl>
1 Control   P1    H         1  8.12  3.06
2 Control   P1    H         2 20.6  25.9

Changing factor levels

dat.1 |> pull(Dose)
 [1] H H H H M M M M L L L L H H H H M M M M L L L L H H H H M M M M L L L L H H H H M M M M L L L L
Levels: H L M
dat.1 |> mutate(
              Dose = fct_relevel(Dose, c("L", "M", "H")),
              Dose = fct_recode(Dose, High = 'H',  Medium = 'M')
              ) |>
    as_tibble() |>
    pull(Dose)
 [1] High   High   High   High   Medium Medium Medium Medium L      L      L      L      High  
[14] High   High   High   Medium Medium Medium Medium L      L      L      L      High   High  
[27] High   High   Medium Medium Medium Medium L      L      L      L      High   High   High  
[40] High   Medium Medium Medium Medium L      L      L      L     
Levels: L Medium High
#OR
dat.1 |>
    mutate(Dose = recode_factor(Dose, "L" = "Low", "M" = "Medium")) |>
    as_tibble() |>
    pull(Dose)
 [1] H      H      H      H      Medium Medium Medium Medium Low    Low    Low    Low    H     
[14] H      H      H      Medium Medium Medium Medium Low    Low    Low    Low    H      H     
[27] H      H      Medium Medium Medium Medium Low    Low    Low    Low    H      H      H     
[40] H      Medium Medium Medium Medium Low    Low    Low    Low   
Levels: Low Medium H

Mutate

dat.1 |> head(2) |> as_tibble()
# A tibble: 2 × 6
  Treatment Plot  Dose   Time Resp1 Resp2
  <fct>     <fct> <fct> <int> <dbl> <dbl>
1 Control   P1    H         1  8.12  3.06
2 Control   P1    H         2 20.6  25.9

Factor levels reflecting order in data

dat.1 |> pull(Dose)
 [1] H H H H M M M M L L L L H H H H M M M M L L L L H H H H M M M M L L L L H H H H M M M M L L L L
Levels: H L M
dat.1 |> mutate(Dose = fct_reorder(Dose, 1:n())) |>
    as_tibble() |>
    pull(Dose)
 [1] H H H H M M M M L L L L H H H H M M M M L L L L H H H H M M M M L L L L H H H H M M M M L L L L
Levels: H M L

Mutate

dat.1 |> head(2) |> as_tibble()
# A tibble: 2 × 6
  Treatment Plot  Dose   Time Resp1 Resp2
  <fct>     <fct> <fct> <int> <dbl> <dbl>
1 Control   P1    H         1  8.12  3.06
2 Control   P1    H         2 20.6  25.9

Factor levels according to a numeric

dat.1 |> pull(Dose)
 [1] H H H H M M M M L L L L H H H H M M M M L L L L H H H H M M M M L L L L H H H H M M M M L L L L
Levels: H L M
dat.1 |> mutate(Dose = fct_reorder(Dose, Resp1, median)) |>
    as_tibble() |>
    pull(Dose)
 [1] H H H H M M M M L L L L H H H H M M M M L L L L H H H H M M M M L L L L H H H H M M M M L L L L
Levels: H M L

Mutate

Window functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> mutate(leadResp2 = lead(Resp2), lagResp2 = lag(Resp2))
   Treatment Plot Dose Time  Resp1  Resp2 leadResp2 lagResp2
1    Control   P1    H    1   8.12   3.06     25.94       NA
2    Control   P1    H    2  20.55  25.94     29.85     3.06
3    Control   P1    H    3  27.49  29.85     25.39    25.94
4    Control   P1    H    4  44.79  25.39     20.31    29.85
5    Control   P1    M    1  20.99  20.31     17.62    25.39
6    Control   P1    M    2  37.54  17.62     98.44    20.31
7    Control   P1    M    3  61.46  98.44    160.01    17.62
8    Control   P1    M    4  82.21 160.01     21.22    98.44
9    Control   P1    L    1  31.73  21.22     37.51   160.01
10   Control   P1    L    2  59.08  37.51    119.22    21.22
11   Control   P1    L    3  94.54 119.22    116.45    37.51
12   Control   P1    L    4 121.17 116.45     23.93   119.22
13   Control   P2    H    1   8.14  23.93     28.02   116.45
14   Control   P2    H    2  13.36  28.02     37.17    23.93
15   Control   P2    H    3  33.37  37.17     38.25    28.02
16   Control   P2    H    4  39.87  38.25     19.73    37.17
17   Control   P2    M    1  19.95  19.73     40.52    38.25
18   Control   P2    M    2  42.83  40.52      4.81    19.73
19   Control   P2    M    3  62.46   4.81    136.66    40.52
20   Control   P2    M    4  81.78 136.66     30.70     4.81
21   Control   P2    L    1  32.76  30.70    123.78   136.66
22   Control   P2    L    2  62.35 123.78    113.87    30.70
23   Control   P2    L    3  90.22 113.87     76.52   123.78
24   Control   P2    L    4 114.03  76.52     23.58   113.87
25 Exclusion   P3    H    1  21.86  23.58     28.03    76.52
26 Exclusion   P3    H    2  39.83  28.03     21.32    23.58
27 Exclusion   P3    H    3  59.53  21.32     90.76    28.03
28 Exclusion   P3    H    4  75.59  90.76     30.63    21.32
29 Exclusion   P3    M    1  38.57  30.63     83.61    90.76
30 Exclusion   P3    M    2  81.25  83.61    124.09    30.63
31 Exclusion   P3    M    3 124.08 124.09    112.65    83.61
32 Exclusion   P3    M    4 159.69 112.65     39.53   124.09
33 Exclusion   P3    L    1  61.16  39.53    110.27   112.65
34 Exclusion   P3    L    2 119.84 110.27    286.33    39.53
35 Exclusion   P3    L    3 175.87 286.33     54.23   110.27
36 Exclusion   P3    L    4 238.76  54.23     28.60   286.33
37 Exclusion   P4    H    1  18.82  28.60     39.07    54.23
38 Exclusion   P4    H    2  39.82  39.07     93.43    28.60
39 Exclusion   P4    H    3  63.30  93.43     60.15    39.07
40 Exclusion   P4    H    4  82.29  60.15     45.90    93.43
41 Exclusion   P4    M    1  39.51  45.90     88.04    60.15
42 Exclusion   P4    M    2  79.24  88.04     84.19    45.90
43 Exclusion   P4    M    3 122.09  84.19    256.34    88.04
44 Exclusion   P4    M    4 161.67 256.34     85.24    84.19
45 Exclusion   P4    L    1  57.93  85.24    167.90   256.34
46 Exclusion   P4    L    2 117.88 167.90    314.49    85.24
47 Exclusion   P4    L    3 181.09 314.49    304.70   167.90
48 Exclusion   P4    L    4 242.31 304.70        NA   314.49

Mutate

Window functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Rank orders

dat.1 |> mutate(rankTime = min_rank(Time),
                 denseRankTime = dense_rank(Time))
   Treatment Plot Dose Time  Resp1  Resp2 rankTime denseRankTime
1    Control   P1    H    1   8.12   3.06        1             1
2    Control   P1    H    2  20.55  25.94       13             2
3    Control   P1    H    3  27.49  29.85       25             3
4    Control   P1    H    4  44.79  25.39       37             4
5    Control   P1    M    1  20.99  20.31        1             1
6    Control   P1    M    2  37.54  17.62       13             2
7    Control   P1    M    3  61.46  98.44       25             3
8    Control   P1    M    4  82.21 160.01       37             4
9    Control   P1    L    1  31.73  21.22        1             1
10   Control   P1    L    2  59.08  37.51       13             2
11   Control   P1    L    3  94.54 119.22       25             3
12   Control   P1    L    4 121.17 116.45       37             4
13   Control   P2    H    1   8.14  23.93        1             1
14   Control   P2    H    2  13.36  28.02       13             2
15   Control   P2    H    3  33.37  37.17       25             3
16   Control   P2    H    4  39.87  38.25       37             4
17   Control   P2    M    1  19.95  19.73        1             1
18   Control   P2    M    2  42.83  40.52       13             2
19   Control   P2    M    3  62.46   4.81       25             3
20   Control   P2    M    4  81.78 136.66       37             4
21   Control   P2    L    1  32.76  30.70        1             1
22   Control   P2    L    2  62.35 123.78       13             2
23   Control   P2    L    3  90.22 113.87       25             3
24   Control   P2    L    4 114.03  76.52       37             4
25 Exclusion   P3    H    1  21.86  23.58        1             1
26 Exclusion   P3    H    2  39.83  28.03       13             2
27 Exclusion   P3    H    3  59.53  21.32       25             3
28 Exclusion   P3    H    4  75.59  90.76       37             4
29 Exclusion   P3    M    1  38.57  30.63        1             1
30 Exclusion   P3    M    2  81.25  83.61       13             2
31 Exclusion   P3    M    3 124.08 124.09       25             3
32 Exclusion   P3    M    4 159.69 112.65       37             4
33 Exclusion   P3    L    1  61.16  39.53        1             1
34 Exclusion   P3    L    2 119.84 110.27       13             2
35 Exclusion   P3    L    3 175.87 286.33       25             3
36 Exclusion   P3    L    4 238.76  54.23       37             4
37 Exclusion   P4    H    1  18.82  28.60        1             1
38 Exclusion   P4    H    2  39.82  39.07       13             2
39 Exclusion   P4    H    3  63.30  93.43       25             3
40 Exclusion   P4    H    4  82.29  60.15       37             4
41 Exclusion   P4    M    1  39.51  45.90        1             1
42 Exclusion   P4    M    2  79.24  88.04       13             2
43 Exclusion   P4    M    3 122.09  84.19       25             3
44 Exclusion   P4    M    4 161.67 256.34       37             4
45 Exclusion   P4    L    1  57.93  85.24        1             1
46 Exclusion   P4    L    2 117.88 167.90       13             2
47 Exclusion   P4    L    3 181.09 314.49       25             3
48 Exclusion   P4    L    4 242.31 304.70       37             4

Mutate

Window functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Rank orders

dat.1 |> mutate(rowresp1 = row_number(Resp1),
                 rowTime = row_number(Time),
                  rankTime = min_rank(Time))
   Treatment Plot Dose Time  Resp1  Resp2 rowresp1 rowTime rankTime
1    Control   P1    H    1   8.12   3.06        1       1        1
2    Control   P1    H    2  20.55  25.94        6      13       13
3    Control   P1    H    3  27.49  29.85        9      25       25
4    Control   P1    H    4  44.79  25.39       20      37       37
5    Control   P1    M    1  20.99  20.31        7       2        1
6    Control   P1    M    2  37.54  17.62       13      14       13
7    Control   P1    M    3  61.46  98.44       25      26       25
8    Control   P1    M    4  82.21 160.01       33      38       37
9    Control   P1    L    1  31.73  21.22       10       3        1
10   Control   P1    L    2  59.08  37.51       22      15       13
11   Control   P1    L    3  94.54 119.22       36      27       25
12   Control   P1    L    4 121.17 116.45       40      39       37
13   Control   P2    H    1   8.14  23.93        2       4        1
14   Control   P2    H    2  13.36  28.02        3      16       13
15   Control   P2    H    3  33.37  37.17       12      28       25
16   Control   P2    H    4  39.87  38.25       18      40       37
17   Control   P2    M    1  19.95  19.73        5       5        1
18   Control   P2    M    2  42.83  40.52       19      17       13
19   Control   P2    M    3  62.46   4.81       27      29       25
20   Control   P2    M    4  81.78 136.66       32      41       37
21   Control   P2    L    1  32.76  30.70       11       6        1
22   Control   P2    L    2  62.35 123.78       26      18       13
23   Control   P2    L    3  90.22 113.87       35      30       25
24   Control   P2    L    4 114.03  76.52       37      42       37
25 Exclusion   P3    H    1  21.86  23.58        8       7        1
26 Exclusion   P3    H    2  39.83  28.03       17      19       13
27 Exclusion   P3    H    3  59.53  21.32       23      31       25
28 Exclusion   P3    H    4  75.59  90.76       29      43       37
29 Exclusion   P3    M    1  38.57  30.63       14       8        1
30 Exclusion   P3    M    2  81.25  83.61       31      20       13
31 Exclusion   P3    M    3 124.08 124.09       42      32       25
32 Exclusion   P3    M    4 159.69 112.65       43      44       37
33 Exclusion   P3    L    1  61.16  39.53       24       9        1
34 Exclusion   P3    L    2 119.84 110.27       39      21       13
35 Exclusion   P3    L    3 175.87 286.33       45      33       25
36 Exclusion   P3    L    4 238.76  54.23       47      45       37
37 Exclusion   P4    H    1  18.82  28.60        4      10        1
38 Exclusion   P4    H    2  39.82  39.07       16      22       13
39 Exclusion   P4    H    3  63.30  93.43       28      34       25
40 Exclusion   P4    H    4  82.29  60.15       34      46       37
41 Exclusion   P4    M    1  39.51  45.90       15      11        1
42 Exclusion   P4    M    2  79.24  88.04       30      23       13
43 Exclusion   P4    M    3 122.09  84.19       41      35       25
44 Exclusion   P4    M    4 161.67 256.34       44      47       37
45 Exclusion   P4    L    1  57.93  85.24       21      12        1
46 Exclusion   P4    L    2 117.88 167.90       38      24       13
47 Exclusion   P4    L    3 181.09 314.49       46      36       25
48 Exclusion   P4    L    4 242.31 304.70       48      48       37

