R/plotRecruits.R

In wStockhausen/rTCSAM2015: A set of tools to set up input for, and interact with output from, a TCSAM2015 model run, as well as to compare TCSAM2015 and rsimTCSAM runs.

#'
#'@title Plot time series of TCSAM 2015 model recruits
#'
#'@description Plots the recruitment time series from a TCSAM 2015 model run.
#'
#'@param res - list object from TCSM 2015 model report file
#'@param logscale - flag (T/F) to plot on ln-scale
#'@param xlab - x axis title
#'@param ylab - y axis title
#'@param xlim - x axis limits
#'@param ylim - y axis limits
#'@param clr - line/points color
#'@param pts.plot - flag (T/F) to plot points
#'@param pts.type - type of point to plot (pch from 'par')
#'@param pts.siz - point size
#'@param line.plot - flag (T/F) to plot line
#'@param line.wd - line width (lwd from par)
#'@param line.type - type of line (lty from 'par')
#'@param overplot - flag (T/F) to plot the data on an existing plot
#'
#'@export
#'
plotRecruits<-function(res,
                        logscale=FALSE,
                        xlab="model year",
                        ylab="recruits",
                        xlim=NULL,
                        ylim=NULL,
                        clr="blue",
                        pts.plot=TRUE,
                        pts.type=21,
                        pts.siz=8,
                        line.plot=TRUE,
                        line.wd=2,
                        line.type=1,
                        overplot=FALSE){
    yrs<-as.numeric(names(res$pop.quants$R.y));
    rec<-res$pop.quants$R.y;
    if (logscale) rec<-log(rec);
    plotXY(yrs,rec,
            xlab=xlab,
            ylab=ylab,
            xlim=xlim,
            ylim=ylim,
            clr=clr,
            pts.plot=pts.plot,
            pts.type=pts.type,
            pts.siz=pts.siz,
            line.plot=line.plot,
            line.wd=line.wd,
            line.type=line.type,
            overplot=overplot);
}