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Gather information for the NOAA Species Information System (SIS)

Source: R/get_SIS_info.R
get_SIS_info.Rd

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 = "first.last@noaa.gov",
  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

See also

SS_output()

Author

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

Examples

if (FALSE) { # \dontrun{
# 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)
} # }