Mutate

Window functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Rank of bins

dat.1 |> mutate(ntile(Resp1, 4))
   Treatment Plot Dose Time  Resp1  Resp2 ntile(Resp1, 4)
1    Control   P1    H    1   8.12   3.06               1
2    Control   P1    H    2  20.55  25.94               1
3    Control   P1    H    3  27.49  29.85               1
4    Control   P1    H    4  44.79  25.39               2
5    Control   P1    M    1  20.99  20.31               1
6    Control   P1    M    2  37.54  17.62               2
7    Control   P1    M    3  61.46  98.44               3
8    Control   P1    M    4  82.21 160.01               3
9    Control   P1    L    1  31.73  21.22               1
10   Control   P1    L    2  59.08  37.51               2
11   Control   P1    L    3  94.54 119.22               3
12   Control   P1    L    4 121.17 116.45               4
13   Control   P2    H    1   8.14  23.93               1
14   Control   P2    H    2  13.36  28.02               1
15   Control   P2    H    3  33.37  37.17               1
16   Control   P2    H    4  39.87  38.25               2
17   Control   P2    M    1  19.95  19.73               1
18   Control   P2    M    2  42.83  40.52               2
19   Control   P2    M    3  62.46   4.81               3
20   Control   P2    M    4  81.78 136.66               3
21   Control   P2    L    1  32.76  30.70               1
22   Control   P2    L    2  62.35 123.78               3
23   Control   P2    L    3  90.22 113.87               3
24   Control   P2    L    4 114.03  76.52               4
25 Exclusion   P3    H    1  21.86  23.58               1
26 Exclusion   P3    H    2  39.83  28.03               2
27 Exclusion   P3    H    3  59.53  21.32               2
28 Exclusion   P3    H    4  75.59  90.76               3
29 Exclusion   P3    M    1  38.57  30.63               2
30 Exclusion   P3    M    2  81.25  83.61               3
31 Exclusion   P3    M    3 124.08 124.09               4
32 Exclusion   P3    M    4 159.69 112.65               4
33 Exclusion   P3    L    1  61.16  39.53               2
34 Exclusion   P3    L    2 119.84 110.27               4
35 Exclusion   P3    L    3 175.87 286.33               4
36 Exclusion   P3    L    4 238.76  54.23               4
37 Exclusion   P4    H    1  18.82  28.60               1
38 Exclusion   P4    H    2  39.82  39.07               2
39 Exclusion   P4    H    3  63.30  93.43               3
40 Exclusion   P4    H    4  82.29  60.15               3
41 Exclusion   P4    M    1  39.51  45.90               2
42 Exclusion   P4    M    2  79.24  88.04               3
43 Exclusion   P4    M    3 122.09  84.19               4
44 Exclusion   P4    M    4 161.67 256.34               4
45 Exclusion   P4    L    1  57.93  85.24               2
46 Exclusion   P4    L    2 117.88 167.90               4
47 Exclusion   P4    L    3 181.09 314.49               4
48 Exclusion   P4    L    4 242.31 304.70               4

Mutate

Window functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Logical bins

dat.1 |> mutate(between(Resp1, 20, 40))
   Treatment Plot Dose Time  Resp1  Resp2 between(Resp1, 20, 40)
1    Control   P1    H    1   8.12   3.06                  FALSE
2    Control   P1    H    2  20.55  25.94                   TRUE
3    Control   P1    H    3  27.49  29.85                   TRUE
4    Control   P1    H    4  44.79  25.39                  FALSE
5    Control   P1    M    1  20.99  20.31                   TRUE
6    Control   P1    M    2  37.54  17.62                   TRUE
7    Control   P1    M    3  61.46  98.44                  FALSE
8    Control   P1    M    4  82.21 160.01                  FALSE
9    Control   P1    L    1  31.73  21.22                   TRUE
10   Control   P1    L    2  59.08  37.51                  FALSE
11   Control   P1    L    3  94.54 119.22                  FALSE
12   Control   P1    L    4 121.17 116.45                  FALSE
13   Control   P2    H    1   8.14  23.93                  FALSE
14   Control   P2    H    2  13.36  28.02                  FALSE
15   Control   P2    H    3  33.37  37.17                   TRUE
16   Control   P2    H    4  39.87  38.25                   TRUE
17   Control   P2    M    1  19.95  19.73                  FALSE
18   Control   P2    M    2  42.83  40.52                  FALSE
19   Control   P2    M    3  62.46   4.81                  FALSE
20   Control   P2    M    4  81.78 136.66                  FALSE
21   Control   P2    L    1  32.76  30.70                   TRUE
22   Control   P2    L    2  62.35 123.78                  FALSE
23   Control   P2    L    3  90.22 113.87                  FALSE
24   Control   P2    L    4 114.03  76.52                  FALSE
25 Exclusion   P3    H    1  21.86  23.58                   TRUE
26 Exclusion   P3    H    2  39.83  28.03                   TRUE
27 Exclusion   P3    H    3  59.53  21.32                  FALSE
28 Exclusion   P3    H    4  75.59  90.76                  FALSE
29 Exclusion   P3    M    1  38.57  30.63                   TRUE
30 Exclusion   P3    M    2  81.25  83.61                  FALSE
31 Exclusion   P3    M    3 124.08 124.09                  FALSE
32 Exclusion   P3    M    4 159.69 112.65                  FALSE
33 Exclusion   P3    L    1  61.16  39.53                  FALSE
34 Exclusion   P3    L    2 119.84 110.27                  FALSE
35 Exclusion   P3    L    3 175.87 286.33                  FALSE
36 Exclusion   P3    L    4 238.76  54.23                  FALSE
37 Exclusion   P4    H    1  18.82  28.60                  FALSE
38 Exclusion   P4    H    2  39.82  39.07                   TRUE
39 Exclusion   P4    H    3  63.30  93.43                  FALSE
40 Exclusion   P4    H    4  82.29  60.15                  FALSE
41 Exclusion   P4    M    1  39.51  45.90                   TRUE
42 Exclusion   P4    M    2  79.24  88.04                  FALSE
43 Exclusion   P4    M    3 122.09  84.19                  FALSE
44 Exclusion   P4    M    4 161.67 256.34                  FALSE
45 Exclusion   P4    L    1  57.93  85.24                  FALSE
46 Exclusion   P4    L    2 117.88 167.90                  FALSE
47 Exclusion   P4    L    3 181.09 314.49                  FALSE
48 Exclusion   P4    L    4 242.31 304.70                  FALSE

Mutate

Window functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Categorical bins

dat.1 |> mutate(fResp1 = ifelse(Resp1 < 30, "Low",
      ifelse(between(Resp1, 31, 50), "Medium", "High")))
## OR
dat.1 |> mutate(fResp1 = case_when(Resp1 < 31 ~ "Low",
                 between(Resp1, 31, 50) ~ "Medium",
                 Resp1 > 50 ~ "High"))
   Treatment Plot Dose Time  Resp1  Resp2 fResp1
1    Control   P1    H    1   8.12   3.06    Low
2    Control   P1    H    2  20.55  25.94    Low
3    Control   P1    H    3  27.49  29.85    Low
4    Control   P1    H    4  44.79  25.39 Medium
5    Control   P1    M    1  20.99  20.31    Low
6    Control   P1    M    2  37.54  17.62 Medium
7    Control   P1    M    3  61.46  98.44   High
8    Control   P1    M    4  82.21 160.01   High
9    Control   P1    L    1  31.73  21.22 Medium
10   Control   P1    L    2  59.08  37.51   High
11   Control   P1    L    3  94.54 119.22   High
12   Control   P1    L    4 121.17 116.45   High
13   Control   P2    H    1   8.14  23.93    Low
14   Control   P2    H    2  13.36  28.02    Low
15   Control   P2    H    3  33.37  37.17 Medium
16   Control   P2    H    4  39.87  38.25 Medium
17   Control   P2    M    1  19.95  19.73    Low
18   Control   P2    M    2  42.83  40.52 Medium
19   Control   P2    M    3  62.46   4.81   High
20   Control   P2    M    4  81.78 136.66   High
21   Control   P2    L    1  32.76  30.70 Medium
22   Control   P2    L    2  62.35 123.78   High
23   Control   P2    L    3  90.22 113.87   High
24   Control   P2    L    4 114.03  76.52   High
25 Exclusion   P3    H    1  21.86  23.58    Low
26 Exclusion   P3    H    2  39.83  28.03 Medium
27 Exclusion   P3    H    3  59.53  21.32   High
28 Exclusion   P3    H    4  75.59  90.76   High
29 Exclusion   P3    M    1  38.57  30.63 Medium
30 Exclusion   P3    M    2  81.25  83.61   High
31 Exclusion   P3    M    3 124.08 124.09   High
32 Exclusion   P3    M    4 159.69 112.65   High
33 Exclusion   P3    L    1  61.16  39.53   High
34 Exclusion   P3    L    2 119.84 110.27   High
35 Exclusion   P3    L    3 175.87 286.33   High
36 Exclusion   P3    L    4 238.76  54.23   High
37 Exclusion   P4    H    1  18.82  28.60    Low
38 Exclusion   P4    H    2  39.82  39.07 Medium
39 Exclusion   P4    H    3  63.30  93.43   High
40 Exclusion   P4    H    4  82.29  60.15   High
41 Exclusion   P4    M    1  39.51  45.90 Medium
42 Exclusion   P4    M    2  79.24  88.04   High
43 Exclusion   P4    M    3 122.09  84.19   High
44 Exclusion   P4    M    4 161.67 256.34   High
45 Exclusion   P4    L    1  57.93  85.24   High
46 Exclusion   P4    L    2 117.88 167.90   High
47 Exclusion   P4    L    3 181.09 314.49   High
48 Exclusion   P4    L    4 242.31 304.70   High
   Treatment Plot Dose Time  Resp1  Resp2 fResp1
1    Control   P1    H    1   8.12   3.06    Low
2    Control   P1    H    2  20.55  25.94    Low
3    Control   P1    H    3  27.49  29.85    Low
4    Control   P1    H    4  44.79  25.39 Medium
5    Control   P1    M    1  20.99  20.31    Low
6    Control   P1    M    2  37.54  17.62 Medium
7    Control   P1    M    3  61.46  98.44   High
8    Control   P1    M    4  82.21 160.01   High
9    Control   P1    L    1  31.73  21.22 Medium
10   Control   P1    L    2  59.08  37.51   High
11   Control   P1    L    3  94.54 119.22   High
12   Control   P1    L    4 121.17 116.45   High
13   Control   P2    H    1   8.14  23.93    Low
14   Control   P2    H    2  13.36  28.02    Low
15   Control   P2    H    3  33.37  37.17 Medium
16   Control   P2    H    4  39.87  38.25 Medium
17   Control   P2    M    1  19.95  19.73    Low
18   Control   P2    M    2  42.83  40.52 Medium
19   Control   P2    M    3  62.46   4.81   High
20   Control   P2    M    4  81.78 136.66   High
21   Control   P2    L    1  32.76  30.70 Medium
22   Control   P2    L    2  62.35 123.78   High
23   Control   P2    L    3  90.22 113.87   High
24   Control   P2    L    4 114.03  76.52   High
25 Exclusion   P3    H    1  21.86  23.58    Low
26 Exclusion   P3    H    2  39.83  28.03 Medium
27 Exclusion   P3    H    3  59.53  21.32   High
28 Exclusion   P3    H    4  75.59  90.76   High
29 Exclusion   P3    M    1  38.57  30.63 Medium
30 Exclusion   P3    M    2  81.25  83.61   High
31 Exclusion   P3    M    3 124.08 124.09   High
32 Exclusion   P3    M    4 159.69 112.65   High
33 Exclusion   P3    L    1  61.16  39.53   High
34 Exclusion   P3    L    2 119.84 110.27   High
35 Exclusion   P3    L    3 175.87 286.33   High
36 Exclusion   P3    L    4 238.76  54.23   High
37 Exclusion   P4    H    1  18.82  28.60    Low
38 Exclusion   P4    H    2  39.82  39.07 Medium
39 Exclusion   P4    H    3  63.30  93.43   High
40 Exclusion   P4    H    4  82.29  60.15   High
41 Exclusion   P4    M    1  39.51  45.90 Medium
42 Exclusion   P4    M    2  79.24  88.04   High
43 Exclusion   P4    M    3 122.09  84.19   High
44 Exclusion   P4    M    4 161.67 256.34   High
45 Exclusion   P4    L    1  57.93  85.24   High
46 Exclusion   P4    L    2 117.88 167.90   High
47 Exclusion   P4    L    3 181.09 314.49   High
48 Exclusion   P4    L    4 242.31 304.70   High

Mutate

Window functions

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Categorical bins

dat.1 |> mutate(fResp1 = cut(Resp1, breaks = c(0, 31, 50, 200),
                              labels = c("Low", "Medium", "High")))
   Treatment Plot Dose Time  Resp1  Resp2 fResp1
1    Control   P1    H    1   8.12   3.06    Low
2    Control   P1    H    2  20.55  25.94    Low
3    Control   P1    H    3  27.49  29.85    Low
4    Control   P1    H    4  44.79  25.39 Medium
5    Control   P1    M    1  20.99  20.31    Low
6    Control   P1    M    2  37.54  17.62 Medium
7    Control   P1    M    3  61.46  98.44   High
8    Control   P1    M    4  82.21 160.01   High
9    Control   P1    L    1  31.73  21.22 Medium
10   Control   P1    L    2  59.08  37.51   High
11   Control   P1    L    3  94.54 119.22   High
12   Control   P1    L    4 121.17 116.45   High
13   Control   P2    H    1   8.14  23.93    Low
14   Control   P2    H    2  13.36  28.02    Low
15   Control   P2    H    3  33.37  37.17 Medium
16   Control   P2    H    4  39.87  38.25 Medium
17   Control   P2    M    1  19.95  19.73    Low
18   Control   P2    M    2  42.83  40.52 Medium
19   Control   P2    M    3  62.46   4.81   High
20   Control   P2    M    4  81.78 136.66   High
21   Control   P2    L    1  32.76  30.70 Medium
22   Control   P2    L    2  62.35 123.78   High
23   Control   P2    L    3  90.22 113.87   High
24   Control   P2    L    4 114.03  76.52   High
25 Exclusion   P3    H    1  21.86  23.58    Low
26 Exclusion   P3    H    2  39.83  28.03 Medium
27 Exclusion   P3    H    3  59.53  21.32   High
28 Exclusion   P3    H    4  75.59  90.76   High
29 Exclusion   P3    M    1  38.57  30.63 Medium
30 Exclusion   P3    M    2  81.25  83.61   High
31 Exclusion   P3    M    3 124.08 124.09   High
32 Exclusion   P3    M    4 159.69 112.65   High
33 Exclusion   P3    L    1  61.16  39.53   High
34 Exclusion   P3    L    2 119.84 110.27   High
35 Exclusion   P3    L    3 175.87 286.33   High
36 Exclusion   P3    L    4 238.76  54.23   <NA>
37 Exclusion   P4    H    1  18.82  28.60    Low
38 Exclusion   P4    H    2  39.82  39.07 Medium
39 Exclusion   P4    H    3  63.30  93.43   High
40 Exclusion   P4    H    4  82.29  60.15   High
41 Exclusion   P4    M    1  39.51  45.90 Medium
42 Exclusion   P4    M    2  79.24  88.04   High
43 Exclusion   P4    M    3 122.09  84.19   High
44 Exclusion   P4    M    4 161.67 256.34   High
45 Exclusion   P4    L    1  57.93  85.24   High
46 Exclusion   P4    L    2 117.88 167.90   High
47 Exclusion   P4    L    3 181.09 314.49   High
48 Exclusion   P4    L    4 242.31 304.70   <NA>

Your turn

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Bin Time into Start (1 and 2) and end (3 and 4)

Your turn

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Bin Time into Start (1 and 2) and end (3 and 4)

Assuming even spread..

