Example use case of PGLMMs for phylogenetic community structure

PGLMM_example.R

# Example Code
# Load functions 
source("/path/where/you/have/this/file/PGLMM.data.R")
source("/path/where/you/have/this/file/PGLMM.fit.R")
source("/path/where/you/have/this/file/PGLMM.reml.R")
source("/path/where/you/have/this/file/PGLMM.sim.R")


# Simulate a dataset for the example
modelflag <- 1
sim.dat <- PGLMM.sim(stree(16, "balanced"), nsites = 30, modelflag = modelflag,
                    second.env = TRUE, compscale = 1)
sim.dat$Vphylo  # I think this is the variance-covariance matrix from the phylogeny
  
  # PGLMM.sim also automatically outputs three figures, shown below


# Organizes the data so that PGLMM can be fit
dat <- PGLMM.data(modelflag=modelflag,sim.dat=sim.dat)
str(dat)  # Structure of the data



# Simulate a dataset for the example
  # low number of iterations, maxit = 25 is probably good, but may need 
  # to increase exitcountermax
out <- PGLMM.fit(dat = dat, maxit = 25, exitcountermax = 30)  
str(out)  # Structure of the data
out$B  # coefficients from PGLMM
out$B0  # coefficients from standard logistic regression
out$s  # parameter(s) of the covariance matrix
out$LL  # log-likelihood
out$flag  # did model converge?