get_results_scenario: Extract SS3 simulation results for one scenario.

In ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

Description

Function that extracts results from all iterations inside a supplied scenario folder. The function writes 3 .csv files to the scenario folder: (1) scalar metrics with one value per iteration (e.g. R_0, h), (2) a timeseries data ('ts') which contains multiple values per iteration (e.g. SSB_y for a range of years y), and (3) [currently disabled and not tested] residuals on the log scale from the surveys across all iterations. The function get_results_all loops through these .csv files and combines them together into a single "final" dataframe.

Usage

get_results_scenario(scenario, directory = getwd(),
  overwrite_files = FALSE)

Arguments

scenario	A single character giving the scenario from which to extract results.
directory	The directory which contains the scenario folder.
overwrite_files	A boolean (default is FALSE) for whether to delete any files previously created with this function. This is intended to be used if iterations were added since the last time it was called, or any changes were made to this function.

Author(s)

Cole Monnahan

See Also

Other get-results: get_results_all, get_results_derived, get_results_scalar, get_results_timeseries

Examples

## Not run: 
d <- system.file("extdata", package = "ss3sim")
case_folder <- file.path(d, "eg-cases")
om <- file.path(d, "models", "cod-om")
em <- file.path(d, "models", "cod-em")
run_ss3sim(iterations = 1:2, scenarios =
  c("D0-F0-cod"),
  case_folder = case_folder, om_dir = om, em_dir = em,
  case_files = list(F = "F",
                    D = c("index", "lcomp", "agecomp")),
  bias_adjust = FALSE)
get_results_scenario(c("D0-F0-cod"), overwrite_files = TRUE)

#clean up
unlink("D0-F0-cod", recursive = TRUE)

## End(Not run)

ss3sim documentation built on Nov. 9, 2019, 1:06 a.m.