PSPMecodyn {PSPManalysis}

Ecological dynamics of a structured population model computed using the Escalator Boxcar Train

Description

PSPMecodyn computes the dynamics of a physiologically structured population model starting from an environmental and population state that is computed with PSPMequi. If starting from an arbitrary state is required, the list specifying the initial state should have the same layout as produced by PSPMequi.

Usage

PSPMecodyn(
  modelname = NULL,
  startstate = NULL,
  timepars = NULL,
  bifpars = 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"

startstate

(list, required)

The initial environmental and population state from which to start the simulation of the dynamics. This list should have the identical layout as a list returned by the function csbread(). As a minimum, the list should contain a vector 'Environment' specifying the initial values of the environmental variables, and a matrix 'Pop00' (assuming there is only a single population in the model), which specifies on each row the number and individual state variables of a cohort of while the different rows specify all the cohorts in the population.

timepars

(row vector of length 4, required)

Vector of length 4 specifying the settings for the time integration:

⁠timepars[1]⁠: Cohort cycle time, i.e. time interval between starts of new boundary cohorts

⁠timepars[2]⁠: Output time interval, i.e. time interval between data output to .out file

⁠timepars[3]⁠: State output interval, i.e. time interval between complete state output to .csb file

⁠timepars[4]⁠: Maximum integration time, i.e. maximum time value until which to continue the integration

bifpars

(row vector of length 6, optional)

Vector of length 6 specifying the settings for the bifurcation settings. If not specified a normal time integration is carried out.

⁠bifpars[1]⁠: Index of the bifurcation parameter

⁠bifpars[2]⁠: Starting value of the bifurcation parameter

⁠bifpars[3]⁠: Step size in the bifurcation parameter

⁠bifpars[4]⁠: Final value of the bifurcation parameter

⁠bifpars[5]⁠: Period of producing data output during each bifurcation interval

⁠bifpars[6]⁠: Period of producing state output during each bifurcation interval

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 pairs of strings, consisting of an option name and a value (for example c("info", "1")). Possible option names and their values are:

⁠"info", "<index>"⁠: Level of performance information on the DOPRI5 integrator written to .err file (1, 2, 3 or 4)

⁠"report", "<index>"⁠: Interval between reporting of data output to console ( > 0)

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 <- PSPMecodyn(modelname = NULL, startstate = NULL, timepars = NULL, bifpars = NULL, parameters = NULL, options = NULL, clean = FALSE, force = FALSE, debug = FALSE, silent = FALSE)

Value

The output is a list containing the following elements:

⁠curvepoints⁠: Matrix with output for all computed points along the curve

⁠curvedesc⁠: Column vector with strings, summarizing the numerical details of the computed curve (i.e., initial point, parameter values, numerical settings used)

Examples

## Not run: 
initstate <- list(Environment = c(1.561e-04, 1.270e-04, 4.008e-06), 
                  Pop00 = matrix(c(0.001, 0, 7.0, 1.0E-5, 300, 111),
                  ncol = 3, byrow = TRUE))
PSPMecodyn("PNAS2002", initstate, c(1, 1, 10, 100))

## End(Not run)