e2e_compare_obs: Box and whisker plots comparing annual or monthly...
In StrathE2E2: End-to-End Marine Food Web Model

Description Usage Arguments Details Value See Also Examples

Generate a multi-panel set of box and whisker diagrams comparing annual or monthly averaged or integrated observational data on the state of the ecosystem with corresponding model outputs. Each panel displays a different category of observational and model data.

e2e_compare_obs(
  selection = "ANNUAL",
  model,
  ci.data = FALSE,
  use.saved = FALSE,
  use.example = FALSE,
  results = NULL
)

`selection`	Text string from a list to select comparison with annual or monthly observations. Select from: "ANNUAL", "MONTHLY". Remember to include the phrase within "" quotes.
`model`	R-list object defining the baseline 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 model output generated by the e2e_run() function (default=NULL).

The observational data are read from the file 'annual_observed_*.csv' or 'monthly_observed_*.csv'in the /Target folder of the model setup defined by a e2e_read() function call. Column 3 of annual_observed_* (header "Use_1.yes_0.no") is a flag to set whether any given row is used in calculating the likelihood of the observed data given the model setup by functions such as e2e_optimize_eco(). Un-used rows of data are omitted from the box and whisker plotting panels.

Arguments determine the source of model data for comparison with the observations. 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 for illustration.

In each plot panel, the distribution of observation data is shown by a black box plot (box spans 50 derived from model outputs are always shown in red - either a red tick mark for data from a single model run, or a red boxplot for data from a Monte Carlo analysis.

graphical display in a new graphics window

e2e_read, e2e_run, e2e_run_mc

# 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,csv.output=FALSE)
# Plot data annual data
    e2e_compare_obs(selection="ANNUAL", model, results=results)
# Note that these are the observational data that were used as the target for optimizing
# the model parameters

# Direct the graphics output to a file ... in this example the graphics file
# is sent to a temporary folder rather than the current working directory:
# or jpeg("plot.jpg"), png("plot.png")
    pdf(file.path(tempdir(), "plot.pdf"),width=8,height=6)
    e2e_compare_obs(selection="ANNUAL", model, results=results)
    dev.off()

# Plot monthly data
    dev.new()
    e2e_compare_obs(model, selection="MONTHLY",results=results)
# Note that these observational data were NOT used for optimizing the 
# model parameters


# To create the same plots from the csv files saved by the e2e_run() function, use:
    model <- e2e_read("North_Sea", "1970-1999")
    results <- e2e_run(model, nyears=2,csv.output=TRUE)
# Here the csv outputs are saved to a temporary folder since results.path is not 
# set in e2e_read()
    e2e_compare_obs(selection="ANNUAL", model, use.saved=TRUE)
    dev.new()
    e2e_compare_obs(selection="MONTHLY", model, use.saved=TRUE)


# Load the 1970-1999 version of the North Sea model supplied with the package and plot
# example data with credible intervals generated by a baseline mode Monte Carlo analysis.
# This example requires the Strathe2E2examples supplementary data package.
if(require(StrathE2E2examples)){
    model <- e2e_read("North_Sea", "1970-1999")
    e2e_compare_obs(model, selection="ANNUAL",ci.data=TRUE,use.example=TRUE)
    dev.new()
    e2e_compare_obs(selection="MONTHLY", model, ci.data=TRUE,use.example=TRUE)
}