e2e_plot_biomass: Plot showing the annual annual average biomass densities of...
In StrathE2E2: End-to-End Marine Food Web Model

Description Usage Arguments Details Value See Also Examples

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.

e2e_plot_biomass(
  model,
  ci.data = FALSE,
  use.saved = FALSE,
  use.example = FALSE,
  results = NULL
)

`model`	R-list object defining the model configuration used to generate the data and compiled by the e2e_read() function.
`ci.data`	Logical. If TRUE plot credible intervals around model results based on Monte Carlo simulation with the e2e_run_mc() function (default=FALSE).
`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).
`use.example`	Logical. If TRUE use pre-computed example data from the internal North Sea model rather than user-generated data (default=FALSE).
`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).

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 by a tick mark.

graphical display in a new graphics window.

e2e_read, e2e_run, e2e_run_mc, e2e_plot_migration, e2e_plot_catch, e2e_plot_trophic, e2e_plot_eco

# 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()


# 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)
}