#' @title Title
#'
#' @description Description
#'
#' @param x A number.
#' @param y A number.
#' @return return value here.
#' @details
#' Additional details here
#' @examples
#' example function call here
#' @export
plot_vl_trajectories_aim2<- function(model,sim,outpath,name)
{
if(is.null(model$vl_list[[sim]])){
cat("\n viral load list not saved; set evoparams$save_vl_list=TRUE to plot VL trajectories")
return(invisible(NULL))
}
vl_df <- do.call(rbind,model$vl_list[[sim]])
agents <- unique(vl_df[,1])
if(is.null(name)){
name="vl_trajectories.pdf"
}else{
name=paste(name,"_vl_traj.pdf",sep="")
}
pdf(file.path(outpath,name),width=12,height=10)
par(mfrow=c(2,2))
for(ind in agents)
{
vl_ix <- which(vl_df[,1]==ind)
if(length(vl_ix>0)){
seq1<- seq(0,model$param[[sim]]$n_steps/365,length=10)
seq2<- seq(-5,8,length=10)
plot(seq1,seq2,type='n', xlab="years",ylab="viral load")
lines(vl_df[vl_ix,5]/365,log10(vl_df[vl_ix,2]),lwd=2,col="blue")
axis(2,col="blue")
par(new=T)
plot(seq1,seq(0,5,length=length(seq1)),type='n', xlab=NA,ylab=NA,axes=F)
lines(vl_df[vl_ix,5]/365,(vl_df[vl_ix,3]),lwd=2,col="green")
axis(4,col="green")
mtext(paste("viral load and cd4 data for agent",ind),side=3)
}
}
dev.off()
}
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