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

dat.1

• 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

Specifying variables is cumbersome

data[,]

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

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

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

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

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

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

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

Piping

• %>%

data %>%
    select(...) %>%
    group_by(...) %>%
    summarise(...)

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

Piping (alternative)

• |>

data |>
    select(...) |>
    group_by(...) |>
    summarise(...)

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

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

dat.1

• re(arranging) data
• subsetting data
• summarising/aggregating data
• joining datasets

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

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

#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

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"

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, …

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 
## # … with 38 more rows

Specifying variables is cumbersome

data[,]

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

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

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

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

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

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

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

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

• data-masking - refer to variables directly
• tidy-selection - refer to variables by position, name or type

select(dat.1, contains("esp"))

select(dat.1, starts_with("Resp"))

select(dat.1, ends_with("e"))

select(dat.1, matches("^R.*[0-9]$"))

select(dat.1, num_range("Resp", 1:2))

select(dat.1, where(is.numeric))

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

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

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

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

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

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

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 %>% 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

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 %>% 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

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

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

Selection helper functions

must evaluate to TRUE/FALSE

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

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

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

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

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

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

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

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

nasa %>% head()

##        lat   long month year cloudhigh cloudlow
## 1 36.20000 -113.8     1 1995      26.0      7.5
## 2 33.70435 -113.8     1 1995      20.0     11.5
## 3 31.20870 -113.8     1 1995      16.0     16.5
## 4 28.71304 -113.8     1 1995      13.0     20.5
## 5 26.21739 -113.8     1 1995       7.5     26.0
## 6 23.72174 -113.8     1 1995       8.0     30.0
##   cloudmid ozone pressure surftemp temperature
## 1     34.5   304      835    272.7       272.1
## 2     32.5   304      940    279.5       282.2
## 3     26.0   298      960    284.7       285.2
## 4     14.5   276      990    289.3       290.7
## 5     10.5   274     1000    292.2       292.7
## 6      9.5   264     1000    294.1       293.6

Select lat, long, and cloud.. columns

nasa %>% head()

##        lat   long month year cloudhigh cloudlow cloudmid ozone pressure surftemp temperature
## 1 36.20000 -113.8     1 1995      26.0      7.5     34.5   304      835    272.7       272.1
## 2 33.70435 -113.8     1 1995      20.0     11.5     32.5   304      940    279.5       282.2
## 3 31.20870 -113.8     1 1995      16.0     16.5     26.0   298      960    284.7       285.2
## 4 28.71304 -113.8     1 1995      13.0     20.5     14.5   276      990    289.3       290.7
## 5 26.21739 -113.8     1 1995       7.5     26.0     10.5   274     1000    292.2       292.7
## 6 23.72174 -113.8     1 1995       8.0     30.0      9.5   264     1000    294.1       293.6

nasa %>% select(lat, long, starts_with("cloud")) %>% head

##        lat   long cloudhigh cloudlow cloudmid
## 1 36.20000 -113.8      26.0      7.5     34.5
## 2 33.70435 -113.8      20.0     11.5     32.5
## 3 31.20870 -113.8      16.0     16.5     26.0
## 4 28.71304 -113.8      13.0     20.5     14.5
## 5 26.21739 -113.8       7.5     26.0     10.5
## 6 23.72174 -113.8       8.0     30.0      9.5

tikus[1:10, c(1:3, 76:77)]

##     Psammocora contigua Psammocora digitata Pocillopora damicornis time rep
## V1                    0                   0                     79   81   1
## V2                    0                   0                     51   81   2
## V3                    0                   0                     42   81   3
## V4                    0                   0                     15   81   4
## V5                    0                   0                      9   81   5
## V6                    0                   0                     72   81   6
## V7                    0                   0                      0   81   7
## V8                    0                   0                     16   81   8
## V9                    0                   0                      0   81   9
## V10                   0                   0                     16   81  10

Select rep, time and only Species that DONT contain pora

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"))

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

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

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

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

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

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

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

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 %>% 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

glimpse(nasa)

## Rows: 41,472
## Columns: 11
## $ lat         <dbl> 36.200000, 33.704348, 31.208696, 28.713043, 26.217391, 23.721739, 21…
## $ long        <dbl> -113.8000, -113.8000, -113.8000, -113.8000, -113.8000, -113.8000, -1…
## $ month       <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,…
## $ year        <int> 1995, 1995, 1995, 1995, 1995, 1995, 1995, 1995, 1995, 1995, 1995, 19…
## $ cloudhigh   <dbl> 26.0, 20.0, 16.0, 13.0, 7.5, 8.0, 14.5, 19.5, 22.5, 21.0, 19.0, 16.5…
## $ cloudlow    <dbl> 7.5, 11.5, 16.5, 20.5, 26.0, 30.0, 29.5, 26.5, 27.5, 26.0, 28.5, 28.…
## $ cloudmid    <dbl> 34.5, 32.5, 26.0, 14.5, 10.5, 9.5, 11.0, 17.5, 18.5, 16.5, 12.5, 13.…
## $ ozone       <dbl> 304, 304, 298, 276, 274, 264, 258, 252, 250, 250, 248, 248, 250, 248…
## $ pressure    <dbl> 835, 940, 960, 990, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000, …
## $ surftemp    <dbl> 272.7, 279.5, 284.7, 289.3, 292.2, 294.1, 295.0, 298.3, 300.1, 300.1…
## $ temperature <dbl> 272.1, 282.2, 285.2, 290.7, 292.7, 293.6, 294.6, 296.9, 297.8, 298.7…

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

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)

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

glimpse(nasa)

