relative_cover {fqacalc}

Calculate Relative Cover

Description

relative_cover calculates the total cover per group of interest (species, taxonomic family, or physiognomic group) divided by the total cover for all observations, then multiplied by 100. If the regional database does not have information on species family or physiognomy, the function will return a data frame with a single NA category.

Usage

relative_cover(
  x,
  key = "name",
  db,
  col = c("species", "family", "physiog"),
  cover_class = "percent_cover",
  allow_no_c = TRUE,
  allow_non_veg = TRUE,
  plot_id = NULL
)

Arguments

x

A data frame containing a list of plant species. This data frame must have one of the following columns: name or acronym. For cover-weighted or relative functions, this data frame must also have a column called cover containing cover values and ideally a column containing plot IDs.

key

A character string representing the column that will be used to join the input data frame x with the regional FQA database. If a value is not specified, the default is "name". "name" and "acronym" are the only acceptable values for key.

db

A character string representing the regional FQA database to use. See db_names for a list of potential values and the fqadata R package where the databases are hosted.

col

A character string representing the categorical variable to calculate the relative cover of. Can be set to "species", "family" or "physiog" (for physiognomy).

cover_class

a character string representing the cover classification used. Acceptable cover classes are: "percent_cover", "carolina_veg_survey", "braun-blanquet", "daubenmire", and "usfs_ecodata". "percent_cover" is the default.

allow_no_c

Boolean (TRUE or FALSE). If TRUE, allow species that are found in the regional FQA database but have not been assigned a C Values. If FALSE, omit species that have not been assigned C Values.

allow_non_veg

Boolean (TRUE or FALSE). If TRUE, allow input to contain un-vegetated ground and un-vegetated water.

plot_id

A character string representing the column in x that contains plot identification values. plot_id is a required argument in plot_summary, where it acts as a grouping variable. plot_id is optional but highly recommended for cover-weighted functions and relative functions. If plot_id is set in a cover-weighted function or a relative function, it only prevents duplicates from occurring in the same plot. It does not act as a grouping variable.

Value

A data frame with categorical variables set by the col argument and their relative cover.

Examples

transect <- data.frame(
acronym  = c("ABEESC", "ABIBAL", "AMMBRE", "ANTELE", "ABEESC", "ABIBAL", "AMMBRE"),
cover = c(50, 4, 20, 30, 40, 7, 60),
plot_id = c(1, 1, 1, 1, 2, 2, 2))

relative_cover(transect, key = "acronym", db = "michigan_2014", col = "species",
plot_id = "plot_id")

#can also include bare ground and unvegetated water
transect_unveg <- data.frame(acronym  = c("GROUND", "ABEESC", "ABIBAL", "AMMBRE",
"ANTELE", "WATER", "GROUND", "ABEESC", "ABIBAL", "AMMBRE"),
cover = c(60, 50, 4, 20, 30, 20, 20, 40, 7, 60),
plot_id = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 2))

relative_cover(transect_unveg, key = "acronym", db = "michigan_2014",
col = "species", plot_id = "plot_id")