R/plot_N.R

In cstawitz/RMAS: Read and Write Input and Output for MAS Model

#' A function to plot N at age
#' @name plot_NAtAge
#' @param SS the matrix of numbers at age from Stock Synthesis, where rows are ages
#' @param MAS the matrix of numbers at age from MAS, where rows are ages
#' @param pdf_on boolean, should the PDF be created? Default is \code{TRUE}
#' @param byage boolean, should the numbers be plotted with each plot representing an age (default to FALSE) or a year?
#' @param years the vector of years in the model
#' @param ages the vector of ages in the model
plot_NAtAge <- function(SS, MAS, pdf_on = TRUE, byage = FALSE, years, ages){

  if(byage){
  if(pdf_on){
  pdf("plots/NAtAge_ByAge.pdf")
  }
  for(i in 1:nrow(SS)){
    plot(NA, xlim= c(min(years), max(years)),
         ylim=c(min(rbind(MAS[i,], SS[i,])),
                max(rbind(SS[i,], MAS[i,]))),
         xlab= "Year", ylab = "Number",
         main=paste("Age", ages[i]))
    points(as.numeric(SS[i,])~years)
    lines(as.numeric(MAS[i,])~years)
  }
  
  if(pdf_on){
  dev.off()
  }
  } else{
    if(pdf_on){
      pdf("plots/NAtAge_ByYr.pdf")
    }
  
  for(i in 1:ncol(SS)){
    
    plot(NA, xlim= c(min(ages), max(ages)),
         ylim=c(min(cbind(MAS[,i], SS[,i])),
                max(cbind(SS[,i], MAS[,i]))),
         main = paste("Year", years[i]), xlab= "Age",
         ylab = "Number")
    points(as.numeric(SS[,i])~ages)
    lines(as.numeric(MAS[,i])~ages)
  }
  
  if(pdf_on){
  dev.off()
  }
  }
}