getSimsNational: Get a set of simulation results from the national demographic...

In LandSciTech/caribouMetrics: Models and Metrics of Boreal Caribou Demography and Habitat Selection

Get a set of simulation results from the national demographic model

Description

Get a set of simulation results from the national demographic model

Usage

getSimsNational(
  replicates = 1000,
  N0 = 1000,
  Anthro = seq(0, 100, by = 1),
  fire_excl_anthro = 0,
  useQuantiles = NULL,
  populationGrowthTable = NULL,
  cPars = getScenarioDefaults(),
  forceUpdate = F,
  interannualVar = eval(formals(caribouPopGrowth)$interannualVar)
)

Arguments

replicates	integer. Number of replicate populations.
N0	initial population size
Anthro, fire_excl_anthro	numeric. A vector of numbers between 0 and 100 representing the percentage of the landscape covered by anthropogenic disturbance buffered by 500 m, and the percentage covered by fire that does not overlap anthropogenic disturbance. The two vectors will be combined with expand.grid() to give the set of scenarios simulated.
useQuantiles	logical or numeric. If it is a numeric vector it must be length 2 and give the low and high limits of the quantiles to use. If useQuantiles != FALSE, each replicate population is assigned to a quantile of the distribution of variation around the expected values, and remains in that quantile as covariates change. If useQuantiles = TRUE, replicate populations will be assigned to quantiles in the default range of 0.025 and 0.975.
populationGrowthTable	data.frame.popGrowthTableJohnsonECCC is included in the package and should be used in most cases. A custom table of model coefficients and standard errors or confidence intervals can be provided but it must match the column names of popGrowthTableJohnsonECCC. If the table does not contain the standard error it is calculated from the confidence interval.
cPars	optional. Parameters for calculating composition survey bias term.
forceUpdate	logical. If the default inputs are used the result is cached. Set forceUpdate to TRUE to ensure the simulations are re-run.
interannualVar	list or logical. List containing interannual variability parameters. These can be either coefficients of variation (R_CV, S_CV), beta precision parameters (R_phi, S_phi), or random effects parameters from a logistic glmm (R_annual, S_annual). Set to FALSE to ignore interannual variability.

Value

a list with two elements:

• summary: a tibble with a summary of parameter values for each scenario. Column names are Anthro, Mean, lower, upper, Parameter.

• samples: a tibble with parameter values for each scenario and replicate 4 rows per replicate \* scenario. Column names are Anthro, Parameter and Value

See Also

Caribou demography functions: caribouBayesianPM(), caribouPopGrowth(), compositionBiasCorrection(), demographicCoefficients(), demographicProjectionApp(), demographicRates(), getOutputTables(), getPriors(), getScenarioDefaults(), plotRes(), popGrowthTableJohnsonECCC, runScnSet(), simulateObservations()

Examples

getSimsNational()

LandSciTech/caribouMetrics documentation built on Feb. 25, 2025, 9:34 a.m.