dat.1 |> mutate(Period = cut(Time, breaks = 2, labels = c("Start", "End")))
   Treatment Plot Dose Time  Resp1  Resp2 Period
1    Control   P1    H    1   8.12   3.06  Start
2    Control   P1    H    2  20.55  25.94  Start
3    Control   P1    H    3  27.49  29.85    End
4    Control   P1    H    4  44.79  25.39    End
5    Control   P1    M    1  20.99  20.31  Start
6    Control   P1    M    2  37.54  17.62  Start
7    Control   P1    M    3  61.46  98.44    End
8    Control   P1    M    4  82.21 160.01    End
9    Control   P1    L    1  31.73  21.22  Start
10   Control   P1    L    2  59.08  37.51  Start
11   Control   P1    L    3  94.54 119.22    End
12   Control   P1    L    4 121.17 116.45    End
13   Control   P2    H    1   8.14  23.93  Start
14   Control   P2    H    2  13.36  28.02  Start
15   Control   P2    H    3  33.37  37.17    End
16   Control   P2    H    4  39.87  38.25    End
17   Control   P2    M    1  19.95  19.73  Start
18   Control   P2    M    2  42.83  40.52  Start
19   Control   P2    M    3  62.46   4.81    End
20   Control   P2    M    4  81.78 136.66    End
21   Control   P2    L    1  32.76  30.70  Start
22   Control   P2    L    2  62.35 123.78  Start
23   Control   P2    L    3  90.22 113.87    End
24   Control   P2    L    4 114.03  76.52    End
25 Exclusion   P3    H    1  21.86  23.58  Start
26 Exclusion   P3    H    2  39.83  28.03  Start
27 Exclusion   P3    H    3  59.53  21.32    End
28 Exclusion   P3    H    4  75.59  90.76    End
29 Exclusion   P3    M    1  38.57  30.63  Start
30 Exclusion   P3    M    2  81.25  83.61  Start
31 Exclusion   P3    M    3 124.08 124.09    End
32 Exclusion   P3    M    4 159.69 112.65    End
33 Exclusion   P3    L    1  61.16  39.53  Start
34 Exclusion   P3    L    2 119.84 110.27  Start
35 Exclusion   P3    L    3 175.87 286.33    End
36 Exclusion   P3    L    4 238.76  54.23    End
37 Exclusion   P4    H    1  18.82  28.60  Start
38 Exclusion   P4    H    2  39.82  39.07  Start
39 Exclusion   P4    H    3  63.30  93.43    End
40 Exclusion   P4    H    4  82.29  60.15    End
41 Exclusion   P4    M    1  39.51  45.90  Start
42 Exclusion   P4    M    2  79.24  88.04  Start
43 Exclusion   P4    M    3 122.09  84.19    End
44 Exclusion   P4    M    4 161.67 256.34    End
45 Exclusion   P4    L    1  57.93  85.24  Start
46 Exclusion   P4    L    2 117.88 167.90  Start
47 Exclusion   P4    L    3 181.09 314.49    End
48 Exclusion   P4    L    4 242.31 304.70    End

Summarising (aggregating) data

Summarise

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> summarise(MeanResp1 = mean(Resp1),
                    VarResp1 = var(Resp1),
                    N = n())
  MeanResp1 VarResp1  N
1  75.26604 3200.305 48

Summarise

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
SE <- function(x) sd(x) / sqrt(length(x))

dat.1 |> summarise(MeanResp1 = mean(Resp1),
                    VarResp1 = var(Resp1),
                    SEM = SE(Resp1))
  MeanResp1 VarResp1      SEM
1  75.26604 3200.305 8.165355

Summarise

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Across (select semantics) versions

dat.1 |> summarise(across(c(Resp1, Resp2),
                           list(Mean = mean, Var = var, SEM = SE)),
                    N = n())
  Resp1_Mean Resp1_Var Resp1_SEM Resp2_Mean Resp2_Var Resp2_SEM  N
1   75.26604  3200.305  8.165355   81.70958  5886.444  11.07403 48

Summarise

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Across (select semantics) versions

dat.1 |> summarise(across(where(is.numeric),
                           list(Mean = mean, Var = var)))
  Time_Mean Time_Var Resp1_Mean Resp1_Var Resp2_Mean Resp2_Var
1       2.5 1.276596   75.26604  3200.305   81.70958  5886.444
dat.1 |> summarize(across(where(is.numeric),  mean),
          across(where(is.factor),  length))
  Time    Resp1    Resp2 Treatment Plot Dose
1  2.5 75.26604 81.70958        48   48   48

Summarise

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Across (select semantics) versions

Var <- c("Resp1", "Resp2")
dat.1 |> summarise(across(all_of(Var), list(Mean = mean, Var = var)))
  Resp1_Mean Resp1_Var Resp2_Mean Resp2_Var
1   75.26604  3200.305   81.70958  5886.444

Summarise

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94

Across (select semantics) versions

Var <- c("Resp1", "Resp2", "Resp3")
dat.1 |> summarise(across(any_of(Var), list(Mean = mean, Var = var)))
  Resp1_Mean Resp1_Var Resp2_Mean Resp2_Var
1   75.26604  3200.305   81.70958  5886.444

Summarise

dat.1 |> count(Dose)
  Dose  n
1    H 16
2    L 16
3    M 16
dat.1 |> count(Dose, between(Resp1, 30, 50))
  Dose between(Resp1, 30, 50)  n
1    H                  FALSE 11
2    H                   TRUE  5
3    L                  FALSE 14
4    L                   TRUE  2
5    M                  FALSE 12
6    M                   TRUE  4

Grouping (=aggregating)

Grouping

dat.1 |> head(6)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
3   Control   P1    H    3 27.49 29.85
4   Control   P1    H    4 44.79 25.39
5   Control   P1    M    1 20.99 20.31
6   Control   P1    M    2 37.54 17.62
dat.1 |> group_by(Treatment, Plot) |>
    summarise(Mean = mean(Resp1))
# A tibble: 4 × 3
# Groups:   Treatment [2]
  Treatment Plot   Mean
  <fct>     <fct> <dbl>
1 Control   P1     50.8
2 Control   P2     50.1
3 Exclusion P3     99.7
4 Exclusion P4    100.

Grouping

dat.1 |> head(6)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
3   Control   P1    H    3 27.49 29.85
4   Control   P1    H    4 44.79 25.39
5   Control   P1    M    1 20.99 20.31
6   Control   P1    M    2 37.54 17.62
dat.1 |>
    group_by(Treatment, Plot) |>
    summarise(Mean = mean(Resp1),
              Var = var(Resp1),
              N = n(),
              First = first(Resp1))
# A tibble: 4 × 6
# Groups:   Treatment [2]
  Treatment Plot   Mean   Var     N First
  <fct>     <fct> <dbl> <dbl> <int> <dbl>
1 Control   P1     50.8 1162.    12  8.12
2 Control   P2     50.1 1069.    12  8.14
3 Exclusion P3     99.7 4285.    12 21.9 
4 Exclusion P4    100.  4470.    12 18.8

Grouping

mutate vs summarise

dat.1 |> group_by(Treatment, Plot) |>
    summarise(Mean = mean(Resp1))
# A tibble: 4 × 3
# Groups:   Treatment [2]
  Treatment Plot   Mean
  <fct>     <fct> <dbl>
1 Control   P1     50.8
2 Control   P2     50.1
3 Exclusion P3     99.7
4 Exclusion P4    100. 
dat.1 |> group_by(Treatment, Plot) |>
    mutate(Mean = mean(Resp1))
# A tibble: 48 × 7
# Groups:   Treatment, Plot [4]
   Treatment Plot  Dose   Time Resp1  Resp2  Mean
   <fct>     <fct> <fct> <int> <dbl>  <dbl> <dbl>
 1 Control   P1    H         1  8.12   3.06  50.8
 2 Control   P1    H         2 20.6   25.9   50.8
 3 Control   P1    H         3 27.5   29.8   50.8
 4 Control   P1    H         4 44.8   25.4   50.8
 5 Control   P1    M         1 21.0   20.3   50.8
 6 Control   P1    M         2 37.5   17.6   50.8
 7 Control   P1    M         3 61.5   98.4   50.8
 8 Control   P1    M         4 82.2  160.    50.8
 9 Control   P1    L         1 31.7   21.2   50.8
10 Control   P1    L         2 59.1   37.5   50.8
# ℹ 38 more rows

Grouping

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> group_by(Treatment, Plot) |>
  mutate(Mean = mean(Resp1), cResp1 = Resp1 - Mean)
# A tibble: 48 × 8
# Groups:   Treatment, Plot [4]
   Treatment Plot  Dose   Time Resp1  Resp2  Mean cResp1
   <fct>     <fct> <fct> <int> <dbl>  <dbl> <dbl>  <dbl>
 1 Control   P1    H         1  8.12   3.06  50.8 -42.7 
 2 Control   P1    H         2 20.6   25.9   50.8 -30.3 
 3 Control   P1    H         3 27.5   29.8   50.8 -23.3 
 4 Control   P1    H         4 44.8   25.4   50.8  -6.02
 5 Control   P1    M         1 21.0   20.3   50.8 -29.8 
 6 Control   P1    M         2 37.5   17.6   50.8 -13.3 
 7 Control   P1    M         3 61.5   98.4   50.8  10.7 
 8 Control   P1    M         4 82.2  160.    50.8  31.4 
 9 Control   P1    L         1 31.7   21.2   50.8 -19.1 
10 Control   P1    L         2 59.1   37.5   50.8   8.27
# ℹ 38 more rows

Grouping

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |> group_by(Treatment, Plot) |>
  summarise(across(everything(), mean))
# A tibble: 4 × 6
# Groups:   Treatment [2]
  Treatment Plot   Dose  Time Resp1 Resp2
  <fct>     <fct> <dbl> <dbl> <dbl> <dbl>
1 Control   P1       NA   2.5  50.8  56.3
2 Control   P2       NA   2.5  50.1  56.2
3 Exclusion P3       NA   2.5  99.7  83.8
4 Exclusion P4       NA   2.5 100.  131.

Grouping

dat.1 |> head(2)
  Treatment Plot Dose Time Resp1 Resp2
1   Control   P1    H    1  8.12  3.06
2   Control   P1    H    2 20.55 25.94
dat.1 |>
    group_by(Treatment, Plot) |>
    summarise(across(starts_with("Resp"),
                     list(Mean=mean, Var=var, SE=SE)))
# A tibble: 4 × 8
# Groups:   Treatment [2]
  Treatment Plot  Resp1_Mean Resp1_Var Resp1_SE Resp2_Mean Resp2_Var
  <fct>     <fct>      <dbl>     <dbl>    <dbl>      <dbl>     <dbl>
1 Control   P1          50.8     1162.     9.84       56.3     2718.
2 Control   P2          50.1     1069.     9.44       56.2     2015.
3 Exclusion P3          99.7     4285.    18.9        83.8     5502.
4 Exclusion P4         100.      4470.    19.3       131.     10877.
# ℹ 1 more variable: Resp2_SE <dbl>

Your turn

Calculate for each year, the mean abundance of Pocillopora damicornis

tikus[1:10, c(1:3, 76:77)]
    time rep Psammocora contigua Millepora intrincata Heliopora coerulea
V1    81   1                   0                   24                461
V2    81   2                   0                    0                271
V3    81   3                   0                    0                221
V4    81   4                   0                    0                154
V5    81   5                   0                    0                  0
V6    81   6                   0                    0                  0
V7    81   7                   0                    0                  0
V8    81   8                   0                    0                  0
V9    81   9                   0                    0                  0
V10   81  10                   0                    0                  0

NOTE to operate on columns whose names contain special characters (including spaces), you must use `` (backticks).

tikus |> arrange(`Pocillopora damicornis`)

Your turn

Calculate for each year, the mean abundance of Pocillopora damicornis

tikus |> group_by(time) |>
    summarise(MeanAbundance = mean(`Pocillopora damicornis`))
# A tibble: 6 × 2
  time  MeanAbundance
  <fct>         <dbl>
1 81             30  
2 83              0  
3 84              0  
4 85              0  
5 87              1.8
6 88              4

Your turn

Calculate for each year, the number of samples as well as the mean and variance of ozone

nasa <- as.data.frame(nasa)
head(nasa)
  time y x   lat      long       date cloudhigh cloudlow cloudmid ozone pressure surftemp temperature  id day
1    1 1 1 -21.2 -113.8000 1995-01-01       0.5     31.0      2.0   260     1000    297.4       296.9 1-1   0
2    1 1 2 -21.2 -111.2957 1995-01-01       1.5     31.5      2.5   260     1000    297.4       296.5 2-1   0
3    1 1 3 -21.2 -108.7913 1995-01-01       1.5     32.5      3.5   260     1000    297.4       296.0 3-1   0
4    1 1 4 -21.2 -106.2870 1995-01-01       1.0     39.0      4.0   258     1000    296.9       296.5 4-1   0
5    1 1 5 -21.2 -103.7826 1995-01-01       0.5     48.0      4.5   258     1000    296.5       295.5 5-1   0
6    1 1 6 -21.2 -101.2783 1995-01-01       0.0     50.0      2.5   258     1000    296.5       295.0 6-1   0
  month year
1     1 1995
2     1 1995
3     1 1995
4     1 1995
5     1 1995
6     1 1995

Your turn

Calculate for each year, the number of samples as well as the mean and variance of ozone

nasa |> group_by(year) |>
    summarise(N = n(), Mean = mean(ozone), Var = var(ozone))
# A tibble: 6 × 4
   year     N  Mean   Var
  <dbl> <int> <dbl> <dbl>
1  1995  6912  264.  258.
2  1996  6912  267.  326.
3  1997  6912  266.  327.
4  1998  6912  267.  507.
5  1999  6912  270.  368.
6  2000  6912  269.  353.