## Rows: 41,472
## Columns: 11
## $ lat         <dbl> 36.200000, 33.704348, 31.208696, 28.713043, 26.217391, 23.721739, 21…
## $ long        <dbl> -113.8000, -113.8000, -113.8000, -113.8000, -113.8000, -113.8000, -1…
## $ month       <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,…
## $ year        <int> 1995, 1995, 1995, 1995, 1995, 1995, 1995, 1995, 1995, 1995, 1995, 19…
## $ cloudhigh   <dbl> 26.0, 20.0, 16.0, 13.0, 7.5, 8.0, 14.5, 19.5, 22.5, 21.0, 19.0, 16.5…
## $ cloudlow    <dbl> 7.5, 11.5, 16.5, 20.5, 26.0, 30.0, 29.5, 26.5, 27.5, 26.0, 28.5, 28.…
## $ cloudmid    <dbl> 34.5, 32.5, 26.0, 14.5, 10.5, 9.5, 11.0, 17.5, 18.5, 16.5, 12.5, 13.…
## $ ozone       <dbl> 304, 304, 298, 276, 274, 264, 258, 252, 250, 250, 248, 248, 250, 248…
## $ pressure    <dbl> 835, 940, 960, 990, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000, …
## $ surftemp    <dbl> 272.7, 279.5, 284.7, 289.3, 292.2, 294.1, 295.0, 298.3, 300.1, 300.1…
## $ temperature <dbl> 272.1, 282.2, 285.2, 290.7, 292.7, 293.6, 294.6, 296.9, 297.8, 298.7…

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))

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

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

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

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"

#subset the dataset to just Plot = "P1"
dat.3 <- dat.1 %>% filter(Plot == "P1")
#examine subset data
dat.3

##    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

#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"

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"

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

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

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

Select helper functions

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

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

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

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

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

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

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 
## # … with 38 more rows

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 
## # … with 38 more rows

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

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

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

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

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)

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

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

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

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

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

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

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

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

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.

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

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
## # … with 38 more rows

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.

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…¹ Resp2…² Resp2…³ Resp2…⁴
##   <fct>     <fct>      <dbl>     <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
## 1 Control   P1          50.8     1162.    9.84    56.3   2718.    15.0
## 2 Control   P2          50.1     1069.    9.44    56.2   2015.    13.0
## 3 Exclusion P3          99.7     4285.   18.9     83.8   5502.    21.4
## 4 Exclusion P4         100.      4470.   19.3    131.   10877.    30.1
## # … with abbreviated variable names ¹​Resp1_SE, ²​Resp2_Mean,
## #   ³​Resp2_Var, ⁴​Resp2_SE

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

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

nasa <- as.data.frame(nasa)
head(nasa)

##        lat   long month year cloudhigh cloudlow cloudmid ozone pressure surftemp temperature
## 1 36.20000 -113.8     1 1995      26.0      7.5     34.5   304      835    272.7       272.1
## 2 33.70435 -113.8     1 1995      20.0     11.5     32.5   304      940    279.5       282.2
## 3 31.20870 -113.8     1 1995      16.0     16.5     26.0   298      960    284.7       285.2
## 4 28.71304 -113.8     1 1995      13.0     20.5     14.5   276      990    289.3       290.7
## 5 26.21739 -113.8     1 1995       7.5     26.0     10.5   274     1000    292.2       292.7
## 6 23.72174 -113.8     1 1995       8.0     30.0      9.5   264     1000    294.1       293.6

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
##   <int> <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.

Wide data

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
##    Between Plot  Time   Count
##    <fct>   <fct> <chr>  <int>
##  1 A1      P1    Time.0     8
##  2 A1      P1    Time.1    14
##  3 A1      P1    Time.2    14
##  4 A1      P2    Time.0    10
##  5 A1      P2    Time.1    12
##  6 A1      P2    Time.2    11
##  7 A2      P3    Time.0     7
##  8 A2      P3    Time.1    11
##  9 A2      P3    Time.2     8
## 10 A2      P4    Time.0    11
## 11 A2      P4    Time.1     9
## 12 A2      P4    Time.2     2
## # A tibble: 12 × 4
##    Between Plot  Time   Count
##    <fct>   <fct> <chr>  <int>
##  1 A1      P1    Time.0     8
##  2 A1      P1    Time.1    14
##  3 A1      P1    Time.2    14
##  4 A1      P2    Time.0    10
##  5 A1      P2    Time.1    12
##  6 A1      P2    Time.2    11
##  7 A2      P3    Time.0     7
##  8 A2      P3    Time.1    11
##  9 A2      P3    Time.2     8
## 10 A2      P4    Time.0    11
## 11 A2      P4    Time.1     9
## 12 A2      P4    Time.2     2

Wide data

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
##    Between Plot  Time  Count
##    <fct>   <fct> <chr> <int>
##  1 A1      P1    0         8
##  2 A1      P1    1        14
##  3 A1      P1    2        14
##  4 A1      P2    0        10
##  5 A1      P2    1        12
##  6 A1      P2    2        11
##  7 A2      P3    0         7
##  8 A2      P3    1        11
##  9 A2      P3    2         8
## 10 A2      P4    0        11
## 11 A2      P4    1         9
## 12 A2      P4    2         2

Long data

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

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

Bio data (missing Subplot 3)

Physio-chemical data (missing S7)

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

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

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

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

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

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

##     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…

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

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
## # … with 4,490 more rows

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
## # … with 4,490 more rows

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
## # … with 4,490 more rows

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
## # … with 1,370 more rows

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
## # … with 50 more rows

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.

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)) 

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