## Script to run GLMM fit on subset of sagebrush data
## Uses STAN to fit the model
##
## Author: Andrew Tredennick
## Email: atredenn@gmail.com
## Last Update: 9-2-2015
####
#### Set some file paths, etc.
####
datapath <- ""
knotpath <- ""
####
#### Load required libraries
####
library(rstan)
library(reshape2)
####
#### Set chain ID from command line prompt
####
args <- commandArgs(trailingOnly = F)
myargument <- args[length(args)]
myargument <- sub("-","",myargument)
chain_id <- as.numeric(myargument)
####
#### Get data
####
fullD <- read.csv(paste0(datapath,"wy_sagecover_subset_noNA.csv"))
if(length(which(is.na(fullD$Cover))) > 0) stop("data contains NA values")
# Get data structure right
growD <- subset(fullD, Year>1984) # get rid of NA lagcover years
growD$Cover <- round(growD$Cover,0) # round for count-like data
growD$CoverLag <- round(growD$CoverLag,0) # round for count-like data
# Load knot data
load(paste0(knotpath,"Knot_cell_distances_subset.Rdata"))
K <- K.data$K
####
#### Write the STAN model
####
model_string <- "
data{
int<lower=0> nobs; // number of observations
int<lower=0> ncovs; // number of climate covariates
int<lower=0> nknots; // number of interpolation knots
int<lower=0> ncells; // number of cells
int<lower=0> cellid[nobs]; // cell id
int<lower=0> dK1; // row dim for K
int<lower=0> dK2; // column dim for K
int y[nobs]; // observation vector
int lag[nobs]; // lag cover vector
matrix[dK1,dK2] K; // spatial field matrix
matrix[nobs,ncovs] X; // spatial field matrix
}
parameters{
real int_mu;
real<lower=0> beta_mu;
real<lower=0.0001> sig_a;
vector[nknots] alpha;
vector[ncovs] beta;
real<lower=0.0001> phi; // neg. binomial dispersion parameter
}
transformed parameters{
vector[ncells] eta;
vector[nobs] mu;
vector[nobs] climEffs;
eta <- K*alpha;
climEffs <- X*beta;
for(n in 1:nobs)
mu[n] <- int_mu + beta_mu*lag[n] + climEffs[n] + eta[cellid[n]];
}
model{
// Priors
alpha ~ normal(0,sig_a);
int_mu ~ normal(0,100);
beta_mu ~ normal(0,10);
beta ~ normal(0,10);
sig_a ~ cauchy(0,5);
phi ~ cauchy(0,5);
// Likelihood
y ~ neg_binomial_2_log(mu, phi);
}
"
####
#### Function to extract STAN mcmc
####
get_mcmc <- function(S){
long <- NULL
sdf <- as.data.frame(S@sim$samples[[1]])
sdf$Iteration <- 1:dim(sdf)[1]
s <- melt(sdf, id.vars = "Iteration")
colnames(s) <- c("Iteration", "Parameter", "value")
long <- rbind(long, s)
return(long)
}
####
#### Send data to STAN function for fitting
####
y = growD$Cover
lag = growD$CoverLag
K = K.data$K
# Set up new, continuous cell IDs
num_ids <- length(unique(growD$ID))
num_reps <- nrow(growD)/num_ids
new_ids <- rep(c(1:num_ids), num_reps)
growD$newID <- new_ids
cellid = growD$newID
X = growD[,c("pptLag", "ppt1", "ppt2", "TmeanSpr1", "TmeanSpr2")]
X = scale(X, center = TRUE, scale = TRUE)
inits <- list()
inits[[1]] <- list(int_mu = 1, beta_mu = 0.05, beta = rep(0, ncol(X)),
alpha = rep(0,ncol(K.data$K)), sig_a=0.05,
phi=10)
inits[[2]] <- list(int_mu = 2, beta_mu = 0.01, beta = rep(0.5, ncol(X)),
alpha = rep(0.5,ncol(K.data$K)), sig_a=0.005,
phi=50)
inits[[3]] <- list(int_mu = 1.5, beta_mu = 0.02, beta = rep(0.2, ncol(X)),
alpha = rep(0.25,ncol(K.data$K)), sig_a=0.025,
phi=100)
datalist <- list(y=y, lag=lag, nobs=length(lag), ncells=length(unique(cellid)),
cellid=cellid, nknots=ncol(K), K=K, dK1=nrow(K), dK2=ncol(K),
X=X, ncovs=ncol(X))
pars <- c("int_mu", "beta_mu", "alpha", "beta", "phi", "sig_a")
# Compile the model
mcmc_config <- stan(model_code=model_string, data=datalist,
pars=pars, chains=0)
mcmc1 <- stan(fit=mcmc_config, data=datalist, pars=pars, chains=1,
iter = 200, warmup = 100, init=list(inits[[chain_id]]))
long <- get_mcmc(mcmc1)
lastones <- subset(long, Iteration==200)
lastmcmc <- mcmc1
saveRDS(long, paste0("iterchunk1_chain", chain_id, ".RDS"))
for(i in 2:10){
betatmp=lastones[grep("beta", lastones$Parameter),]
beta=as.numeric(unlist(betatmp[which(betatmp$Parameter!="beta_mu"),"value"]))
newinits <- list(list(int_mu=as.numeric(lastones[which(lastones$Parameter=="int_mu"),"value"]),
beta_mu=as.numeric(lastones[which(lastones$Parameter=="beta_mu"),"value"]),
beta=beta,
alpha=as.numeric(unlist(lastones[grep("alpha", lastones$Parameter),"value"])),
sig_a=as.numeric(lastones[which(lastones$Parameter=="sig_a"),"value"]),
phi=as.numeric(lastones[which(lastones$Parameter=="phi"),"value"])))
mcmc <- stan(fit = lastmcmc, data = datalist, pars = pars, chains = 1,
iter=200, warmup=100, init = newinits)
long <- get_mcmc(mcmc)
lastones <- subset(long, Iteration==200)
lastmcmc <- mcmc
saveRDS(long, paste0("iterchunk",i,"_chain", chain_id, ".RDS"))
}
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