get_SIS_info: Gather information for the NOAA Species Information System...

In r4ss/r4ss: R Code for Stock Synthesis

Gather information for the NOAA Species Information System (SIS)

Description

Processes model results contained in the list created by SS_output() in a format that is more convenient for submission to SIS. Currently the results are returned invisibly as a list of two tables and written to a CSV file from which results could be copied into SIS. In the future some more direct link could be explored to avoid the manual copy step.

Usage

get_SIS_info(
  model,
  dir = model[["inputs"]][["dir"]],
  writecsv = TRUE,
  stock = "StockName",
  assessment_type = "Operational",
  final_year = model[["endyr"]] + 1,
  data_year = model[["endyr"]],
  month,
  sciencecenter = "NWFSC",
  Mgt_Council = "PFMC",
  SpawnOutputLabel = model[["SpawnOutputLabel"]],
  contact = "[e-mail]",
  review_result = "XXXX",
  catch_input_data = "XXXX",
  abundance_input_data = "XXXX",
  bio_input_data = "XXXX",
  comp_input_data = "XXXX",
  ecosystem_linkage = "XXXX"
)

Arguments

model	Output from SS_output
dir	Directory in which to write the CSV files.
writecsv	Write results to a CSV file (where the name will have the format "[stock]_2019_SIS_info.csv" where stock is an additional input
stock	String to prepend id info to filename for CSV file
assessment_type	"Operational" or "Stock Monitoring Updates" (or perhaps additional options as well)
final_year	Year of assessment and reference points (typically will be model[["endyr"]] + 1)
data_year	Last year of of timeseries data
month	Month when assessment was conducted (within final_year)
sciencecenter	Origin of assessment report
Mgt_Council	Council jurisdiction. Currently only "PFMC" (Pacific Fishery Management Council) and "GM" (Gulf of Mexico) are the only options.
SpawnOutputLabel	Units for spawning output if not in mt (e.g. "Millions of eggs"). In the future this can be included in the model list created by r4ss::SS_output()
contact	Name and/or email address for lead author.
review_result	Something like "Full Acceptance"
catch_input_data	Qualitative category for catch input data
abundance_input_data	Qualitative category for abundance input data
bio_input_data	Qualitative category for biological input data
comp_input_data	Qualitative category for size/age composition input data
ecosystem_linkage	Qualitative category for ecosystem linkage

Author(s)

Ian G. Taylor, Andi Stephens, LaTreese S. Denson

See Also

SS_output()

Examples

## Not run: 
# read the model output
model <- SS_output(
  dir = system.file("extdata/simple_small", package = "r4ss"),
  printstats = FALSE, verbose = FALSE
)
# run get_SIS_info:
info <- get_SIS_info(model, stock = "SimpleExample", month = 1)

## End(Not run)

r4ss/r4ss documentation built on April 30, 2024, 4:42 a.m.