filter_MCBE: Identify which runs should be filtered out of results of MCBE...

In nikolaifish/bamExtras: Functions and Data in Support of Stock Assessments with the Beaufort Assessment Model (BAM)

Identify which runs should be filtered out of results of MCBE uncertainty analysis

Description

Identify which runs should be filtered out of results of MCBE uncertainty analysis

Usage

filter_MCBE(
  sim_summary,
  filter_info = list(gradient.max = c(0, 0.01), Fref = c(0, 5), F.Fref = c(0, 5),
    R.sigma.par = c(0.2, 1), R0_prob = c(0.005, 0.995), avoid_bounds = TRUE),
  nm_rp = list(parms = c(Fref = "Fmsy", F.Fref = "Fend.Fmsy.mean"))
)

Arguments

sim_summary	Output object from summarize_MCBE
filter_info	list of ranges used to filter out MCBE results. set to NULL to retain all results.

Value

This function returns a list including: 1. sim_pass is a numeric vector indicating which simulation runs should be retained after filtering. 2. test_vals is a data frame of the values used to conduct filtering for all runs. 3. test_logical is a logical matrix indicating the results of each filtering test.

Author(s)

Kyle Shertzer, Erik Williams, and Nikolai Klibansky

Examples

## Not run: 
# Run MCBE, writing files to dir_bam_sim
run_MCBE("GrayTriggerfish", dir_bam_sim="sim_GrTr")
# Summarize results of MCBE and assign to object
ss_GrTr <- summarize_MCBE(dir_bam_sim="sim_GrTr")
sim2keep <- filter_MCBE(ss_GrTr,nm_rp = list("spr.brps"=c("Fref"="F30","F.Fref"="Fend.F30.mean")))
# Plot MCBE results

## End(Not run)

nikolaifish/bamExtras documentation built on April 17, 2025, 9:44 p.m.