SSexecutivesummary {r4ss}

A function to create a executive summary tables from an SS Report.sso file

Description

Takes the output from SS_output and creates executive summary tables as required by the current Terms of Reference for US West Coast groundfish stock. Additionally, historical catches, time-series and numbers-at-ages tables are created.

Usage

SSexecutivesummary(
  replist,
  plotfolder = "default",
  ci_value = 0.95,
  es_only = FALSE,
  fleetnames = NULL,
  tables = c("a", "b", "c", "d", "e", "f", "g", "h", "i", "catch", "timeseries",
    "numbers", "biomass", "likes"),
  divide_by_2 = FALSE,
  endyr = NULL,
  adopted_ofl = NULL,
  adopted_abc = NULL,
  adopted_acl = NULL,
  forecast_ofl = NULL,
  forecast_abc = NULL,
  format = TRUE,
  match_digits = FALSE,
  verbose = TRUE
)

Arguments

replist

A list object created by SS_output().

plotfolder

Directory where the 'tables' directory will be created. The default is the dir location where the Report.sso file is located.

ci_value

To calculate confidence intervals, default is set at 0.95

es_only

TRUE/FALSE switch to produce only the executive summary tables will be produced, default is FALSE which will return all executive summary tables, historical catches, and numbers-at-ages

fleetnames

A vector of user-defined names providing a name for each fleet in the model.

tables

Which tables to produce (default is everything). Note: some tables depend on calculations related to previous tables, so will fail if requested on their own (e.g. Table 'f' can't be created without also creating Table 'a')

divide_by_2

This will allow the user to calculate single sex values based on the new sex specification (-1) in SS for single sex models. Default value is FALSE. TRUE will divide by 2.

endyr

Optional input to choose a different ending year for tables (could be useful for catch-only updates)

adopted_ofl

Vector of adopted ofl values to be printed in the management performance table. This should be a vector of 10 values.

adopted_abc

Vector of adopted abc values to be printed in the management performance table. This should be a vector of 10 values.

adopted_acl

Vector of adopted acl values to be printed in the management performance table. This should be a vector of 10 values.

forecast_ofl

Optional input vector for management adopted OFL values for table g. These values will be overwrite the OFL values in the projection table, rather than the model estimated OFL values. Example input: c(1500, 1300)

forecast_abc

Optional input vector for management adopted ABC values for table g. These values will be overwrite the ABC values in the projection table, rather than the model estimated ABC values. Example input: c(1500, 1300)

format

Logical. Option to control whether tables are formatted (e.g. commas added, CIs separated with "-"). The formatting is intended to create tables that can be cut and pasted easily into a word document without additional formatting work. If the tables are being used by LaTex/Markdown or other documenting software, having formatting turned on prevents the tables from being formatted further since the objects are no longer numeric.

match_digits

TRUE/FALSE switch on whether the low and high interval values in e_ReferencePoints_ES will be reported with the same number of decimal digits as the estimate.

verbose

Return updates of function progress to the R console?

Value

Individual csv files for each executive summary table and additional tables (catch, timeseries, numbers-at-age).

Author(s)

Chantel Wetzel