csim2pam: csim2pam: Converts community simulation to a Presence Absence...

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

csim2pam: Converts community simulation to a Presence Absence Matrix (PAM)

Description

Converts community simultion object into a Presence Absence Matrices (PAM) for a given simultation steps.

Usage

csim2pam(community_sim, which_steps)

Arguments

community_sim	An object of class community_bam.
which_steps	Steps in the simulation object to be converted into a PAM

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 <- bam::community_sim(en_models = enm_path,
                               ngbs_vect = ngbs_vect,
                               init_coords = init_coords,
                               nsteps = nsteps,
                               threshold = 0.1)

pamt10 <-bam::csim2pam(community_sim = sdm_comm ,
                       which_steps = 10)
pams <- bam::csim2pam(community_sim = sdm_comm ,
                      which_steps = c(1:10))

## End(Not run)

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