PSPMind {PSPManalysis}

Computes the individual life history of a physiologically structured population model in a given environment

Description

PSPMind is a utility function to compute the individual life history as defined by a physiologically structured population model, given a specific set of values for the environmental variables

Usage

PSPMind(
  modelname = NULL,
  environment = NULL,
  parameters = NULL,
  options = NULL,
  clean = FALSE,
  force = FALSE,
  debug = FALSE,
  silent = FALSE
)

Arguments

modelname

(string, required)

Basename of the file with the model specification. The file should have an extension ".h". For example, the model "PNAS2002" is specified in the file "PNAS2002.h". If the model is specified in R include the .R extension explicitly, i.e. specify the model name as "PNAS2002.R"

environment

(row vector, required)

Vector of length ENVIRON_DIM (set in the model program file; This is the length of the variable 'EnvironmentState' if the model is specified in R), specifying the value of the environmental variables at which to calculate the individual life history. This vector can also be extended with values of the birth rates for all structured populations in the model, which would scale the output of the model with these birth rates.

parameters

(row vector, optional, can be left equal to its default NULL)

Vector of length PARAMETER_NR (set in the model program file; This is the length of the variable 'DefaultParameters' if the model is specified in R), specifying the values for the model parameters to use in the computation. Vectors of other lengths, including an empty vector will be ignored.

options

(row vector of strings, optional, can be left equal to its default NULL)

Vector with a pair of strings, consisting of an option name and a value (for example c("isort", "1")). The only possible option name and its values is:

⁠"isort", "<index>"⁠: Index of i-state variable to use as ruling variable for sorting the structured populations

clean

(Boolean, optional argument)

Specify clean = TRUE as argument to remove all the result files of the model before the computation

force

(Boolean, optional argument)

Specify force = TRUE as argument to force a rebuilding of the model before the computation

debug

(Boolean, optional argument) Specify debug = TRUE as argument to compile the model in verbose mode and with debugging flag set

silent

(Boolean, optional argument)

Specify silent = TRUE as argument to suppress reporting of compilation commands and results on the console

Details

output <- PSPMind(modelname = NULL, environment = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE)

Value

The output is a structure with the population state as normally stored in the .csb output file of PSPMdemo, PSPMequi, PSPMecodyn and PSPMevodyn.

Examples

## Not run: 
PSPMind("PNAS2002_5bs", c(1.30341E-05, 3.84655E-05, 4.00802E-06), 
        options = c("isort", "1"), clean=TRUE, force=TRUE)

## End(Not run)