pam2richness: pam2richness: Converts Presence Absence Matrix (pam object)...

In luismurao/bam: Species Distribution Models in the light of the BAM theory

pam2richness: Converts Presence Absence Matrix (pam object) to richness raster

Description

Converts Presence Absence Matrix (pam object) to richness raster

Usage

pam2richness(pamobj, which_steps)

Arguments

pamobj	An object of class pam see csim2pam
which_steps	Time steps in the pam to convert

Examples

## Not run: 
library(bam)
lagos_path <- system.file("extdata/conejos",
                          package = "bam")
enm_path <- list.files(lagos_path,
                       pattern = ".tif",
                    full.names = TRUE)
en_models <- raster::stack(enm_path)
ngbs_vect <- sample(1:2,replace = T,
                    size = raster::nlayers(en_models))
init_coords <- read.csv(file.path(lagos_path,
                                  "lagos_initit.csv"))
nsteps <- 30
sdm_comm <- community_sim(en_models = enm_path,
                          ngbs_vect = ngbs_vect,
                          init_coords = init_coords,
                          nsteps = nsteps,
                          threshold = 0.1)

pams <-csim2pam(community_sim = sdm_comm ,
                which_steps = c(1:20))
richness_stack <- pam2richness(pams,which_steps=pams@which_steps)
raster::plot(richness_stack)

## End(Not run)

luismurao/bam documentation built on Nov. 28, 2022, 3:02 p.m.