pam2richness {bamm} | R Documentation |
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 |
which_steps |
Time steps in the pam to convert |
Value
A RasterStack richness for each simulation step
Author(s)
Luis Osorio-Olvera & Jorge SoberĂ³n.
Examples
lagos_path <- system.file("extdata/conejos",
package = "bamm")
enm_path <- list.files(lagos_path,
pattern = ".tif",
full.names = TRUE)[seq(1,10)]
en_models <- raster::stack(enm_path)
ngbs_vect <- sample(2,replace = TRUE,
size = raster::nlayers(en_models))
init_coords <- read.csv(file.path(lagos_path,
"lagos_initit.csv"))[seq(1,10),]
nsteps <- 10
sdm_comm <- bamm::community_sim(en_models = en_models,
ngbs_vect = ngbs_vect,
init_coords = init_coords,
nsteps = nsteps,
threshold = 0.1)
pams <-bamm::csim2pam(community_sim = sdm_comm ,
which_steps = seq_len(nsteps))
richness_stack <- bamm::pam2richness(pamobj = pams,
which_steps = pams@which_steps)
raster::plot(richness_stack)
[Package bamm version 0.5.0 Index]