runAnalysis: Run the fish density simulation

Description Usage Arguments Value Examples

View source: R/runAnalysis.R

Description

Executes the simulation for a given region and species.

Usage

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runAnalysis(Mcmc_prediction = TRUE, Abundance_or_catch = "Catch",
  Mcmc_sample = 1, Mcmc_seed = 200, Which_species, Which_region,
  Years = NULL, Env_covariate = c("SURFACE_TEMPERATURE",
  "GEAR_TEMPERATURE", "BOTTOM_DEPTH"), Transform_covariate = c("ID",
  "ID", "LOG"), Include_year_effect = FALSE, Include_2_order = TRUE,
  Standardize_variable = FALSE, Spacetime = "AR",
  YEARS_pred = 1982:2016, Overwrite = FALSE)

Arguments

year

Either a single year or 2 element vector with maximum and minimum year to retrieve.

survey

String for intended survey (EBS_SHELF, EBS_SLOPE, NBS_SHELF, GOA, AI).

Value

The output is a list of years and densities. The output must be re-joined to the Predict_data object for spatial analysis.

YEARS_USE

Vector of available years

SDM_result

Matrix of densities per year, rows for a given year correspond to Predict_data rows.

Examples

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## TBD

oceanconner/simfish documentation built on Nov. 5, 2019, 7:35 p.m.