Reshaping data

Reshaping data frames

Wide data

  Plot Between Time.0 Time.1 Time.2
R1 P1 A1 8 14 14
R2 P2 A1 10 12 11
R3 P3 A2 7 11 8
R4 P4 A2 11 9 2

Wide to long (melt)

data.w |> pivot_longer(Time.0:Time.2,  names_to = "Time",
                        values_to = "Count")
## OR
data.w |> pivot_longer(c(-Between, -Plot),  names_to = "Time",
                        values_to = "Count")
# A tibble: 12 × 4
   Plot  Between Time   Count
   <fct> <fct>   <chr>  <int>
 1 P1    A1      Time.0     8
 2 P1    A1      Time.1    14
 3 P1    A1      Time.2    14
 4 P2    A1      Time.0    10
 5 P2    A1      Time.1    12
 6 P2    A1      Time.2    11
 7 P3    A2      Time.0     7
 8 P3    A2      Time.1    11
 9 P3    A2      Time.2     8
10 P4    A2      Time.0    11
11 P4    A2      Time.1     9
12 P4    A2      Time.2     2
# A tibble: 12 × 4
   Plot  Between Time   Count
   <fct> <fct>   <chr>  <int>
 1 P1    A1      Time.0     8
 2 P1    A1      Time.1    14
 3 P1    A1      Time.2    14
 4 P2    A1      Time.0    10
 5 P2    A1      Time.1    12
 6 P2    A1      Time.2    11
 7 P3    A2      Time.0     7
 8 P3    A2      Time.1    11
 9 P3    A2      Time.2     8
10 P4    A2      Time.0    11
11 P4    A2      Time.1     9
12 P4    A2      Time.2     2

Reshaping data frames

Wide data

  Plot Between Time.0 Time.1 Time.2
R1 P1 A1 8 14 14
R2 P2 A1 10 12 11
R3 P3 A2 7 11 8
R4 P4 A2 11 9 2

Wide to long (melt)

## OR
data.w |> pivot_longer(starts_with("Time"),  names_to = "Time",
                        values_to = "Count",
                        names_prefix = "Time.")
# A tibble: 12 × 4
   Plot  Between Time  Count
   <fct> <fct>   <chr> <int>
 1 P1    A1      0         8
 2 P1    A1      1        14
 3 P1    A1      2        14
 4 P2    A1      0        10
 5 P2    A1      1        12
 6 P2    A1      2        11
 7 P3    A2      0         7
 8 P3    A2      1        11
 9 P3    A2      2         8
10 P4    A2      0        11
11 P4    A2      1         9
12 P4    A2      2         2

Reshaping data frames

Long data

Resp1 Resp2 Between Plot Subplot Within
8 17 A1 P1 S1 B1
10 18 A1 P1 S1 B2
7 17 A1 P1 S2 B1
11 21 A1 P1 S2 B2
14 19 A2 P2 S3 B1
12 13 A2 P2 S3 B2
11 24 A2 P2 S4 B1
9 18 A2 P2 S4 B2
14 25 A3 P3 S5 B1
11 18 A3 P3 S5 B2
8 27 A3 P3 S6 B1
2 22 A3 P3 S6 B2
8 17 A1 P4 S7 B1
10 22 A1 P4 S7 B2
7 16 A1 P4 S8 B1
12 13 A1 P4 S8 B2
11 23 A2 P5 S9 B1
12 19 A2 P5 S9 B2
12 23 A2 P5 S10 B1
10 21 A2 P5 S10 B2
3 17 A3 P6 S11 B1
11 16 A3 P6 S11 B2
13 26 A3 P6 S12 B1
7 28 A3 P6 S12 B2

Reshaping data frames

data |> head(2)
  Resp1 Resp2 Between Plot Subplot Within
1     8    17      A1   P1      S1     B1
2    10    18      A1   P1      S1     B2

Widen (cast) Widen Resp1 for repeated measures (Within)

data |> select(-Resp2) |>
  pivot_wider(names_from = Within,  values_from = c(Resp1))
# A tibble: 12 × 5
   Between Plot  Subplot    B1    B2
   <fct>   <fct> <fct>   <int> <int>
 1 A1      P1    S1          8    10
 2 A1      P1    S2          7    11
 3 A2      P2    S3         14    12
 4 A2      P2    S4         11     9
 5 A3      P3    S5         14    11
 6 A3      P3    S6          8     2
 7 A1      P4    S7          8    10
 8 A1      P4    S8          7    12
 9 A2      P5    S9         11    12
10 A2      P5    S10        12    10
11 A3      P6    S11         3    11
12 A3      P6    S12        13     7

Reshaping data frames

Widen Resp1 and Resp2 for repeated measures (Within)

data |> head(2)
  Resp1 Resp2 Between Plot Subplot Within
1     8    17      A1   P1      S1     B1
2    10    18      A1   P1      S1     B2
data |> pivot_wider(names_from = Within, values_from = c(Resp1, Resp2))
# A tibble: 12 × 7
   Between Plot  Subplot Resp1_B1 Resp1_B2 Resp2_B1 Resp2_B2
   <fct>   <fct> <fct>      <int>    <int>    <int>    <int>
 1 A1      P1    S1             8       10       17       18
 2 A1      P1    S2             7       11       17       21
 3 A2      P2    S3            14       12       19       13
 4 A2      P2    S4            11        9       24       18
 5 A3      P3    S5            14       11       25       18
 6 A3      P3    S6             8        2       27       22
 7 A1      P4    S7             8       10       17       22
 8 A1      P4    S8             7       12       16       13
 9 A2      P5    S9            11       12       23       19
10 A2      P5    S10           12       10       23       21
11 A3      P6    S11            3       11       17       16
12 A3      P6    S12           13        7       26       28

Combining data

Merging data frames

Bio data (missing Subplot 3)

  Resp1 Resp2 Between Plot Subplot
1 8 18 A1 P1 S1
2 10 21 A1 P1 S2
4 11 23 A1 P2 S4
5 14 22 A2 P3 S5
6 12 24 A2 P3 S6
7 11 23 A2 P4 S7
8 9 20 A2 P4 S8
9 14 11 A3 P5 S9
10 11 22 A3 P5 S10
11 8 24 A3 P6 S11
12 2 16 A3 P6 S12

Physio-chemical data (missing S7)

  Chem1 Chem2 Between Plot Subplot
1 1.453 0.8858 A1 P1 S1
2 3.266 0.18 A1 P1 S2
3 1.179 5.078 A1 P2 S3
4 13.4 1.576 A1 P2 S4
5 3.779 1.622 A2 P3 S5
6 1.197 4.237 A2 P3 S6
8 5.688 2.986 A2 P4 S8
9 4.835 4.133 A3 P5 S9
10 2.003 3.604 A3 P5 S10
11 12.33 1.776 A3 P6 S11
12 4.014 0.2255 A3 P6 S12

Merging data frames

Merge bio and chem data (only keep full matches - an inner join)

data.bio |> inner_join(data.chem)
   Resp1 Resp2 Between Plot Subplot     Chem1     Chem2
1      8    18      A1   P1      S1  1.452878 0.8858208
2     10    21      A1   P1      S2  3.266253 0.1800177
3     11    23      A1   P2      S4 13.400350 1.5762780
4     14    22      A2   P3      S5  3.779183 1.6222430
5     12    24      A2   P3      S6  1.196657 4.2369184
6      9    20      A2   P4      S8  5.687807 2.9859003
7     14    11      A3   P5      S9  4.834518 4.1328919
8     11    22      A3   P5     S10  2.002931 3.6043314
9      8    24      A3   P6     S11 12.326867 1.7763576
10     2    16      A3   P6     S12  4.014221 0.2255188
  • S3 and S7 absent

Merging data frames

Merge bio and chem data (keep all data - outer join)

data.bio |> full_join(data.chem)
   Resp1 Resp2 Between Plot Subplot     Chem1     Chem2
1      8    18      A1   P1      S1  1.452878 0.8858208
2     10    21      A1   P1      S2  3.266253 0.1800177
3     11    23      A1   P2      S4 13.400350 1.5762780
4     14    22      A2   P3      S5  3.779183 1.6222430
5     12    24      A2   P3      S6  1.196657 4.2369184
6     11    23      A2   P4      S7        NA        NA
7      9    20      A2   P4      S8  5.687807 2.9859003
8     14    11      A3   P5      S9  4.834518 4.1328919
9     11    22      A3   P5     S10  2.002931 3.6043314
10     8    24      A3   P6     S11 12.326867 1.7763576
11     2    16      A3   P6     S12  4.014221 0.2255188
12    NA    NA      A1   P2      S3  1.178652 5.0780682
  • note the order of Subplot

Merging data frames

Merge bio and chem data (only keep full BIO matches - left join)

data.bio |> left_join(data.chem)
   Resp1 Resp2 Between Plot Subplot     Chem1     Chem2
1      8    18      A1   P1      S1  1.452878 0.8858208
2     10    21      A1   P1      S2  3.266253 0.1800177
3     11    23      A1   P2      S4 13.400350 1.5762780
4     14    22      A2   P3      S5  3.779183 1.6222430
5     12    24      A2   P3      S6  1.196657 4.2369184
6     11    23      A2   P4      S7        NA        NA
7      9    20      A2   P4      S8  5.687807 2.9859003
8     14    11      A3   P5      S9  4.834518 4.1328919
9     11    22      A3   P5     S10  2.002931 3.6043314
10     8    24      A3   P6     S11 12.326867 1.7763576
11     2    16      A3   P6     S12  4.014221 0.2255188

Merging data frames

Merge bio and chem data (only keep full CHEM matches - right join)

data.bio |> right_join(data.chem)
   Resp1 Resp2 Between Plot Subplot     Chem1     Chem2
1      8    18      A1   P1      S1  1.452878 0.8858208
2     10    21      A1   P1      S2  3.266253 0.1800177
3     11    23      A1   P2      S4 13.400350 1.5762780
4     14    22      A2   P3      S5  3.779183 1.6222430
5     12    24      A2   P3      S6  1.196657 4.2369184
6      9    20      A2   P4      S8  5.687807 2.9859003
7     14    11      A3   P5      S9  4.834518 4.1328919
8     11    22      A3   P5     S10  2.002931 3.6043314
9      8    24      A3   P6     S11 12.326867 1.7763576
10     2    16      A3   P6     S12  4.014221 0.2255188
11    NA    NA      A1   P2      S3  1.178652 5.0780682

VLOOKUP

VLOOKUP

Biological data set (data.bio)

   Resp1 Resp2 Between Plot Subplot
1      8    18      A1   P1      S1
2     10    21      A1   P1      S2
4     11    23      A1   P2      S4
5     14    22      A2   P3      S5
6     12    24      A2   P3      S6
7     11    23      A2   P4      S7
8      9    20      A2   P4      S8
9     14    11      A3   P5      S9
10    11    22      A3   P5     S10
11     8    24      A3   P6     S11
12     2    16      A3   P6     S12

Geographical data set (lookup table) (data.geo)

  Plot     LAT     LONG
1   P1 17.9605 145.4326
2   P2 17.5210 146.1983
3   P3 17.0011 146.3839
4   P4 18.2350 146.7934
5   P5 18.9840 146.0345
6   P6 20.1154 146.4672

VLOOKUP

Incorporate (merge) the lat/longs into the bio data

data.bio |> left_join(data.geo, by = c("Plot"))
   Resp1 Resp2 Between Plot Subplot     LAT     LONG
1      8    18      A1   P1      S1 17.9605 145.4326
2     10    21      A1   P1      S2 17.9605 145.4326
3     11    23      A1   P2      S4 17.5210 146.1983
4     14    22      A2   P3      S5 17.0011 146.3839
5     12    24      A2   P3      S6 17.0011 146.3839
6     11    23      A2   P4      S7 18.2350 146.7934
7      9    20      A2   P4      S8 18.2350 146.7934
8     14    11      A3   P5      S9 18.9840 146.0345
9     11    22      A3   P5     S10 18.9840 146.0345
10     8    24      A3   P6     S11 20.1154 146.4672
11     2    16      A3   P6     S12 20.1154 146.4672

Applied examples

Tikus Island coral data

    Psammocora contigua Psammocora digitata time rep
V1                    0                   0   81   1
V2                    0                   0   81   2
V3                    0                   0   81   3
V4                    0                   0   81   4
V5                    0                   0   81   5
V6                    0                   0   81   6
V7                    0                   0   81   7
V8                    0                   0   81   8
V9                    0                   0   81   9
V10                   0                   0   81  10
Rows: 60
Columns: 77
$ `Psammocora contigua`    <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Psammocora digitata`    <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Pocillopora damicornis` <int> 79, 51, 42, 15, 9, 72, 0, 16, 0, 16…
$ `Pocillopora verrucosa`  <int> 32, 21, 35, 0, 0, 0, 41, 25, 38, 0,…
$ `Stylopora pistillata`   <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Acropora bruegemanni`   <int> 0, 44, 0, 11, 9, 10, 0, 0, 0, 37, 0…
$ `Acropora robusta`       <int> 0, 35, 40, 0, 0, 0, 0, 0, 0, 0, 0, …
$ `Acropora grandis`       <int> 0, 0, 0, 0, 0, 0, 60, 0, 0, 0, 0, 0…
$ `Acropora intermedia`    <int> 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Acropora formosa`       <int> 75, 0, 15, 0, 125, 0, 0, 0, 10, 0, …
$ `Acropora splendida`     <int> 0, 22, 0, 31, 0, 9, 16, 0, 0, 20, 0…
$ `Acropera aspera`        <int> 17, 18, 9, 8, 23, 0, 17, 13, 16, 18…
$ `Acropora hyacinthus`    <int> 141, 34, 55, 54, 0, 0, 0, 0, 0, 0, …
$ `Acropora palifera`      <int> 32, 0, 44, 0, 17, 0, 0, 0, 0, 0, 0,…
$ `Acropora cytherea`      <int> 108, 33, 14, 122, 0, 0, 0, 8, 0, 0,…
$ `Acropora tenuis`        <int> 0, 25, 0, 0, 0, 22, 28, 0, 0, 0, 0,…
$ `Acropora pulchra`       <int> 0, 0, 15, 52, 62, 33, 0, 0, 24, 0, …
$ `Acropora nasuta`        <int> 43, 21, 19, 0, 0, 0, 10, 0, 0, 0, 0…
$ `Acropora humilis`       <int> 31, 25, 0, 19, 0, 0, 0, 0, 0, 0, 0,…
$ `Acropora diversa`       <int> 22, 19, 20, 13, 23, 14, 0, 12, 12, …
$ `Acropora digitifera`    <int> 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Acropora divaricata`    <int> 0, 32, 55, 0, 0, 0, 0, 0, 0, 0, 0, …
$ `Acropora subglabra`     <int> 51, 0, 0, 44, 15, 0, 0, 25, 0, 0, 0…
$ `Acropora cerealis`      <int> 0, 75, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Acropora valida`        <int> 0, 0, 0, 30, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Acropora acuminata`     <int> 20, 0, 71, 0, 15, 0, 25, 25, 0, 0, …
$ `Acropora elsevi`        <int> 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Acropora millepora`     <int> 17, 14, 0, 20, 0, 0, 0, 0, 0, 0, 0,…
$ `Montipora monasteriata` <int> 60, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Montipora tuberculosa`  <int> 0, 15, 15, 0, 0, 0, 0, 0, 0, 0, 0, …
$ `Montipora hispida`      <int> 0, 0, 0, 32, 40, 24, 0, 0, 0, 0, 0,…
$ `Montipora digitata`     <int> 0, 0, 0, 0, 0, 77, 84, 53, 71, 351,…
$ `Montipora foliosa`      <int> 0, 0, 0, 0, 50, 71, 62, 81, 24, 0, …
$ `Montipora verrucosa`    <int> 0, 0, 30, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Fungia fungites`        <int> 0, 0, 18, 17, 0, 0, 0, 0, 0, 0, 0, …
$ `Fungia paumotensis`     <int> 0, 33, 0, 0, 0, 0, 0, 0, 0, 0, 12, …
$ `Fungia concina`         <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 10…
$ `Fungia scutaria`        <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Halomitra limax`        <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Pavona varians`         <int> 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 30, …
$ `Pavona venosa`          <int> 0, 24, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Pavona cactus`          <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Coeloseris mayeri`      <int> 20, 0, 15, 0, 9, 19, 0, 0, 25, 0, 0…
$ `Galaxea fascicularis`   <int> 51, 27, 31, 24, 0, 13, 0, 0, 0, 0, …
$ `Symphyllia radians`     <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Lobophyllia corymbosa`  <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 12…
$ `Lobophyllia hemprichii` <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Porites cylindrica`     <int> 61, 24, 0, 20, 0, 0, 0, 0, 0, 0, 10…
$ `Porites lichen`         <int> 0, 47, 49, 0, 0, 0, 0, 0, 0, 0, 0, …
$ `Porites lobata`         <int> 36, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Porites lutea`          <int> 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Porites nigrescens`     <int> 0, 0, 0, 21, 0, 9, 25, 0, 45, 26, 0…
$ `Porites solida`         <int> 0, 0, 10, 0, 17, 0, 31, 41, 0, 0, 0…
$ `Porites stephensoni`    <int> 0, 0, 0, 0, 0, 0, 0, 30, 0, 0, 0, 0…
$ `Goniopora lobata`       <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Favia pallida`          <int> 10, 20, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
$ `Favia speciosa`         <int> 0, 0, 30, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Favia stelligera`       <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Favia rotumana`         <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Favites abdita`         <int> 33, 41, 23, 27, 91, 63, 72, 48, 71,…
$ `Favites chinensis`      <int> 0, 44, 78, 61, 44, 0, 55, 30, 30, 0…
$ `Goniastrea rectiformis` <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 0,…
$ `Goniastrea pectinata`   <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Goniastrea sp`          <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Dulophyllia crispa`     <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9,…
$ `Platygyra daedalea`     <int> 0, 27, 55, 0, 71, 74, 55, 48, 0, 0,…
$ `Platygyra sinensis`     <int> 47, 27, 56, 26, 0, 0, 0, 0, 0, 0, 0…
$ `Hydnopora rigida`       <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Leptastrea purpurea`    <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Leptastrea pruinosa`    <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Cyphastrea serailia`    <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0…
$ `Millepora platyphylla`  <int> 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Millepora dichotoma`    <int> 21, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Millepora intrincata`   <int> 24, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Heliopora coerulea`     <int> 461, 271, 221, 154, 0, 0, 0, 0, 0, …
$ time                     <fct> 81, 81, 81, 81, 81, 81, 81, 81, 81,…
$ rep                      <fct> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 2…

