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Subset Species/Environmental Dataset to Ecologically-Relevant Dynamic Variables

match_guilds.Rd

This function reduces the number of environmental covariates in the species/environmental data frame based on defined feeding and habitat guilds

Usage

match_guilds(
  spp_env,
  spp,
  spp_col = "name",
  spp_guild,
  feeding_key,
  feeding_col = "Feeding.Guild",
  habitat_key,
  habitat_col = "Habitat.Guild",
  static_vars = c("x", "y", "month", "year", "bathy", "rugosity", "dist2coast"),
  pa_col = "value"
)

Arguments

spp_env

data.frame of fisheries and environmental data

spp

Species name to add to log files and save data to correct directory (see vignette for recommended directory set up)

spp_col

name of column with species name in spp_guild key

spp_guild

file path to csv file containing a list of species and corresponding feeding and habitat guilds. See vignette for recommended set up of this file

feeding_key, habitat_key

file path to csv for feeding and habitat guild keys respectively. See vignette for recommended set up of these files.

feeding_col, habitat_col

columns names indicating the guild column in the feeding and habitat guild csvs

static_vars

a vector with the column names to be retained

pa_col

column name for presence/absence column

Value

a data frame that contains the static variables listed and only environmental covariates associated with the species' feeding and habitat guilds