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Subset an environmental PAM by species names

Source: R/lets_subsetPAMenv.R
lets.subsetPAMenv.Rd

Subsets an environmental-space presence-absence matrix (PAM) generated by lets.envpam by retaining only a selected set of species. Species not included in species are removed from both tabular components of the object, and species richness is recalculated and written back to the corresponding raster layers.

Usage

lets.subsetPAMenv(x, species, remove.cells = TRUE)

Arguments

x

An environmental PAM produced by lets.envpam.

species

A character vector with species names to retain in the PAM.

remove.cells

Logical. If TRUE, rows with zero richness after subsetting are removed from matrices. Default is TRUE.

Value

A list with the same structure as the input object:

  • x[[1]]: the subsetted env PAM table.

  • x[[2]]: the subsetted geo PAM table.

  • x[[3]]: the raster associated with env PAM, updated with recalculated richness values.

  • x[[4]]: the raster associated with geo PAM, updated with recalculated richness values.

Details

Optionally, cells with zero richness after subsetting can be removed from the tabular components.

If none of the supplied species names match the species present in the PAM, the function stops with an error before modifying the object.

See also

lets.envpam, lets.plot.envpam, lets.presab, lets.addvar

Examples

if (FALSE) { # \dontrun{
data("Phyllomedusa")
data("prec")
data("temp")

prec <- unwrap(prec)
temp <- unwrap(temp)

PAM <- lets.presab(Phyllomedusa, remove.cells = FALSE)
envs <- lets.addvar(PAM, c(temp, prec), onlyvar = TRUE)
colnames(envs) <- c("Temperature", "Precipitation")
wrld_simpl <- get(utils::data("wrld_simpl", package = "letsR"))
PAM <- lets.pamcrop(PAM, vect(wrld_simpl))

res <- lets.envpam(PAM, envs)

lets.plot.envpam(
  x = res,
  species = NULL,
  cell_id_env = NULL,
  cell_id_geo = NULL,
  plot.grid = TRUE,
  world = TRUE,
  mar = c(4, 4, 4, 4)
)

sub <- sample(PAM$Species_name, 10)
pam_sub <- lets.subsetPAMenv(res, sub)
lets.plot.envpam(pam_sub)
} # }