R/popSizesPlot.R

In droglenc/FSAmisc: Miscellaneous functions for simple fisheries stock assessment methods

#' @title Constructs a plot of population size versus time from the projection of Leslie matrix.
#'
#' @description Constructs a plot of population size versus time from the projection of Leslie matrix using \code{pop.projection} from the \pkg{popbio} package.
#'
#' @note This function is meant to work with an object saved from \code{pop.projection()} in the \pkg{popbio} package.  It is not a general function for plotting population size versus time.
#'
#' @param object An object saved from \code{pop.projection} from the \pkg{popbio} package.
#' @param use.log A logical that indicates if the population sizes should be logged before plotting.
#' @param xlab A string for labelling the x-axis.
#' @param ylab A string for labelling the y-axis.
#' @param type A type of plot -- use \code{l} for lines, \code{p} for points, and \code{b} for both.
#' @param lwd A numeric that indicates the line width to use.
#' @param add A logical that indicates whether the data should be added to a currently existing plot.
#' @param \dots Extra arguments to be sent to the default plot routine.
#'
#' @return A plot of either population sizes or log population sizes versus time.
#'
#' @author Derek H. Ogle, \email{dogle@@northland.edu}
#'
#' @seealso \code{pop.projection} and \code{stage.vector.plot} in \pkg{popbio}.
#'
#' @keywords hplot
#'
#' @examples
#' ## ONLY RUN IN INTERACTIVE MODE
#' if (interactive()) {
#'
#' require(popbio)
#' example(pop.projection)
#' popSizesPlot(p)
#'
#' } ## END IF INTERACTIVE MODE
#'
#' @export
popSizesPlot <- function(object,use.log=FALSE,xlab="Time",ylab="Population Size",type="l",lwd=2,add=FALSE,...) {
  t <- 0:(length(object$pop.sizes)-1)
  N <- object$pop.sizes
  if (use.log) {
    N <- log(N)
    if (ylab=="Population Size") ylab="log Population Size"
  }
  df <- data.frame(t,N)
  if (!add) plot(N~t,data=df,type=type,lwd=lwd,xlab=xlab,ylab=ylab,...)
    else graphics::points(N~t,data=df,type=type,lwd=lwd,...)
}