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# R Code to run the mark-recovery model
local(envir=.PBSmodEnv,expr={
locale = sys.frame(sys.nframe() - 1) # local environment
# ************************************************************
# Functions required for the GUI
# ************************************************************
# Initialize and compile the WinBUGS model
modCompile <- function() {
getWinVal(scope="L"); # get data from the GUI
mdat <- list(M=M,S=S,R=R,eps=eps); # collect input data
bugsData(mdat,"MarkRecDat.txt"); # write data in bugs format
modelCheck("MarkRecMod.txt"); # check model syntax
modelData("MarkRecDat.txt"); # load current data
modelCompile(nc); # compile with nc chains
modelGenInits(); # generate randoms inits
samplesSet(c("p","N")); # set parameters to monitor
Nest <- M*S/R;
setWinVal(list(Nest=Nest)); # update estimate in GUI
}
# Update the model and save complete history in global "MRhist"
modUpdate <- function() {
getWinVal(scope="L");
modelUpdate(clen,cthin);
MRhist <- as.data.frame( samplesHistory("*",beg=0,plot=FALSE) ); tput(MRhist)
ctot <- dim(MRhist)[1]; # total length so far
setWinVal(list(ctot=ctot)); par(ask=FALSE); }
# Functions to report results
modHist <- function() {
getWinVal(scope="L"); resetGraph();
samplesHistory("*",beg=s1-1,end=s2-1,thin=sthin,
mfrow=c(2,1),ask=FALSE); };
modDens <- function() {
getWinVal(scope="L"); resetGraph();
samplesDensity("*",beg=s1-1,end=s2-1,thin=sthin,
mfrow=c(2,1),ask=FALSE); };
modACF <- function(chn=1) { # default chain 1
getWinVal(scope="L"); resetGraph();
samplesAutoC("*",chn,beg=s1-1,end=s2-1,thin=sthin,
mfrow=c(2,1),ask=FALSE); };
modPairs <- function() {
getWinVal(scope="L"); resetGraph();
i1 <- max(s1,1); i2 <- min(s2,ctot); # ensure valid range
idx <- seq(i1,i2,by=sthin);
tget(MRhist)
par(ask=FALSE); pairs(MRhist[idx,],pch=19,cex=0.5); };
# ************************************************************
# Load libraries and start the GUI
# ************************************************************
if (!require(BRugs, quietly=TRUE)) stop("The `BRugs` package is required for this example")
if (!require(PBSmodelling, quietly=TRUE)) stop("The `PBSmodelling` package is required for this example")
createWin("MarkRecWin.txt")
}) # end local scope
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