PSPMevodyn: Evolutionary dynamics for a structured population model...

In PSPManalysis: Analysis of Physiologically Structured Population Models

Evolutionary dynamics for a structured population model computed following the canonical equation

Description

PSPMevodyn computes the dynamics of a physiologically structured population model over evolutionary time for an arbitrary number of evolving parameters. The evolutionary trajectory of these evolving parameters is determined by the canonical equation of Adaptive Dynamics, which is solved using a simple Euler integration scheme.

Usage

PSPMevodyn(
  modelname = NULL,
  startpoint = NULL,
  curvepars = NULL,
  evopars = NULL,
  covars = 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"
startpoint	(row vector, required) The initial point from which to start the simulation of the dynamics over evolutionary time, including the initial values of the evolving parameters
curvepars	(row vector of length 2, required) Vector of length 2 specifying: curvepars[1]: the maximum step size in evolutionary time during the integration of the canonical equation curvepars[2]: the maximum evolutionary time at which to stop the integration of the canonical equation
evopars	(row vector of length n*4, required) Vector of length n*4 specifying: evopars[1]: the index of the structured population whose life history is influenced by the first evolving parameter evopars[2]: the index of the first evolution parameter (in case the model is specified in R, this can be a string with the name of the parameter as specified in the variable 'DefaultParameters') evopars[3]: lower threshold, below which value of the first evolution parameter the computation stops evopars[4]: upper threshold, above which value of the first evolution parameter the computation stops ...... evopars[n*4-3]: the index of the structured population whose life history is influenced by the last evolving parameter evopars[n*4-2]: the index of the last evolution parameter (in case the model is specified in R, this can be a string with the name of the parameter as specified in the variable 'DefaultParameters') evopars[n*4-1]: lower threshold, below which value of the last evolution parameter the computation stops evopars[n*4]: upper threshold, above which value of the last evolution parameter the computation stops
covars	(row vector or matrix, optional, can be left equal to its default NULL) Vector of length N*N or NxN matrix, where N is the number of evolving parameters. The vector or matrix elements specify the values of the covariance matrix in the selection gradients. Vectors of other lengths, including an empty vector will be ignored.
parameters	(row vector, optional, can be left equal to its default NULL) Vector of length PARAMETER_NR (set in the model program file), 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("popZE", "1")) or single options (i.e. c("test")). Possible option names and their values are: "envZE", "<index>": Index of environment variable in trivial equilibrium (can be used multiple times) "popZE", "<index>": Index of structured population in trivial equilibrium (can be used multiple times) "isort", "<index>": Index of i-state variable to use as ruling variable for sorting the structured populations "report", "<value>": Interval between consecutive output of computed points to the console ( >= 1). Minimum value of 1 implies output of every point "test": Perform only a single integration over the life history, reporting dynamics of survival, R0, i-state and interaction variables
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 <- PSPMevodyn(modelname = NULL, startpoint = NULL, curvepars = NULL, evopars = NULL, covars = 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: 
PSPMevodyn("Indet_growth", c(0.22, 0.03554, 1.0), c(0.05, 1), 
            c(0, 6, 0.5, 1.5))

## End(Not run)

PSPManalysis documentation built on Jan. 22, 2023, 1:10 a.m.