Map envPAM descriptors

Plots each column of the descriptor table returned by lets.envcells back onto the environmental richness raster embedded in the environmental space PAM object.

Usage

lets.plot.envcells(
  x,
  y,
  ras = FALSE,
  plot_ras = TRUE,
  mfrow = c(4, 4),
  which.plot = NULL,
  col_func = NULL,
  ...
)

Arguments

x

The envPAM list returned by lets.envpam (must include $Env_Richness_Raster and $Presence_and_Absence_Matrix_env).

y

A data.frame returned by lets.envcells with one row per environmental cell (aligned with x).

ras

Logical; if TRUE, returns a named list of terra SpatRaster layers corresponding to each column plotted. Default FALSE.

plot_ras

Logical; if TRUE, the function plot the graphs. Default TRUE.

mfrow

A vector of the form c(nr, nc). The figures will be drawn in an nr-by-nc array on the device by rows as in par documentation.

which.plot

Indicate the number of the columns in y to be ploted.

col_func

A custom color ramp palette function to use for plotting variables (e.g., from colorRampPalette).

...

other arguments passed to terra::plot function.

Value

If ras = TRUE, returns a named list of SpatRaster objects corresponding to each descriptor column.

Details

Plot environmental descriptors over the environmental raster grid

Each descriptor column is assigned as values of the environmental raster template and plotted sequentially. Rows with zero frequency are masked as NA. The plotting grid defaults to par(mfrow = c(4,4)).

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, terra::vect(wrld_simpl))
res <- lets.envpam(PAM, envs, n_bins = 30)
out <- lets.envcells(res, perc = 0.2)
lets.plot.envcells(res, out)
} # }