Tikus Island coral data

Explore/Process data

  • Convert abundance to cover (abundance is the length in cm of a 10m transect containing the species)
  • Mean cover of total Acropora per year
  • NOTE there is a typo ‘Acropera’
Rows: 60
Columns: 77
$ `Psammocora contigua`    <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Psammocora digitata`    <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Pocillopora damicornis` <int> 79, 51, 42, 15, 9, 72, 0, 16, 0, 16…
$ `Pocillopora verrucosa`  <int> 32, 21, 35, 0, 0, 0, 41, 25, 38, 0,…
$ `Stylopora pistillata`   <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Acropora bruegemanni`   <int> 0, 44, 0, 11, 9, 10, 0, 0, 0, 37, 0…
$ `Acropora robusta`       <int> 0, 35, 40, 0, 0, 0, 0, 0, 0, 0, 0, …
$ `Acropora grandis`       <int> 0, 0, 0, 0, 0, 0, 60, 0, 0, 0, 0, 0…
$ `Acropora intermedia`    <int> 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Acropora formosa`       <int> 75, 0, 15, 0, 125, 0, 0, 0, 10, 0, …
$ `Acropora splendida`     <int> 0, 22, 0, 31, 0, 9, 16, 0, 0, 20, 0…
$ `Acropera aspera`        <int> 17, 18, 9, 8, 23, 0, 17, 13, 16, 18…
$ `Acropora hyacinthus`    <int> 141, 34, 55, 54, 0, 0, 0, 0, 0, 0, …
$ `Acropora palifera`      <int> 32, 0, 44, 0, 17, 0, 0, 0, 0, 0, 0,…
$ `Acropora cytherea`      <int> 108, 33, 14, 122, 0, 0, 0, 8, 0, 0,…
$ `Acropora tenuis`        <int> 0, 25, 0, 0, 0, 22, 28, 0, 0, 0, 0,…
$ `Acropora pulchra`       <int> 0, 0, 15, 52, 62, 33, 0, 0, 24, 0, …
$ `Acropora nasuta`        <int> 43, 21, 19, 0, 0, 0, 10, 0, 0, 0, 0…
$ `Acropora humilis`       <int> 31, 25, 0, 19, 0, 0, 0, 0, 0, 0, 0,…
$ `Acropora diversa`       <int> 22, 19, 20, 13, 23, 14, 0, 12, 12, …
$ `Acropora digitifera`    <int> 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Acropora divaricata`    <int> 0, 32, 55, 0, 0, 0, 0, 0, 0, 0, 0, …
$ `Acropora subglabra`     <int> 51, 0, 0, 44, 15, 0, 0, 25, 0, 0, 0…
$ `Acropora cerealis`      <int> 0, 75, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Acropora valida`        <int> 0, 0, 0, 30, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Acropora acuminata`     <int> 20, 0, 71, 0, 15, 0, 25, 25, 0, 0, …
$ `Acropora elsevi`        <int> 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Acropora millepora`     <int> 17, 14, 0, 20, 0, 0, 0, 0, 0, 0, 0,…
$ `Montipora monasteriata` <int> 60, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Montipora tuberculosa`  <int> 0, 15, 15, 0, 0, 0, 0, 0, 0, 0, 0, …
$ `Montipora hispida`      <int> 0, 0, 0, 32, 40, 24, 0, 0, 0, 0, 0,…
$ `Montipora digitata`     <int> 0, 0, 0, 0, 0, 77, 84, 53, 71, 351,…
$ `Montipora foliosa`      <int> 0, 0, 0, 0, 50, 71, 62, 81, 24, 0, …
$ `Montipora verrucosa`    <int> 0, 0, 30, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Fungia fungites`        <int> 0, 0, 18, 17, 0, 0, 0, 0, 0, 0, 0, …
$ `Fungia paumotensis`     <int> 0, 33, 0, 0, 0, 0, 0, 0, 0, 0, 12, …
$ `Fungia concina`         <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 10…
$ `Fungia scutaria`        <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Halomitra limax`        <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Pavona varians`         <int> 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 30, …
$ `Pavona venosa`          <int> 0, 24, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Pavona cactus`          <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Coeloseris mayeri`      <int> 20, 0, 15, 0, 9, 19, 0, 0, 25, 0, 0…
$ `Galaxea fascicularis`   <int> 51, 27, 31, 24, 0, 13, 0, 0, 0, 0, …
$ `Symphyllia radians`     <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Lobophyllia corymbosa`  <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 12…
$ `Lobophyllia hemprichii` <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Porites cylindrica`     <int> 61, 24, 0, 20, 0, 0, 0, 0, 0, 0, 10…
$ `Porites lichen`         <int> 0, 47, 49, 0, 0, 0, 0, 0, 0, 0, 0, …
$ `Porites lobata`         <int> 36, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Porites lutea`          <int> 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Porites nigrescens`     <int> 0, 0, 0, 21, 0, 9, 25, 0, 45, 26, 0…
$ `Porites solida`         <int> 0, 0, 10, 0, 17, 0, 31, 41, 0, 0, 0…
$ `Porites stephensoni`    <int> 0, 0, 0, 0, 0, 0, 0, 30, 0, 0, 0, 0…
$ `Goniopora lobata`       <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Favia pallida`          <int> 10, 20, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
$ `Favia speciosa`         <int> 0, 0, 30, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Favia stelligera`       <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Favia rotumana`         <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Favites abdita`         <int> 33, 41, 23, 27, 91, 63, 72, 48, 71,…
$ `Favites chinensis`      <int> 0, 44, 78, 61, 44, 0, 55, 30, 30, 0…
$ `Goniastrea rectiformis` <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 0,…
$ `Goniastrea pectinata`   <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Goniastrea sp`          <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Dulophyllia crispa`     <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9,…
$ `Platygyra daedalea`     <int> 0, 27, 55, 0, 71, 74, 55, 48, 0, 0,…
$ `Platygyra sinensis`     <int> 47, 27, 56, 26, 0, 0, 0, 0, 0, 0, 0…
$ `Hydnopora rigida`       <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Leptastrea purpurea`    <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Leptastrea pruinosa`    <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ `Cyphastrea serailia`    <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19, 0…
$ `Millepora platyphylla`  <int> 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Millepora dichotoma`    <int> 21, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Millepora intrincata`   <int> 24, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ `Heliopora coerulea`     <int> 461, 271, 221, 154, 0, 0, 0, 0, 0, …
$ time                     <fct> 81, 81, 81, 81, 81, 81, 81, 81, 81,…
$ rep                      <fct> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 2…

Tikus Island coral data

  • Step 1. fix typo
  • Step 2. pivot to longer
  • Step 3. convert abundance to cover (abundance is the length in cm of a 10m transect containing the species)
    • Cover=Abundance/1000 (proportions)
    • Cover=Cover x 100 (%)
    • so Cover=Abundance/10
  • Step 4. isolate genera
  • Step 5. filter to Acropora
  • Step 6. sum all Acropora per year, site
  • Step 7. summarise per year

Tikus Island coral data

Step 1. fix the typo (rename)

