Calculate species cover — cover

Convert the number of observations for each species or non-species to proportion or percent cover within each row based on the total number of observations in each row. Useful for quadrats with varying numbers of observations to calculate each row's percent cover all at once.

Usage

cover_calc(data, spp, prop = TRUE, total = FALSE)

Arguments

data: A data frame with each row representing a sampling unit (ex. a quadrat or photo).
spp: The column names containing all observations to be used in the proportion calculation. It is important to note that the proportions will be scaled to the total observations in these columns for each quadrat.
prop: If prop = TRUE, the resulting cover will be proportions. If prop = FALSE, the resulting cover will be in percentages.
total: If total = TRUE, a column containing the total number of observations at each sampling unit will be returned in a new column called total_pts. This will not be returned if total = FALSE.

Value

A data frame containing scaled observation cover.

Examples

#create data set for example
Sites <- as.factor(c("One", "One", "Two", "Two", "Three", "Three"))
Transect <- as.factor(c("1-Shallow", "2-Shallow", "1-Shallow", "2-Shallow",
    "1-Shallow", "2-Shallow"))
Acropora.sp <- c(1, 2, 3, 4, 5, 6)
Gardineroseris.sp <- c(6, 1, 2, 3, 4, 5)
Psammocora.sp <- c(5, 6, 1, 2, 3, 4)
Leptastrea.sp <- c(4, 5, 6, 1, 2, 3)
coral_cover <- data.frame(Sites, Transect, Acropora.sp, Gardineroseris.sp,
                          Psammocora.sp, Leptastrea.sp)

cover_calc(data = coral_cover, spp = names(coral_cover[3:6]), prop = TRUE, total = TRUE)
#>   Sites  Transect Acropora.sp Gardineroseris.sp Psammocora.sp Leptastrea.sp
#> 1   One 1-Shallow   0.0625000        0.37500000    0.31250000     0.2500000
#> 2   One 2-Shallow   0.1428571        0.07142857    0.42857143     0.3571429
#> 3   Two 1-Shallow   0.2500000        0.16666667    0.08333333     0.5000000
#> 4   Two 2-Shallow   0.4000000        0.30000000    0.20000000     0.1000000
#> 5 Three 1-Shallow   0.3571429        0.28571429    0.21428571     0.1428571
#> 6 Three 2-Shallow   0.3333333        0.27777778    0.22222222     0.1666667
#>   total_pts
#> 1        16
#> 2        14
#> 3        12
#> 4        10
#> 5        14
#> 6        18

cover_calc(data = coral_cover, spp = names(coral_cover[3:6]), prop = FALSE, total = FALSE)
#>   Sites  Transect Acropora.sp Gardineroseris.sp Psammocora.sp Leptastrea.sp
#> 1   One 1-Shallow     6.25000         37.500000     31.250000      25.00000
#> 2   One 2-Shallow    14.28571          7.142857     42.857143      35.71429
#> 3   Two 1-Shallow    25.00000         16.666667      8.333333      50.00000
#> 4   Two 2-Shallow    40.00000         30.000000     20.000000      10.00000
#> 5 Three 1-Shallow    35.71429         28.571429     21.428571      14.28571
#> 6 Three 2-Shallow    33.33333         27.777778     22.222222      16.66667