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plotStrains=function(out,numSpecies,numStages,numStrains,speciesNames,stageNames,figName='strainFig',figType='eps',saveFig=FALSE){
#set size of labels
cexlabsize=2.0
cexaxissize=2.0
cexlegendsize=1.0
cexmainsize=1.75
if (!is.list(stageNames)){stageNames=list(stageNames)}
for (species in seq(1,numSpecies)){
if (numStrains[species]>1){
cols=grDevices::rainbow(numStrains[species])
if (numStages[species]>1){wlen=5*numStages[species];hlen=5}else{wlen=7;hlen=7}
grDevices::dev.new(bg="white",horizontal=FALSE,onefile = FALSE, paper = 'special',width=wlen,height=hlen)
graphics::par(mfrow=c(1,numStages[species]))
for (stage in seq(1,numStages[species])){
str1=paste(speciesNames[species],'.',stageNames[[species]][stage],sep='')
titlestr=paste(speciesNames[species],' (',stageNames[[species]][stage],')',sep='')
graphics::plot(c(min(out[,'time']),1.1*max(out[,'time'])),c(min(0,min(out[,grepl(paste('^',str1,sep=''),colnames(out))])),max(out[,grepl(paste('^',str1,sep=''),colnames(out))])),type='n',main=titlestr,xlab='time',ylab='density',cex.lab=cexlabsize,cex.axis=cexaxissize,cex.main=cexmainsize)
# plot(c(min(out[,'time']),1.1*max(out[,'time'])),c(min(0,min(out[,grepl(paste('^',str1,sep=''),colnames(out))])),max(out[,grepl(paste('^',str1,sep=''),colnames(out))])),type='n',main=titlestr,xlab='time',ylab='density',cex.lab=2,cex.axis=2,cex.main=1.75)
for (i in seq(1,numStrains[species])){
str=paste(str1,'.strain',i,sep='')
graphics::lines(out[,'time'],out[,str],col=cols[i],lwd=2)
}
graphics::legend('topleft',paste('strain',seq(1,numStrains[species])),col=cols,lty=1,lwd=2,bty='n',cex=cexlegendsize)
}
if (saveFig){
if (numSpecies>1){figName=paste(figName,speciesNames[species],sep=''); print(paste('Fig saved to',figName))}
#if (figType=='pdf'){grDevices::dev.copy2pdf(file=paste(figName,'.pdf',sep=""))}
if (figType=='eps'){grDevices::dev.copy2eps(file=paste(figName,'.eps',sep=""))}
if (figType=='png'){grDevices::dev.print(grDevices::png,filename=paste(figName,'.png',sep=""),res=100,width=wlen,height=hlen,units='in')}
if (figType=='tiff'){grDevices::dev.print(grDevices::tiff,filename=paste(figName,'.tiff',sep=""),res=100,width=wlen,height=hlen,units='in')}
}
}
}
}
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