tikus |> rename(`Acropora aspera` = `Acropera aspera`)
    Psammocora contigua Psammocora digitata Pocillopora damicornis
V1                    0                   0                     79
V2                    0                   0                     51
V3                    0                   0                     42
V4                    0                   0                     15
V5                    0                   0                      9
V6                    0                   0                     72
V7                    0                   0                      0
V8                    0                   0                     16
V9                    0                   0                      0
V10                   0                   0                     16
V11                   0                   0                      0
V12                   0                   0                      0
V13                   0                   0                      0
V14                   0                   0                      0
V15                   0                   0                      0
V16                   0                   0                      0
V17                   0                   0                      0
V18                   0                   0                      0
V19                   0                   0                      0
V20                   0                   0                      0
V21                   0                   0                      0
V22                   0                   0                      0
V23                   0                   0                      0
V24                   0                   0                      0
V25                   0                   0                      0
V26                   0                   0                      0
V27                   0                   0                      0
V28                   0                   0                      0
V29                   0                   0                      0
V30                   0                   0                      0
V31                   0                   0                      0
V32                   0                   0                      0
V33                   0                   0                      0
V34                   0                   0                      0
V35                   0                   0                      0
V36                   0                   0                      0
V37                   0                   0                      0
V38                   0                   0                      0
V39                   0                   0                      0
V40                   0                   0                      0
V41                   0                   0                     18
V42                   0                   0                      0
V43                   0                   0                      0
V44                   0                   0                      0
V45                   0                   0                      0
V46                   0                   0                      0
V47                   0                   0                      0
V48                   0                   0                      0
V49                   0                   0                      0
V50                   0                   0                      0
V51                   0                   0                      0
V52                   0                   0                      0
V53                   0                   0                      0
V54                   0                   0                      0
V55                   0                   0                      0
V56                   0                   0                      0
V57                   0                   0                     10
V58                   0                   0                      0
V59                   0                   0                     30
V60                   0                   0                      0
    Pocillopora verrucosa Stylopora pistillata Acropora bruegemanni
V1                     32                    0                    0
V2                     21                    0                   44
V3                     35                    0                    0
V4                      0                    0                   11
V5                      0                    0                    9
V6                      0                    0                   10
V7                     41                    0                    0
V8                     25                    0                    0
V9                     38                    0                    0
V10                     0                    0                   37
V11                     0                    0                    0
V12                     0                    0                    0
V13                     0                    0                    0
V14                     0                    0                    0
V15                     0                    0                    0
V16                     0                    0                    0
V17                     0                    0                    0
V18                     0                    0                    0
V19                     0                    0                    0
V20                     0                    0                    0
V21                     0                    0                    0
V22                     0                    0                    0
V23                     0                    0                    0
V24                     0                    0                    0
V25                     0                    0                    0
V26                     0                    0                    0
V27                     0                    0                    0
V28                     0                    0                    0
V29                     0                    0                    0
V30                     0                    0                    0
V31                     0                    0                   33
V32                     0                    0                    0
V33                     0                    0                    0
V34                     0                    0                    0
V35                     0                    0                    0
V36                     0                    0                    0
V37                     0                    0                    0
V38                     0                    0                    0
V39                     0                    0                    0
V40                     0                    0                    0
V41                     0                    0                   60
V42                     0                    0                   55
V43                     0                    0                   42
V44                     0                    0                   14
V45                     0                    0                    0
V46                     0                    0                    0
V47                     0                    0                    0
V48                     0                    0                    0
V49                     0                    0                    0
V50                     0                    0                    0
V51                     0                    0                   63
V52                     0                    0                   48
V53                     0                    0                   52
V54                     0                    0                    0
V55                     0                    0                    0
V56                     0                    0                    0
V57                     0                    0                    0
V58                     0                    0                   32
V59                     0                    0                    0
V60                     0                    0                    0
    Acropora robusta Acropora grandis Acropora intermedia
V1                 0                0                  30
V2                35                0                   0
V3                40                0                   0
V4                 0                0                   0
V5                 0                0                   0
V6                 0                0                   0
V7                 0               60                   0
V8                 0                0                   0
V9                 0                0                   0
V10                0                0                   0
V11                0                0                   0
V12                0                0                   0
V13                0                0                   0
V14                0                0                   0
V15                0                0                   0
V16                0                0                   0
V17                0                0                   0
V18                0                0                   0
V19                0                0                   0
V20                0                0                   0
V21                0                0                   0
V22                0                0                   0
V23                0                0                   0
V24                0                0                   0
V25                0                0                   0
V26                0                0                   0
V27                0                0                   0
V28                0                0                   0
V29                0                0                   0
V30                0                0                   0
V31                0                0                   0
V32                0                0                   0
V33               30                0                   0
V34                0                0                   0
V35                0                0                   0
V36                0                0                   0
V37                0                0                   0
V38                0                0                   0
V39                0                0                   0
V40                0                0                   0
V41                0               18                   0
V42               42                0                   0
V43               40               13                   0
V44                9               10                   0
V45               20                0                   0
V46                0                0                   0
V47                0                0                   0
V48                0               22                   0
V49                0                0                   0
V50                0                0                   0
V51                0                0                   0
V52               45                0                   0
V53               40                0                   0
V54                8                0                   0
V55                0                0                   0
V56               30                0                   0
V57                0                0                   0
V58                0                0                   0
V59                0                0                   0
V60                0                0                   0
    Acropora formosa Acropora splendida Acropora aspera
V1                75                  0              17
V2                 0                 22              18
V3                15                  0               9
V4                 0                 31               8
V5               125                  0              23
V6                 0                  9               0
V7                 0                 16              17
V8                 0                  0              13
V9                10                  0              16
V10                0                 20              18
V11                0                  0               0
V12                0                  0               0
V13                0                  0               0
V14                0                  0               0
V15                0                  0               0
V16                0                  0               0
V17                0                  0               0
V18                0                  0               0
V19                0                  0               0
V20                0                  0               0
V21                0                  0               0
V22                0                  0               0
V23                0                  0               0
V24                0                  0               0
V25                0                  0               0
V26                0                  0               0
V27                0                  0               0
V28                0                  0               0
V29                0                  0               0
V30                0                  0               0
V31               25                  0              15
V32               20                  0               0
V33               30                  0               0
V34                0                  0               0
V35                0                  0               0
V36                0                  0               0
V37                0                  0               0
V38                0                  0               0
V39                0                  0               0
V40                0                  0               0
V41                0                  0               0
V42                0                  0               0
V43                0                  0               0
V44                0                  0               0
V45                0                  0               0
V46                0                  0               0
V47                0                  0               0
V48                0                  0               0
V49                0                  0               0
V50                0                  0               0
V51               55                  0               0
V52               26                  0               0
V53                0                  0               0
V54                0                  0               0
V55                0                  0               0
V56                0                  0               0
V57                0                  0               0
V58                0                  0               0
V59                0                  0               0
V60                0                  0               0
    Acropora hyacinthus Acropora palifera Acropora cytherea
V1                  141                32               108
V2                   34                 0                33
V3                   55                44                14
V4                   54                 0               122
V5                    0                17                 0
V6                    0                 0                 0
V7                    0                 0                 0
V8                    0                 0                 8
V9                    0                 0                 0
V10                   0                 0                 0
V11                   0                 0                 0
V12                   0                 0                 0
V13                   0                 0                 0
V14                   0                 0                 0
V15                   0                 0                 0
V16                   0                 0                 0
V17                   0                 0                 0
V18                   0                 0                 0
V19                   0                 0                 0
V20                   0                 0                 0
V21                   0                 0                 0
V22                   0                 0                 0
V23                   0                 0                 0
V24                   0                 0                 0
V25                   0                 0                 0
V26                   0                 0                 0
V27                   0                 0                 0
V28                   0                 0                 0
V29                   0                 0                 0
V30                   0                 0                 0
V31                  21                 0                 0
V32                   0                12                 0
V33                   0                 0                 0
V34                   0                12                 0
V35                   0                 0                 0
V36                   0                 0                 0
V37                   0                 0                 0
V38                   0                 0                 0
V39                   0                 0                 0
V40                   0                 0                 0
V41                  72                 0                 0
V42                  93                 0                 0
V43                  45                 0                 0
V44                  36                 0                 0
V45                   9                 0                 0
V46                   0                 0                 0
V47                   0                 0                 0
V48                   0                 0                 0
V49                   0                 0                 0
V50                   0                 0                 0
V51                  75                 0                 0
V52                  56                 0                 0
V53                  61                 0                 0
V54                  45                 0                 0
V55                   0                 0                 0
V56                   0                 0                 0
V57                   0                 0                 0
V58                   0                 0                 0
V59                   0                 0                 0
V60                   0                 0                 0
    Acropora tenuis Acropora pulchra Acropora nasuta Acropora humilis
V1                0                0              43               31
V2               25                0              21               25
V3                0               15              19                0
V4                0               52               0               19
V5                0               62               0                0
V6               22               33               0                0
V7               28                0              10                0
V8                0                0               0                0
V9                0               24               0                0
V10               0                0               0                0
V11               0                0               0                0
V12               0                0               0                0
V13               0                0               0                0
V14               0                0               0                0
V15               0                0               0                0
V16               0                0               0                0
V17               0                0               0                0
V18               0                0               0                0
V19               0                0               0                0
V20               0                0               0                0
V21               0                0               0                0
V22               0                0               0                0
V23               0                0               0                0
V24               0                0               0                0
V25               0                0               0                0
V26               0                0               0                0
V27               0                0               0                0
V28               0                0               0                0
V29               0                0               0                0
V30               0                0               0                0
V31               0                0               0                0
V32               0                0               0                0
V33               0                0               0               30
V34               0                0              15                0
V35               0                0               0                0
V36               0                0               0                0
V37               0                0               0                0
V38               0                0               0                0
V39               0                0               0                0
V40               0                0               0                0
V41               0                0               9                0
V42              30                0              17                0
V43              25                0               0                0
V44               0                0              45                0
V45               0                0               0                0
V46               0                0              40                0
V47              35                0               0                0
V48               0                0               0                0
V49               0                0               0                0
V50               0                0               0                0
V51               9                0               0                0
V52              37                0               0                0
V53              42                0               0               30
V54               0                0               0                0
V55              17                0               0                0
V56               0                0               0                0
V57               0                0               0                0
V58               0                0               0                0
V59               0                0               0                0
V60               0                0               0                0
    Acropora diversa Acropora digitifera Acropora divaricata
V1                22                  30                   0
V2                19                   0                  32
V3                20                   0                  55
V4                13                   0                   0
V5                23                   0                   0
V6                14                   0                   0
V7                 0                   0                   0
V8                12                   0                   0
V9                12                   0                   0
V10                0                   0                   0
V11                0                   0                   0
V12                0                   0                   0
V13                0                   0                   0
V14                0                   0                   0
V15                0                   0                   0
V16                0                   0                   0
V17                0                   0                   0
V18                0                   0                   0
V19                0                   0                   0
V20                0                   0                   0
V21                0                   0                   0
V22                0                   0                   0
V23                0                   0                   0
V24                0                   0                   0
V25                0                   0                   0
V26                0                   0                   0
V27                0                   0                   0
V28                0                   0                   0
V29                0                   0                   0
V30                0                   0                   0
V31                0                   0                   0
V32                0                   0                   0
V33                0                   0                   0
V34                0                   0                   0
V35                0                   0                   0
V36                0                   0                   0
V37                0                   0                   0
V38                0                   0                   0
V39                0                   0                   0
V40                0                   0                   0
V41                0                   0                   0
V42                0                   0                   0
V43                0                   0                   0
V44                0                   0                   0
V45                0                   0                   0
V46                0                   0                   0
V47                0                   0                   0
V48                0                   0                   0
V49                0                   0                   0
V50                0                   0                   0
V51                0                   0                  30
V52                0                   0                   0
V53                0                   0                   0
V54                0                   0                   0
V55                0                   0                   0
V56                0                   0                   0
V57               24                   0                   0
V58                0                   0                   0
V59                0                   0                   0
V60                0                   0                   0
    Acropora subglabra Acropora cerealis Acropora valida
V1                  51                 0               0
V2                   0                75               0
V3                   0                 0               0
V4                  44                 0              30
V5                  15                 0               0
V6                   0                 0               0
V7                   0                 0               0
V8                  25                 0               0
V9                   0                 0               0
V10                  0                 0               0
V11                  0                 0               0
V12                  0                 0               0
V13                  0                 0               0
V14                  0                 0               0
V15                  0                 0               0
V16                  0                 0               0
V17                  0                 0               0
V18                  0                 0               0
V19                  0                 0               0
V20                  0                 0               0
V21                  0                 0               0
V22                  0                 0               0
V23                  0                 0               0
V24                  0                 0               0
V25                  0                 0               0
V26                  0                 0               0
V27                  0                 0               0
V28                  0                 0               0
V29                  0                 0               0
V30                  0                 0               0
V31                  0                 0               0
V32                  0                 0               0
V33                  0                 0               0
V34                  0                 0               0
V35                  0                 0               0
V36                  0                 0               0
V37                  0                 0               0
V38                  0                 0               0
V39                  0                 0               0
V40                  0                 0               0
V41                  0                 0               0
V42                  0                 0               0
V43                  0                 0               0
V44                  0                 0               0
V45                  0                 0               0
V46                  0                 0               0
V47                  0                 0               0
V48                  0                 0               0
V49                  0                 0               0
V50                  0                 0               0
V51                  0                 0               0
V52                  0                 0               0
V53                  0                 0               0
V54                  0                 0               0
V55                  0                 0               0
V56                  0                 0               0
V57                  0                 0               0
V58                  0                 0               0
V59                  0                 0               0
V60                  0                 0               0
    Acropora acuminata Acropora elsevi Acropora millepora
V1                  20              30                 17
V2                   0               0                 14
V3                  71               0                  0
V4                   0               0                 20
V5                  15               0                  0
V6                   0               0                  0
V7                  25               0                  0
V8                  25               0                  0
V9                   0               0                  0
V10                  0               0                  0
V11                  0               0                  0
V12                  0               0                  0
V13                  0               0                  0
V14                  0               0                  0
V15                  0               0                  0
V16                  0               0                  0
V17                  0               0                  0
V18                  0               0                  0
V19                  0               0                  0
V20                  0               0                  0
V21                  0               0                  0
V22                  0               0                  0
V23                  0               0                  0
V24                  0               0                  0
V25                  0               0                  0
V26                  0               0                  0
V27                  0               0                  0
V28                  0               0                  0
V29                  0               0                  0
V30                  0               0                  0
V31                  0               0                  0
V32                  0               0                  0
V33                  0               0                  0
V34                  0               0                  0
V35                  0               0                  0
V36                  0               0                  0
V37                  0               0                  0
V38                  0               0                  0
V39                  0               0                  0
V40                  0               0                  0
V41                  0               0                  0
V42                  0               0                  0
V43                  0               0                  0
V44                  0               0                  0
V45                  0               0                  0
V46                  0               0                  0
V47                  0               0                  0
V48                  0               0                  0
V49                  0               0                  0
V50                  0               0                  0
V51                  0               0                  0
V52                  0               0                 30
V53                  0               0                  0
V54                  0               0                  0
V55                  0               0                  0
V56                  0               0                  0
V57                  0               0                  0
V58                  0               0                  0
V59                  0               0                  0
V60                  0               0                  0
    Montipora monasteriata Montipora tuberculosa Montipora hispida
V1                      60                     0                 0
V2                       0                    15                 0
V3                       0                    15                 0
V4                       0                     0                32
V5                       0                     0                40
V6                       0                     0                24
V7                       0                     0                 0
V8                       0                     0                 0
V9                       0                     0                 0
V10                      0                     0                 0
V11                      0                     0                 0
V12                      0                    24                 0
V13                      0                     0                 0
V14                      0                     0                 0
V15                      0                     0                15
V16                      0                     0                 0
V17                      0                     0                 0
V18                      0                     0                 0
V19                      0                     0                 0
V20                      0                     0                 0
V21                      9                     0                 9
V22                     15                    12                 0
V23                     31                     0                15
V24                     33                    12                 0
V25                     41                     0                25
V26                     15                     0                 0
V27                      0                     0                26
V28                     30                     0                 0
V29                      0                     0                 0
V30                      0                     0                 0
V31                     15                     0                15
V32                     40                    31                 0
V33                     33                    37                22
V34                     35                    42                 0
V35                     18                    61                28
V36                      0                    46                 0
V37                      0                     0                41
V38                      0                     8                 0
V39                      0                     0                 0
V40                      0                     0                 0
V41                     17                     0                 0
V42                     42                     0                 0
V43                     21                     0                 0
V44                     19                     0                 0
V45                      0                     0                 0
V46                      0                     0                 0
V47                      0                     0                 0
V48                      0                     0                 0
V49                      0                     0                 0
V50                      0                     0                 0
V51                      0                     0                 0
V52                      0                     0                 0
V53                      0                     0                 0
V54                      0                     0                 0
V55                      0                     0                 0
V56                      0                     0                 0
V57                      0                     0                 0
V58                      0                     0                 0
V59                      0                     0                 0
V60                      0                     0                 0
    Montipora digitata Montipora foliosa Montipora verrucosa
V1                   0                 0                   0
V2                   0                 0                   0
V3                   0                 0                  30
V4                   0                 0                   0
V5                   0                50                   0
V6                  77                71                   0
V7                  84                62                   0
V8                  53                81                   0
V9                  71                24                   0
V10                351                 0                   0
V11                  0                 0                   0
V12                  0                 0                   0
V13                  0                 0                   0
V14                  0                 0                   0
V15                  0                 0                   0
V16                  0                 0                   0
V17                  0                 0                   0
V18                  0                24                   0
V19                  0                 0                   0
V20                 30                 0                   0
V21                  0                 0                   0
V22                 20                 0                  40
V23                 43                 7                  20
V24                 22                 0                   0
V25                 15                30                   0
V26                 51                25                   0
V27                 24                 0                   0
V28                 43                65                   0
V29                 51                41                   0
V30                301                27                   0
V31                  0                 0                   0
V32                 98                 0                   0
V33                 71                 0                   0
V34                 45                 0                   0
V35                 51                71                   0
V36                 92                71                   0
V37                 37                50                   0
V38                 82               172                   0
V39                 91               120                   0
V40                456                71                   0
V41                  0                 0                   0
V42                 15                 0                   0
V43                  0                 0                   0
V44                 69                 0                   0
V45                 54               100                   0
V46                 93                84                   0
V47                141                95                   0
V48                144               185                   0
V49                612               173                   0
V50                783                98                   0
V51                  0                 0                   0
V52                  0                 0                   0
V53                  0                 0                   0
V54                  0                 0                   0
V55                  0                13                   0
V56                 25                 0                   0
V57                 25                 0                   0
V58                 18                40                   0
V59                632               175                   0
V60                210                39                   0
    Fungia fungites Fungia paumotensis Fungia concina Fungia scutaria
V1                0                  0              0               0
V2                0                 33              0               0
V3               18                  0              0               0
V4               17                  0              0               0
V5                0                  0              0               0
V6                0                  0              0               0
V7                0                  0              0               0
V8                0                  0              0               0
V9                0                  0              0               0
V10               0                  0              0               0
V11               0                 12              0               0
V12               9                 20             10               0
V13               0                  0             10               0
V14              15                 28             10               0
V15               0                  0              0               0
V16               0                  0              0               0
V17               0                  0              0               0
V18               0                  0              0               0
V19               0                  0              0               0
V20               0                  0              0               0
V21              21                  0              0              15
V22               0                 15             12               0
V23               0                  0              0               0
V24               0                  0              0               0
V25               0                  0              0               0
V26               0                  0              0               0
V27               0                  0              0               0
V28               0                  0              0               0
V29               0                  0              0               0
V30               0                  0              0               0
V31               0                  0              0               0
V32               9                  0              0               0
V33               0                  0              0               0
V34               0                  0              0               0
V35               0                  0              0               0
V36               0                  0              0               0
V37               0                  0              0               0
V38               0                  0              0               0
V39               0                  0              0               0
V40               0                  0              0               0
V41               0                  0              0               0
V42               0                  0              0               0
V43               0                  0              0               0
V44               0                  0              0               0
V45               0                  0              0               0
V46               0                  0              0               0
