getScenarioDefaults: Default parameters for simulation of example demographic...

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

Default parameters for simulation of example demographic trajectories.

Description

Returns default parameter values for simulations of example demographic trajectories. See simulateObservations() for additional details.

Usage

getScenarioDefaults(
  paramTable = NULL,
  iFire = 0,
  iAnthro = 0,
  obsAnthroSlope = 2,
  projAnthroSlope = 2,
  rSlopeMod = 1,
  sSlopeMod = 1,
  rQuantile = 0.5,
  sQuantile = 0.5,
  projYears = 35,
  obsYears = 15,
  preYears = 0,
  N0 = 1000,
  assessmentYrs = 3,
  qMin = 0,
  qMax = 0.6,
  uMin = 0,
  uMax = 0.2,
  zMin = 0,
  zMax = 0.2,
  cowMult = 6,
  collarInterval = NA,
  cowCount = NA,
  collarCount = NA,
  startYear = NA,
  interannualVar = list(eval(formals(caribouPopGrowth)$interannualVar)),
  curYear = 2023
)

Arguments

paramTable	a data.frame with column names matching the arguments below. Any columns that are missing will be filled with the default values.
iFire	number. Initial fire disturbance percentage.
iAnthro	number. Initial anthropogenic disturbance percentage
obsAnthroSlope	number. Percent change in anthropogenic disturbance per year in the observation period
projAnthroSlope	number. Percent change in anthropogenic disturbance per year in the projection period
rSlopeMod	number. Disturbance-recruitment slope multiplier
sSlopeMod	number. Disturbance-survival slope multiplier
rQuantile	number in 0, 1. Recruitment quantile
sQuantile	number in 0, 1. Survival quantile
projYears	Number of years of projections
obsYears	Number of years of observations
preYears	Number of years before monitoring begins
N0	Number or vector of numbers. Initial population size for one or more sample populations.
assessmentYrs	Number of years over which to assess population growth rate lambda.
qMin	number in 0, 1. Minimum ratio of bulls to cows in composition survey groups.
qMax	number in 0, 1. Maximum ratio of bulls to cows in composition survey groups.
uMin	number in 0, 1. Minimum probability of misidentifying young bulls as adult females and vice versa in composition survey.
uMax	number in 0, 1. Maximum probability of misidentifying young bulls as adult females and vice versa in composition survey.
zMin	number in 0, 1. Minimum probability of missing calves in composition survey.
zMax	number in 0, <1. Maximum probability of missing calves in composition survey.
cowMult	number >= 1. The apparent number of adult females per collared animal in composition survey. Set to NA to use cowCount.
collarInterval	number. Optional. Number of years between collar deployments. If missing assumed to be every year
cowCount	Optional. Only used in runScnSet() to set the number of cows per year in recruitment survey
collarCount	number >= 1. The target number of collars active each year. Set to NA to use freqStartsPerYear in simulateObservations()
startYear	year. First year in observation period. Optional, if not provided it will be calculated from curYear and obsYears
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.
curYear	year. The current year. All years before are part of the observation period and years after are part of the projection period.

Value

a data.frame of parameter values including a label that combines all the parameter names and values into a string

See Also

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

Examples

getScenarioDefaults()

# paramTable list takes precedence over argument values
getScenarioDefaults(paramTable = data.frame(iFire = 10, iAnthro = 20, obsYears = 1), obsYears = 5)

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