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Population Model Run

Source: R/PopulationModel_Run.R
PopulationModel_Run.Rd

Runs the population model with stressors and stressor-response relationships

Usage

PopulationModel_Run(
  dose = NA,
  sr_wb_dat = NA,
  life_cycle_params = NA,
  HUC_ID = NA,
  n_years = 100,
  MC_sims = 10,
  stressors = NA,
  output_type = "full",
  habitat_dd_k = NULL,
  s0_calibrate = TRUE
)

Arguments

dose

dataframe. Stressor magnitude dataset imported from StressorMagnitudeWorkbook().

sr_wb_dat

list object. Stressor response workbook imported from StressorResponseWorkbook().

life_cycle_params

dataframe. Life cycle parameters.

HUC_ID

character. HUC_ID for the location unit. Can only be one HUC_ID (not an array).

n_years

numeric. Number of years to run the population.

MC_sims

numeric. set number of Monte Carlo simulations for the Population Model.

stressors

(optional) character vector of stressor names to include in the Population Model. Leave the default value as NA if you wish to include all stressors applicable to the population model.

output_type

(optional) character. Set to "full" for all data of "adults" for only adult data.

habitat_dd_k

(optional) dataframe of location and stage-specific habitat capacity k values for the target species. If used this dataframe will override the capacity estimates. Blank or NA K cells mean "no constraint for that life stage" (not unknown/to-be-determined). Supplying a row for a HUC switches that location into habitat-capacity mode: fry survival (s0) is not recalibrated to force lambda = 1, because growth is expected to be restrained by the K constraints. A row whose K cells are all blank leaves every stage unconstrained and triggers a warning. Optional k_...cv columns hold the coefficient of variation for the matching k..._mean capacity estimate: each capacity with a cv > 0 is redrawn every projection year and every batch replicate from a normal distribution (mean = the K value, sd = K * cv) clamped at zero, with the CE and baseline runs of a replicate sharing the same draws (see build_stage_k_noise). Missing cv columns or blank/NA cv cells mean cv = 0 (capacity treated as exact; no random draws).

s0_calibrate

(optional) logical. If TRUE (default) fry survival (s0) is re-calibrated so lambda = 1 when an adult capacity k is set and no Beverton-Holt flags are present. Set to FALSE to keep the raw s0 from the life cycles file (used by pop_model_ltre so that lambda responds to vital-rate perturbations instead of being re-tuned to 1).

Value

List object of population model outputs. These include the population vectors for each Monte Carlo simulation and year. List objects names include "ce" for the runs with stressors and "baseline" for the runs without stressors.

Details

Runs the population model within the Joe Model stress-response framework. The population model is run independently for each single sub-watershed unit (HUC_ID). Inputs for PopulationModel_Run include the stressor-response and stressor magnitude workbooks as well as the life cycle parameters object.

If the life cycle parameters include a p.cat row (probability of a catastrophic event per generation), catastrophe years first run the normal annual projection (aging, reproduction, natural mortality, density dependence) and then remove a random 50-100 percent of every life stage. Catastrophic mortality is applied in addition to normal annual mortality, not instead of it (see Projection_DD).

Examples

if (FALSE) { # \dontrun{
library(CEMPRA)
} # }