Filter species with a given sites coverage threshold — fb_filter_species_by_site

Selects species (columns) for which the percentage of sites where the species is present (distribution value higher than 0 and non-NA) is higher than a threshold.

Usage

fb_filter_species_by_site_coverage(
  site_species,
  threshold_sites_proportion = 0
)

Arguments

site_species: a data.frame with sites in rows and species in columns. NOTE: the first column should be named "site" and indicate site names. The other columns should be named according to species names.
threshold_sites_proportion: a numeric of length 1 between 0 and 1. The percentage of sites coverage threshold.

Value

A subset of site_species with species with a prevalence higher than threshold_sites_proportion.

Examples

library("funbiogeo")

data("site_species")

# Filter species present in at least 10% of the sites
new_site_species <- fb_filter_species_by_site_coverage(
  site_species,
  threshold_sites_proportion = 0.1
)

new_site_species[1:3, 1:4]
#>   site sp_078 sp_006 sp_119
#> 1    1      1      1      1
#> 2    2      1      1      1
#> 3    3      1      1      1

# There are now only 84 species (instead of 149)
ncol(new_site_species)
#> [1] 84