R/e2e_plot_biomass.R

In StrathE2E2: End-to-End Marine Food Web Model

#
# e2e_plot_biomass.R
#
#' Plot showing the annual annual average biomass densities of each guild in the inshore and offshore zones, optionally with credible intervals.
#'
#' Generate plots showing the annual average biomass densities of each guild in the ecology model in the inshore and offshore zones during the final year of a run. The default is to plot data from a single model run but if available, 
#' credible intervals of model output from a Monte Carlo analysis can also be plotted.
#'
#' Note that in this plot the biomass are expressed as mMN/m2, meaning that the mass in each zone has been scaled to the zonal sea surface area. So the data in
#' this plot are area densities and not mass.
#'
#' Arguments determine the source of model data to be plotted. These can be outputs from a single model run with data held in memory as a list object or in a saved csv file, or from 
#' a Monte Carlo simulation (using the function e2e_run_mc()) to estimate credible intervals of model outputs. Generation of credible interval data is a long computing task, so 
#' example data for the North Sea model provided with the package are available as example data sets.
#'
#' If credible intervals are plotted these are displayed as box-and-whiskers. The box spans 50% of the likelihood distribution of values and the whiskers 99%. The median is shown 
#' by a tick mark.
#'
#' @param model R-list object defining the model configuration used to generate the data and compiled by the e2e_read() function.
#' @param ci.data Logical. If TRUE plot credible intervals around model results based on Monte Carlo simulation with the e2e_run_mc() function (default=FALSE).
#' @param use.saved Logical. If TRUE use data from a prior user-defined run held as csv files data in the current results folder (default=FALSE).
#' @param use.example Logical. If TRUE use pre-computed example data from the internal North Sea model rather than user-generated data (default=FALSE).
#' @param results R-list object of baseline model output generated by the e2e_run() function. Only needed if ci.data=FALSE, use.saved=FALSE and use.example=FALSE. (Default=NULL).
#'
#' @return graphical display in a new graphics window.
#'
#' @seealso \code{\link{e2e_read}}, \code{\link{e2e_run}}, \code{\link{e2e_run_mc}}, \code{\link{e2e_plot_migration}}, \code{\link{e2e_plot_catch}}, \code{\link{e2e_plot_trophic}}, \code{\link{e2e_plot_eco}}
#'
#' @importFrom graphics text
#'
#' @export
#'
#' @examples
#' # Load the 1970-1999 version of the North Sea model supplied with the package, 
#' # run, and generate a plot:
#'     model <- e2e_read("North_Sea", "1970-1999")
#'     results <- e2e_run(model, nyears=2)
#'     e2e_plot_biomass(model, results=results)
#'
#' # Direct the graphics output to a pdf file ... 
#' # or jpeg("plot.jpg"), png("plot.png")
#'     pdf(file.path(tempdir(), "plot.pdf"),width=4,height=6)
#'     e2e_plot_biomass(model, results=results)
#'     dev.off()
#'
#' \donttest{
#' # Alternatively, plot the same data from a csv file saved by the e2e_run() function. Here the
#' # csv output is directed to a temporary folder since results.path is not set in the e2e_read()
#' # function call:
#'     results <- e2e_run(model, nyears=2,csv.output=TRUE)
#'     dev.new()
#'     e2e_plot_biomass(model, use.saved=TRUE)
#' }
#'
#' # For the same model, plot the example data with credible intervals:
#' # This example requires the Strathe2E2examples supplementary data package.
#' if(require(StrathE2E2examples)){
#'     e2e_plot_biomass(model, ci.data=TRUE, use.example=TRUE)
#' }
#'
#
# ---------------------------------------------------------------------
# |                                                                   |
# | Author: Mike Heath                                                |
# | Department of Mathematics and Statistics                          |
# | University of Strathclyde, Glasgow                                |
# |                                                                   |
# | Date of this version: May 2020                                    |
# |                                                                   |
# ---------------------------------------------------------------------

e2e_plot_biomass <- function(model,ci.data=FALSE, use.saved=FALSE, use.example=FALSE, results=NULL  ) {

   oo <- options()
   on.exit(options(oo))

	if (use.example == TRUE) hasExamples()

start_par = par()$mfrow
on.exit(par(mfrow = start_par))

if(use.saved==TRUE & use.example==TRUE){
        stop("use.saved and use.example cannot both be TRUE ! \n")
}

if(use.saved==TRUE & is.list(results)==TRUE){
        stop("use.saved is TRUE but a dataframe object has also been specified ! \n")
}

if(use.example==TRUE & is.list(results)==TRUE){
        stop("use.example is TRUE but a dataframe object has also been specified ! \n")
}

if(use.saved==FALSE & use.example==FALSE & is.list(results)==FALSE){
        stop("no source of data has been specified ! \n")
}

if(ci.data==FALSE & use.example==TRUE){
        stop("no example data available for a single model run - run the model to generate some data ! \n")
}

if(ci.data==TRUE & use.saved==FALSE & use.example==FALSE & is.list(results)==TRUE){
        stop("credible intervals available only from saved or example data ! \n")
}

#.........................................................................

if(ci.data == FALSE & use.saved==FALSE & is.list(results)==TRUE ){
	plot_inshore_vs_offshore_anavmass(model, use.saved=FALSE,results=results)
}

if(ci.data == FALSE & use.saved==TRUE ){
	plot_inshore_vs_offshore_anavmass(model, use.saved=TRUE)
}

if(ci.data == TRUE & use.saved==FALSE & use.example==TRUE ){
	plot_inshore_vs_offshore_anavmass_with_ci(model, use.example=TRUE)
}

if(ci.data == TRUE & use.saved==TRUE & use.example==FALSE ){
	plot_inshore_vs_offshore_anavmass_with_ci(model, use.example=FALSE)
}

#.........................................................................


}

#-----------------------------------------------------------------