model_setup: Load models and set up lists and classes for the base model,...

In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

Load models and set up lists and classes for the base model, bridge model groups, and sensitivity model groups

Description

Load models and set up lists and classes for the base model, bridge model groups, and sensitivity model groups

Usage

model_setup(
  drs = NA,
  base_models_desc = NA,
  bridge_models_desc = NA,
  sens_models_desc = NA,
  request_models_desc = NA,
  test_models_desc = NA,
  retro_models_desc = NA,
  prepend_to_bridge = NA,
  ...
)

Arguments

drs	Output list from set_dirs()
base_models_desc	A list of descriptions for the base models
bridge_models_desc	A list of vectors of text strings to show in the legends for bridge model plots, one name for each model, where the list elements represent a group of models
sens_models_desc	A list of vectors of text strings to show in the legends for sensitivity model plots, one name for each model, where the list elements represent a group of models
request_models_desc	A list of vectors of text strings to show in the legends for request model plots, one name for each model, where the list elements represent a group of models
test_models_desc	A list of vectors of text strings to show in the legends for test model plots, one name for each model, where the list elements represent a group of models
retro_models_desc	A list of vectors of text strings to show in the legends for retrospective model plots, one name for each model, where the list elements represent a group of models
prepend_to_bridge	A logical vector of length the same as bridge_models_desc. If TRUE, the base model will be prepended to the group at that index
...	Arguments to pass to create_rds_file()

Details

If any of the text lists are NULL, default description text will be assigned and a warning given.

Value

A list of items, the base_model inside a single-element list, the list of bridge model groups, sensitivity model groups, request model groups, test model groups, and retrospective model groups. These groups are lists of models which are to be compared with each other in the document. This simplifies plotting and table functions

Examples

## Not run: 
library(tidyverse)
library(lubridate)
bridge_models_dirs <- list(c("01-new-ss-exe",
                             "02-new-catch-age",
                             "03-update-survey"),
                           c("04-age-1-index",
                             "05-new-wt-at-age"))
bridge_models_descs <- list(c("Update Stock Synthesis version to 3.30.20",
                              "Update all fishery catch and comps",
                              "Update pre-2021 survey data"),
                            c("Update wt-at-age data",
                              "Add 2021 survey data"))
sens_models_dirs <- list(c("01-h-prior-mean-low",
                           "02-h-fix-high",
                           "03-sigma-r-fix-low",
                           "04-sigma-r-fix-high",
                           "05-m-02-sd",
                           "06-m-03-sd"),
                         c("07-age-1-survey",
                           "08-comp-weight-harmonic-mean"),
                         c("09-tv-select-phi-extra-low",
                           "10-tv-select-phi-low",
                           "11-tv-select-phi-high"),
                           c("12-max-sel-age-5",
                           "13-max-sel-age-7",
                           "14-max-sel-age-8"))
sens_models_descs <- list(c("Steepness Mean Prior Low (0.5)",
                            "Steepness Fix 1.0",
                            "Sigma R 1.0",
                            "Sigma R 1.6",
                            "Natural Mortality (SD=0.2)",
                            "Natural Mortality (SD=0.3)"),
                          c("Remove Age 1 Index",
                            "Downweight Fishery Comps"),
                          c("Phi t.v. selectivity (0.21)",
                            "Phi t.v. selectivity (0.70)",
                            "Phi t.v. selectivity (2.10)"),
                          c("Max. age selectivity 5",
                            "Max. age selectivity 7",
                            "Max. age selectivity 8"))

drs <- set_dirs(bridge_models_dirs = bridge_models_dirs,
                sens_models_dirs = sens_models_dirs,
                request_models_dirs = request_models_dirs,
                test_models_dirs = test_models_dirs,
                retro_models_dirs = retro_models_dirs,
                prepend_to_bridge = c(TRUE, FALSE))

model_setup <- function(drs,
                        bridge_models_desc = bridge_models_desc,
                        sens_models_desc = sens_models_desc,
                        retro_models_desc = retro_models_desc,
                        overwrite_rds_files = TRUE)

## End(Not run)

pacific-hake/hake-assessment documentation built on Jan. 14, 2025, 9:12 p.m.