runFAC: Run a single FAC model to equilibirum

In brouwern/FACavian: An R implementation and extension of full-annual cycle (FAC) model of Runge & Marra *2005)

Run a single FAC model to equilibirum

Description

Iterates a single parameterization of the Runge & Marra 2004 FAC model until equilbirium is reached. Typically the desired output is the equilibrium population size(s) and all intermediate output is discarded.

Usage

runFAC(
  iterations = 350,
  Ninit = c(10, 0, 10, 0),
  param.set = param_set(),
  scenario = NA,
  vary = NA,
  verbose = FALSE,
  check.errors = TRUE,
  check.errors.in = c("B0.RM", "P.cgg", "P.cgp", "P.cpg", "P.cpp", "P.kgg", "P.kgp",
    "P.kpg", "P.kpp", "Y1"),
  check.eq = TRUE,
  minimum.i = 20,
  eq.tol = 6,
  diagnostic.plot = F,
  return.output = T,
  save.ts = T,
  use.IBM = F,
  use.IBM.S.b = F,
  ...
)

Arguments

iterations	how many iterations of model to run before stopping
Ninit	vector of initial abundances at the begining of winter for W.mg, W.mp, W.fg and W.fp
param.set	initila parameters for this run of the model.
scenario	character string representing name of scenario explored in original Runge and Marra paper (not currently implemented 7/10/2018)
vary	...
verbose	verbose general output
check.errors	Run error checks on model subcomponents
check.errors.in	run error checks and report
check.eq	should equilibrium be assessed?
minimum.i	number of iterations to run if equilibrium is being checked
eq.tol	Tolerance for equilibirum check; the number of digistic lambda and variace of lambda should be rounded to when comparing against 1. Larger numbers reduce the likelihood of model passing the equilbirium check
diagnostic.plot	Return a diagnostic plot show population size over time
return.output	Output the full model dataframe?
save.ts	Save the full time series of the model run? If FALSE then only final time point will be returned. Additionally, equilibrium monitoring will not be done and the time series cannot be plotted
use.IBM	use individual based model for habitat and mate acquisition
use.IBM.S.b	use IBM for summer adult survival
...	other arguements passed

Value

runFAC.i A dataframe containing the status of the population at each time step for all parameters

References

Runge, MC and PP Marra. 2004. Modeling seasonal interactions in the population dynamics of migratory birds. In Greenberg, R and PP Marra, eds. Birds of two worlds. Johns Hopkins University Press, Baltimore.

Examples

# Run an FAC
test.FAC <- runFAC(verbose = TRUE)

# Look at structure of output
str(test.FAC,1)

brouwern/FACavian documentation built on June 1, 2024, 10:32 p.m.