V47               0                  0              0               0
V48               0                  0              0               0
V49               0                  0              0               0
V50               0                  0              0               0
V51              33                  0              0               0
V52               0                  0              0               0
V53              12                  0              0               0
V54              17                  0              0               0
V55              17                  0              0               0
V56              24                  0              0               0
V57              20                  0              0               0
V58               0                  0              0               0
V59               0                  0              0               0
V60               0                  0              0               0
    Halomitra limax Pavona varians Pavona venosa Pavona cactus
V1                0             30             0             0
V2                0              0            24             0
V3                0              0             0             0
V4                0              0             0             0
V5                0              0             0             0
V6                0              0             0             0
V7                0              0             0             0
V8                0              0             0             0
V9                0              0             0             0
V10               0              0             0             0
V11               0             30             0             0
V12               0              0             0             0
V13              15              0             0             0
V14               0              0             0             0
V15               0              0             0             0
V16               0              0             0             0
V17               0              0             0             0
V18               0              0             0             0
V19               0             15             0             0
V20               0              0             0             0
V21               0              8            30            15
V22               0              0             0            15
V23               0             21             0             0
V24               0              0             0             0
V25               0             31             0             0
V26               0              0             0             0
V27               0              0             0             0
V28               0              0             0             0
V29               0              0             0             0
V30               0              0             0             0
V31               0             31             0             0
V32               0              0             0             0
V33               0             37             0             0
V34               0              0             0             0
V35               0             52             0             0
V36               0              0             0             0
V37               0              0             0             0
V38               0              0             0             0
V39               0              0             0             0
V40               0              0             0             0
V41               0              0             0             0
V42               0              0             0             0
V43               0              0             0             0
V44               0              0             0             0
V45               0              0             0             0
V46               0              0             0             0
V47               0              0             0             0
V48               0              0             0             0
V49               0              0             0             0
V50               0              0             0             0
V51               0             15            30             0
V52               0             15             0             0
V53               0              0            21             0
V54               0              0             0             0
V55               0              0             0             0
V56               0              0             0             0
V57               0              0             0             0
V58               0              0             0             0
V59               0              0             0             0
V60               0              0             0             0
    Coeloseris mayeri Galaxea fascicularis Symphyllia radians
V1                 20                   51                  0
V2                  0                   27                  0
V3                 15                   31                  0
V4                  0                   24                  0
V5                  9                    0                  0
V6                 19                   13                  0
V7                  0                    0                  0
V8                  0                    0                  0
V9                 25                    0                  0
V10                 0                    0                  0
V11                 0                    9                  0
V12                 0                    0                  0
V13                12                    0                  0
V14                 0                    0                  0
V15                 0                    0                  0
V16                 0                    0                  0
V17                 0                    0                  0
V18                 0                    0                  0
V19                12                    0                  0
V20                 0                    0                  0
V21                 0                   21                  0
V22                 0                   15                  0
V23                 0                    0                  0
V24                 0                   15                  0
V25                 0                    0                  0
V26                 0                    0                  0
V27                 0                    0                  0
V28                 0                    0                  0
V29                 0                    0                  0
V30                 0                    0                  0
V31                 0                   27                  0
V32                 0                    0                  0
V33                 0                    0                 15
V34                 0                    0                  0
V35                 0                    0                  0
V36                 0                    0                  0
V37                 0                    0                  0
V38                 0                    0                  0
V39                 0                    0                  0
V40                 0                    0                  0
V41                 0                   35                  0
V42                 0                   32                  0
V43                24                    0                  0
V44                 0                   11                  0
V45                 0                    0                  0
V46                 0                    0                  0
V47                 0                    0                  0
V48                 0                    0                  0
V49                 0                    0                  0
V50                 0                    0                  0
V51                 0                   30                  0
V52                 0                    0                  0
V53                 0                    0                  0
V54                 0                    0                  0
V55                 0                    0                  0
V56                 0                    0                  0
V57                 0                    0                  0
V58                 0                    0                  0
V59                 0                    0                  0
V60                 0                    0                  0
    Lobophyllia corymbosa Lobophyllia hemprichii Porites cylindrica
V1                      0                      0                 61
V2                      0                      0                 24
V3                      0                      0                  0
V4                      0                      0                 20
V5                      0                      0                  0
V6                      0                      0                  0
V7                      0                      0                  0
V8                      0                      0                  0
V9                      0                      0                  0
V10                     0                      0                  0
V11                     0                      0                 10
V12                    12                      0                  0
V13                     0                      0                  0
V14                     0                      0                 20
V15                     0                      0                  0
V16                     0                      0                  0
V17                     0                      0                  0
V18                     0                      0                  0
V19                     0                      0                  0
V20                     0                      0                  0
V21                     0                      0                 30
V22                     0                      0                  0
V23                     0                      0                 11
V24                     0                      0                 32
V25                     0                      0                  0
V26                     0                      0                 11
V27                     0                      0                  0
V28                     0                      0                  0
V29                     0                      0                  0
V30                     0                      0                  0
V31                    15                     15                121
V32                    30                      0                 51
V33                     0                      0                131
V34                     0                      0                 61
V35                     0                      0                 87
V36                     0                      0                100
V37                     0                      0                  0
V38                     0                      0                 60
V39                     0                      0                 91
V40                     0                      0                  0
V41                     0                      0                 52
V42                     0                      0                 65
V43                     0                      0                 19
V44                     0                      0                  0
V45                     0                      0                  0
V46                     0                      0                 74
V47                     0                      0                  0
V48                     0                      0                  0
V49                     0                      0                  0
V50                     0                      0                  0
V51                     0                      0                 55
V52                    15                      0                 70
V53                    27                      0                 42
V54                     0                      0                  0
V55                    30                      0                  0
V56                     0                      0                 27
V57                     0                      0                  0
V58                     0                      0                  0
V59                     0                      0                 47
V60                     0                      0                 53
    Porites lichen Porites lobata Porites lutea Porites nigrescens
V1               0             36            30                  0
V2              47              0             0                  0
V3              49              0             0                  0
V4               0              0             0                 21
V5               0              0             0                  0
V6               0              0             0                  9
V7               0              0             0                 25
V8               0              0             0                  0
V9               0              0             0                 45
V10              0              0             0                 26
V11              0              0             0                  0
V12             40              0             0                  0
V13             19              0             0                  0
V14              0              0             0                 12
V15              0              0             0                  0
V16              0              0             0                 28
V17              0              0             0                  0
V18              0              0             0                  0
V19              0              0             0                  0
V20              0              0             0                  0
V21              0             12             0                  0
V22             42              0             0                  0
V23             18              0            15                  0
V24              0              0             0                 27
V25              0              0             0                  0
V26              0              0             0                  0
V27              0              0             0                  0
V28              0              0             0                  0
V29              0              0             0                  0
V30              0              0             0                  0
V31              9             55             0                 13
V32             12              0             0                 71
V33             33             20            30                 79
V34              6              0             0                 98
V35              0              0             0                165
V36              0              0             0                 15
V37              0              0             0                 20
V38              0              0             0                 68
V39              0              0             0                107
V40              0              0             0                 51
V41             27              0             0                  0
V42             31              0             0                 72
V43             38              0             0                 53
V44             18              0             0                  0
V45              0              0             0                  0
V46              0              0             0                  0
V47              0              0             0                  0
V48              0              0             0                  0
V49              0              0             0                  0
V50              0              0             0                  0
V51             27              0             0                 83
V52             39              0             0                 83
V53             42              0            30                 67
V54             12              0             0                 10
V55              0              0            45                 37
V56              0              0             0                 65
V57              0              0             0                 35
V58              0              0            15                  0
V59              0              0             0                 45
V60              0              0             0                 55
    Porites solida Porites stephensoni Goniopora lobata Favia pallida
V1               0                   0                0            10
V2               0                   0                0            20
V3              10                   0                0             0
V4               0                   0                0             0
V5              17                   0                0             0
V6               0                   0                0             0
V7              31                   0                0             0
V8              41                  30                0             0
V9               0                   0                0             0
V10              0                   0                0             0
V11              0                   0                0             0
V12              0                   0                0             0
V13              0                   0               30             0
V14              0                   0                0             0
V15              0                  20                0             0
V16              0                   0                0             0
V17              0                  25                0             0
V18              0                   0                0             0
V19              0                   0                0             0
V20              0                   0                0             0
V21             12                   0                0             0
V22             24                   0                0             0
V23              0                   0                0             0
V24              0                   0                0             0
V25              0                  27                0             0
V26              0                   0                0             0
V27              0                  33                0             0
V28              0                   0                0             0
V29              0                   0                0             0
V30              0                   0                0             0
V31             35                   0               30             0
V32             52                   0                0             8
V33              0                   0                0             0
V34              9                   0                0             0
V35              0                  55                0             0
V36             39                   0                0             0
V37              0                  71                0             0
V38              0                  37                0             0
V39              0                   0                0             0
V40              0                  50                0             0
V41              0                   0                0             0
V42              0                   0                0             0
V43              0                   0                0             0
V44              0                   0                0             0
V45              0                   0                0             0
V46              0                   0                0             0
V47              0                   0                0             0
V48              0                   0                0             0
V49              0                   0                0             0
V50              0                   0                0             0
V51              0                   0                0             0
V52              0                   0                0            21
V53              0                   0                0             0
V54              0                   0                0             0
V55              0                   0                0             0
V56              0                   0                0             0
V57              0                   0                0             0
V58              0                   0                0             0
V59              0                   0                0             0
V60              0                   0                0             0
    Favia speciosa Favia stelligera Favia rotumana Favites abdita
V1               0                0              0             33
V2               0                0              0             41
V3              30                0              0             23
V4               0                0              0             27
V5               0                0              0             91
V6               0                0              0             63
V7               0                0              0             72
V8               0                0              0             48
V9               0                0              0             71
V10              0                0              0             11
V11              0                0              0              0
V12              0                0              0              0
V13              0                0              0              0
V14              0                0              0              0
V15              0                0              0              0
V16              0                0              0              0
V17              0                0              0              0
V18              0                0              0              0
V19              0                0              0              0
V20              0                0              0              0
V21              0                0              0              0
V22              0                0              0              0
V23              0                0              0              0
V24              0                0              0              0
V25              0                0              0              0
V26              0                0              0              0
V27              0                0              0              0
V28              0                0              0              0
V29              0                0              0              0
V30              0                0              0              0
V31              0                0              0              9
V32              0                0              0              0
V33              0                0              0              0
V34              0                0              0              0
V35              0                0              0              0
V36              0                0              0              0
V37              0                0              0              0
V38              0                0              0              0
V39              0                0              0              0
V40              0                0              0              0
V41              0                0              0             27
V42              0                0              0             11
V43              0                0              0             10
V44              0                0              0              0
V45              0                0              0              0
V46              0                0              0              0
V47              0                0              0              0
V48              0                0              0              0
V49              0                0              0              0
V50              0                0              0              0
V51              0                0              0              0
V52              0                0              0              0
V53              0                0              0             12
V54              0                0              0              0
V55              0                0              0              0
V56              0                0              0              0
V57              0                0              0              0
V58              0                0              0              0
V59              0                0              0              0
V60              0                0              0              0
    Favites chinensis Goniastrea rectiformis Goniastrea pectinata
V1                  0                      0                    0
V2                 44                      0                    0
V3                 78                      0                    0
V4                 61                      0                    0
V5                 44                      0                    0
V6                  0                      0                    0
V7                 55                      0                    0
V8                 30                      0                    0
V9                 30                      0                    0
V10                 0                      0                    0
V11                 0                      6                    0
V12                21                      0                    0
V13                 0                      0                    0
V14                23                      0                    0
V15                20                      0                    0
V16                 0                      0                    0
V17                 0                      0                    0
V18                 0                      0                    0
V19                 0                      0                    0
V20                 0                      0                    0
V21                 0                     21                    0
V22                 0                      9                    0
V23                 0                      0                   15
V24                 0                      0                    0
V25                 0                      0                    0
V26                 0                      0                    0
V27                 0                      0                    0
V28                 0                      0                   15
V29                 0                      0                    0
V30                 0                      0                    0
V31                 9                      0                    0
V32                 0                      0                    0
V33                 0                      0                    0
V34                 0                      0                    0
V35                 0                      0                    0
V36                 0                      0                    0
V37                 0                      0                    0
V38                 0                      0                    0
V39                 0                      0                    0
V40                 0                      0                    0
V41                 0                      0                    0
V42                 0                      0                    0
V43                 0                      0                    0
V44                 0                      0                    0
V45                 0                      0                    0
V46                 0                      0                    0
V47                 0                      0                    0
V48                 0                      0                    0
V49                 0                      0                    0
V50                 0                      0                    0
V51                 0                      0                    0
V52                 0                      0                    0
V53                 0                      0                    0
V54                 0                      0                    0
V55                 0                      0                    0
V56                 0                      0                    0
V57                 0                      0                    0
V58                 0                      0                    0
V59                 0                      0                    0
V60                 0                      0                    0
    Goniastrea sp Dulophyllia crispa Platygyra daedalea
V1              0                  0                  0
V2              0                  0                 27
V3              0                  0                 55
V4              0                  0                  0
V5              0                  0                 71
V6              0                  0                 74
V7              0                  0                 55
V8              0                  0                 48
V9              0                  0                  0
V10             0                  0                  0
V11             0                  0                  0
V12             0                  9                  0
V13             0                  0                  0
V14             0                  0                  0
V15             0                  0                  0
V16             0                  0                  0
V17             0                  0                  0
V18             0                  0                  0
V19             0                  0                  0
V20             0                  0                  0
V21             0                  0                  0
V22             0                  0                  0
V23             0                  0                  0
V24             0                  0                  0
V25             0                  0                  0
V26             0                  0                 30
V27             0                  0                  0
V28             0                  0                  0
V29            17                  0                  0
V30            34                  0                  0
V31             0                  0                  0
V32             0                  0                 25
V33             0                  0                 18
V34             0                  0                 57
V35             0                  0                  0
V36             0                  0                 50
V37             0                  0                  0
V38             0                  0                  0
V39             0                  0                  0
V40             0                  0                  0
V41             0                  0                  0
V42             0                  0                  0
V43             0                  0                  0
V44             0                  0                  0
V45             0                  0                  0
V46             0                  0                  0
V47             0                  0                  0
V48             0                  0                  0
V49             0                  0                  0
V50             0                  0                  0
V51             0                  0                  0
V52             0                  0                  0
V53             0                  0                  0
V54             0                  0                  0
V55             0                  0                  0
V56             0                  0                  0
V57             0                  0                  0
V58             0                  0                  0
V59             0                  0                  0
V60             0                  0                  0
    Platygyra sinensis Hydnopora rigida Leptastrea purpurea
V1                  47                0                   0
V2                  27                0                   0
V3                  56                0                   0
V4                  26                0                   0
V5                   0                0                   0
V6                   0                0                   0
V7                   0                0                   0
V8                   0                0                   0
V9                   0                0                   0
V10                  0                0                   0
V11                  0                0                   0
V12                  0                0                   0
V13                  0                0                   0
V14                  0                0                   0
V15                  0                0                   0
V16                  0                0                   0
V17                  0                0                   0
V18                  0                0                   0
V19                  0                0                   0
V20                  0                0                   0
V21                  0                0                  17
V22                  0                0                  18
V23                  0                0                  16
V24                 24                0                   0
V25                  0                0                   9
V26                  0                0                   0
V27                  0                0                   0
V28                  0                0                   0
V29                  0                0                   0
V30                  0                0                   0
V31                  0                0                   0
V32                  0                0                   0
V33                  0                0                   0
V34                 35                0                   0
V35                  0                0                   0
V36                  0                0                   0
V37                 33                0                   0
V38                  0                0                   0
V39                 37                0                   0
V40                  0                0                   0
V41                  0               35                   0
V42                  0                0                   0
V43                  0               14                   0
V44                  0                0                   0
V45                  0               21                   0
V46                  0               18                   0
V47                  0               17                   0
V48                  0                0                   0
V49                  0                0                   0
V50                  0                0                   0
V51                  0                0                   0
V52                  0                0                   0
V53                  0                0                   0
V54                  0                0                   0
V55                  0                0                   0
V56                  0                0                   0
V57                  0                0                   0
V58                  0                0                   0
V59                  0                0                   0
V60                  0                0                   0
    Leptastrea pruinosa Cyphastrea serailia Millepora platyphylla
V1                    0                   0                    30
V2                    0                   0                     0
V3                    0                   0                     0
V4                    0                   0                     0
V5                    0                   0                     0
V6                    0                   0                     0
V7                    0                   0                     0
V8                    0                   0                     0
V9                    0                   0                     0
V10                   0                   0                     0
V11                   0                  19                     0
V12                   0                   0                     0
V13                   0                  17                     0
V14                   0                   0                     0
V15                   0                   0                     0
V16                   0                  18                     0
V17                   0                   0                     0
V18                   0                   0                     0
V19                   0                   0                     0
V20                   0                   0                     0
V21                  19                  20                     0
V22                  20                   0                     0
V23                   0                  22                     0
V24                   0                   0                     0
V25                   0                   6                     0
V26                   0                  28                     0
V27                   0                   0                     0
V28                   0                   0                     0
V29                   0                   0                     0
V30                   0                   0                     0
V31                   0                  15                     0
V32                   0                   0                     0
V33                   0                   0                     0
V34                   0                   0                     0
V35                   0                   0                     0
V36                   0                   0                     0
V37                   0                   0                     0
V38                   0                   0                     0
V39                   0                   0                     0
V40                   0                   0                     0
V41                   0                   0                    21
V42                   0                   0                     0
V43                   0                   0                     0
V44                   0                   0                     0
V45                   0                   0                     0
V46                   0                   0                     0
V47                   0                   0                     0
V48                   0                   0                     0
V49                   0                   0                     0
V50                   0                   0                     0
V51                   0                  24                     0
V52                   0                   0                     0
V53                   0                   0                     0
V54                   0                   0                     0
V55                   0                   0                     0
V56                   0                   0                     0
V57                   0                   0                     0
V58                   0                   0                     0
V59                   0                   0                     0
V60                   0                   0                     0
    Millepora dichotoma Millepora intrincata Heliopora coerulea time
V1                   21                   24                461   81
V2                    0                    0                271   81
V3                    0                    0                221   81
V4                    0                    0                154   81
V5                    0                    0                  0   81
V6                    0                    0                  0   81
V7                    0                    0                  0   81
V8                    0                    0                  0   81
V9                    0                    0                  0   81
V10                   0                    0                  0   81
V11                   0                    0                  0   83
V12                   0                    0                  0   83
V13                   0                    0                  0   83
V14                   0                    0                  0   83
V15                   0                    0                  0   83
V16                   0                    0                  0   83
V17                   0                    0                  0   83
V18                   0                    0                  0   83
V19                   0                    0                  0   83
V20                   0                    0                  0   83
V21                   0                    0                  0   84
V22                   0                    0                  0   84
V23                   0                    0                  0   84
V24                   0                    0                  0   84
V25                   0                    0                  0   84
V26                   0                    0                  0   84
V27                   0                    0                  0   84
V28                   0                    0                  0   84
V29                   0                    0                  0   84
V30                   0                    0                  0   84
V31                   0                    0                  0   85
V32                   0                    0                  0   85
V33                   0                    0                  0   85
V34                   0                    0                  0   85
V35                   0                    0                  0   85
V36                   0                    0                  0   85
V37                   0                    0                  0   85
V38                   0                    0                  0   85
V39                   0                    0                  0   85
V40                   0                    0                  0   85
V41                   0                    0                  0   87
V42                   0                    0                  0   87
V43                   0                    0                  0   87
V44                   0                    0                  0   87
V45                   0                    0                  0   87
V46                   0                    0                  0   87
V47                   0                    0                  0   87
V48                   0                    0                  0   87
V49                   0                    0                  0   87
V50                   0                    0                  0   87
V51                   0                    0                  8   88
V52                   0                    0                  0   88
V53                   0                    0                  0   88
V54                   0                    0                  0   88
V55                   0                    0                  0   88
V56                   0                    0                  0   88
V57                   0                    0                  0   88
V58                   0                    0                  0   88
V59                   0                    0                  0   88
V60                   0                    0                  0   88
    rep
V1    1
V2    2
V3    3
V4    4
V5    5
V6    6
V7    7
V8    8
V9    9
V10  10
V11   1
V12   2
V13   3
V14   4
V15   5
V16   6
V17   7
V18   8
V19   9
V20  10
V21   1
V22   2
V23   3
V24   4
V25   5
V26   6
V27   7
V28   8
V29   9
V30  10
V31   1
V32   2
V33   3
V34   4
V35   5
V36   6
V37   7
V38   8
V39   9
V40  10
V41   1
V42   2
V43   3
V44   4
V45   5
V46   6
V47   7
V48   8
V49   9
V50  10
V51   1
V52   2
V53   3
V54   4
V55   5
V56   6
V57   7
V58   8
V59   9
V60  10

