cover_calc {quadcleanR}

Calculate species cover

Description

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)

cover_calc(data = coral_cover, spp = names(coral_cover[3:6]), prop = FALSE, total = FALSE)