Tikus Island coral data

Step 2. melt data (pivot_longer)

tikus |> rename(`Acropora aspera` = `Acropera aspera`) |>
    pivot_longer(cols = c(-time, -rep), names_to = "Species",
                 values_to = "Abundance")
# A tibble: 4,500 × 4
   time  rep   Species                Abundance
   <fct> <fct> <chr>                      <int>
 1 81    1     Psammocora contigua            0
 2 81    1     Psammocora digitata            0
 3 81    1     Pocillopora damicornis        79
 4 81    1     Pocillopora verrucosa         32
 5 81    1     Stylopora pistillata           0
 6 81    1     Acropora bruegemanni           0
 7 81    1     Acropora robusta               0
 8 81    1     Acropora grandis               0
 9 81    1     Acropora intermedia           30
10 81    1     Acropora formosa              75
# ℹ 4,490 more rows

Tikus Island coral data

Step 3. Calculate Cover (mutate) (Abundance/10)

tikus |> rename(`Acropora aspera` = `Acropera aspera`) |>
    pivot_longer(cols = c(-time, -rep), names_to = "Species",
                 values_to = "Abundance") |>
    mutate(Cover = Abundance / 10)
# A tibble: 4,500 × 5
   time  rep   Species                Abundance Cover
   <fct> <fct> <chr>                      <int> <dbl>
 1 81    1     Psammocora contigua            0   0  
 2 81    1     Psammocora digitata            0   0  
 3 81    1     Pocillopora damicornis        79   7.9
 4 81    1     Pocillopora verrucosa         32   3.2
 5 81    1     Stylopora pistillata           0   0  
 6 81    1     Acropora bruegemanni           0   0  
 7 81    1     Acropora robusta               0   0  
 8 81    1     Acropora grandis               0   0  
 9 81    1     Acropora intermedia           30   3  
10 81    1     Acropora formosa              75   7.5
# ℹ 4,490 more rows

Tikus Island coral data

Step 4. Split species into Genera and Species (separate)

tikus |> rename(`Acropora aspera` = `Acropera aspera`) |>
    pivot_longer(cols = c(-time, -rep), names_to = "Species",
                 values_to = "Abundance") |>
    mutate(Cover = Abundance / 10) |>
    separate(Species, c("Genera", "Species"))
# A tibble: 4,500 × 6
   time  rep   Genera      Species     Abundance Cover
   <fct> <fct> <chr>       <chr>           <int> <dbl>
 1 81    1     Psammocora  contigua            0   0  
 2 81    1     Psammocora  digitata            0   0  
 3 81    1     Pocillopora damicornis         79   7.9
 4 81    1     Pocillopora verrucosa          32   3.2
 5 81    1     Stylopora   pistillata          0   0  
 6 81    1     Acropora    bruegemanni         0   0  
 7 81    1     Acropora    robusta             0   0  
 8 81    1     Acropora    grandis             0   0  
 9 81    1     Acropora    intermedia         30   3  
10 81    1     Acropora    formosa            75   7.5
# ℹ 4,490 more rows

Tikus Island coral data

Step 5. Subset just ‘Acropora’ (filter)

tikus |> rename(`Acropora aspera` = `Acropera aspera`) |>
    pivot_longer(cols = c(-time, -rep), names_to = "Species",
                 values_to = "Abundance") |>
    mutate(Cover = Abundance / 10) |>
    separate(Species, c("Genera", "Species")) |>
    filter(Genera == "Acropora")
# A tibble: 1,380 × 6
   time  rep   Genera   Species     Abundance Cover
   <fct> <fct> <chr>    <chr>           <int> <dbl>
 1 81    1     Acropora bruegemanni         0   0  
 2 81    1     Acropora robusta             0   0  
 3 81    1     Acropora grandis             0   0  
 4 81    1     Acropora intermedia         30   3  
 5 81    1     Acropora formosa            75   7.5
 6 81    1     Acropora splendida           0   0  
 7 81    1     Acropora aspera             17   1.7
 8 81    1     Acropora hyacinthus        141  14.1
 9 81    1     Acropora palifera           32   3.2
10 81    1     Acropora cytherea          108  10.8
# ℹ 1,370 more rows

Tikus Island coral data

Step 6. Sum over all Species (group_by and summarise)

tikus |> rename(`Acropora aspera` = `Acropera aspera`) |>
    pivot_longer(cols = c(-time, -rep), names_to = "Species",
                 values_to = "Abundance") |>
    mutate(Cover = Abundance / 10) |>
    separate(Species, c("Genera", "Species")) |>
    filter(Genera == "Acropora") |>
    group_by(time, rep) |>
    summarise(SumCover = sum(Cover))
# A tibble: 60 × 3
# Groups:   time [6]
   time  rep   SumCover
   <fct> <fct>    <dbl>
 1 81    1         64.7
 2 81    2         39.7
 3 81    3         35.7
 4 81    4         40.4
 5 81    5         28.9
 6 81    6          8.8
 7 81    7         15.6
 8 81    8          8.3
 9 81    9          6.2
10 81    10         7.5
# ℹ 50 more rows

Tikus Island coral data

Step 7. Summarise per year

tikus |> rename(`Acropora aspera` = `Acropera aspera`) |>
    pivot_longer(cols = c(-time, -rep), names_to = "Species",
                 values_to = "Abundance") |>
    mutate(Cover = Abundance / 10) |>
    separate(Species, c("Genera", "Species")) |>
    filter(Genera == "Acropora") |>
    group_by(time, rep) |>
    summarise(SumCover = sum(Cover)) |>
    group_by(time) |>
    summarise(Mean = mean(SumCover),
              Var = var(SumCover))
# A tibble: 6 × 3
  time   Mean   Var
  <fct> <dbl> <dbl>
1 81    25.6  383. 
2 83     0      0  
3 84     0      0  
4 85     2.43  14.2
5 87     8.01  68.5
6 88     8.55 106.

Tikus Island coral data

Store the result

tikas_sum <-
    tikus |> rename(`Acropora aspera` = `Acropera aspera`) |>
    pivot_longer(cols = c(-time, -rep), names_to = "Species",
                 values_to = "Abundance") |>
    mutate(Cover = Abundance / 10) |>
    separate(Species, c("Genera", "Species")) |>
    filter(Genera == "Acropora") |>
    group_by(time, rep) |>
    summarise(SumCover = sum(Cover)) |>
    group_by(time) |>
    summarise(Mean = mean(SumCover),
              Var = var(SumCover))

Tikus Island coral data

Can you modify so that we get the means and var for each Genera per year?

tikus |> rename(`Acropora aspera` = `Acropera aspera`) |>
    pivot_longer(cols = c(-time, -rep), names_to = "Species",
                 values_to = "Abundance") |>
    mutate(Cover = Abundance / 10) |>
    separate(Species, c("Genera", "Species")) |>
    group_by(time, rep, Genera) |>
    summarise(SumCover = sum(Cover)) |>
    group_by(time, Genera) |>
    summarise(Mean = mean(SumCover),
              Var = var(SumCover))
# A tibble: 144 × 4
# Groups:   time [6]
   time  Genera       Mean    Var
   <fct> <chr>       <dbl>  <dbl>
 1 81    Acropora    25.6  383.  
 2 81    Coeloseris   0.88   1.02
 3 81    Cyphastrea   0      0   
 4 81    Dulophyllia  0      0   
 5 81    Favia        0.6    1.16
 6 81    Favites      8.22  14.9 
 7 81    Fungia       0.68   1.38
 8 81    Galaxea      1.46   3.23
 9 81    Goniastrea   0      0   
10 81    Goniopora    0      0   
# ℹ 134 more rows

Tikus Island coral data

What about the means and var for the top 3 Genera per year (sorted from highest to lowest)?

tikus |> rename(`Acropora aspera` = `Acropera aspera`) |>
    pivot_longer(cols = c(-time, -rep), names_to = "Species",
                 values_to = "Abundance") |>
    mutate(Cover = Abundance / 10) |>
    separate(Species, c("Genera", "Species")) |>
    group_by(time, rep, Genera) |>
    summarise(SumCover = sum(Cover)) |>
    group_by(time, Genera) |>
    summarise(Mean = mean(SumCover),
              Var = var(SumCover)) |>
    top_n(3, Mean) |>
    arrange(-Mean)
# A tibble: 18 × 4
# Groups:   time [6]
   time  Genera     Mean    Var
   <fct> <chr>     <dbl>  <dbl>
 1 87    Montipora 27.4  966.  
 2 81    Acropora  25.6  383.  
 3 85    Montipora 20.5  171.  
 4 85    Porites   19.0   51.3 
 5 88    Montipora 11.8  644.  
 6 81    Montipora 11.4   95.7 
 7 81    Heliopora 11.1  262.  
 8 84    Montipora 11.0   70.5 
 9 88    Porites    9.84  41.4 
10 88    Acropora   8.55 106.  
11 87    Acropora   8.01  68.5 
12 87    Porites    4.49  35.8 
13 84    Porites    2.94   6.65
14 85    Platygyra  2.55   8.74
15 83    Porites    1.74   2.07
16 84    Pavona     1.2    3.33
17 83    Fungia     1.14   3.64
18 83    Montipora  0.93   1.57