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Indicator Dependencies

All relevant package dependencies are listed in the DESCRIPTIONS file under Imports. When all indicators have been added to the repo we can provide a list of package versions

Survey Based Indicators

The survey data will pulled from the Oracle database via a cron job (quarterly?) using R function

SOEworkflows::get_survey_data(channel,outputPathDatasets)
  • channel is a connection object created using ROracle::dbConnect()
  • outputPathDatasets is the path to the folder where "raw" data is stored (EDAB_Datasets)
  • Currently the data sets created are:
    • surveyNoLengths.rds - used in aggregate_biomass
    • bigelowData.rds - used in survey_shannon
    • albatrosData.rds - used in survey_shannon
    • condition.rds - used in condition

aggregate_biomass

To run the "workflow" below, it is assumed that the "raw" survey data has been pulled using the get_survey_data function above.

Note: the following function resides in the folder data-raw and is NOT part of the package

workflow_aggregate_biomass(outputPath,inputPathSurvey,inputPathSpecies)
  • inputPathSpecies is the path to static data set EDAB_Datasets/SOE_species_list_24.rds.
  • inputPathSurvey is the path to the dynamically created survey data EDAB_Datasets/surveyNoLengths.rds.
  • outputPath is the path to folder where indicator data should be saved, EDAB_Indicators. The rds file name is hardcoded as aggregate_biomass.rds to match the ecodata package dataset

survey_shannon

To run the "workflow" below, it is assumed that the "raw" survey data has been pulled using the get_survey_data function above.

Note: the following function resides in the folder data-raw and is NOT part of the package

workflow_survey_shannon(outputPath,inputPathBigelow,inputPathAlbatross)
  • inputPathBigelow is the path to static data set EDAB_Datasets/bigelowData.rds.
  • inputPathAlbatross is the path to the dynamically created survey data EDAB_Datasets/albatrossData.rds.
  • outputPath is the path to folder where indicator data should be saved, EDAB_Indicators. The rds file name is hardcoded as survey_shannon.rds to match the ecodata package dataset

exp_n

To run the "workflow" below, it is assumed that the "raw" survey data has been pulled using the get_survey_data function above.

Note: the following function resides in the folder data-raw and is NOT part of the package

workflow_exp_n(outputPath,inputPathBigelow,inputPathAlbatross)
  • inputPathBigelow is the path to static data set EDAB_Datasets/bigelowData.rds.
  • inputPathAlbatross is the path to static data set EDAB_Datasets/albatrossData.rds.
  • outputPath is the path to folder where indicator data should be saved, EDAB_Indicators. The rds file name is hardcoded as exp_n.rds to match the ecodata package dataset

species_dist

To run the "workflow" below, it is assumed that the "raw" survey data has been pulled using the get_survey_data function above.

Note: the following function resides in the folder data-raw and is NOT part of the package

workflow_species_dist(outputPath,inputPathSurvey,inputPathSpecies)
  • inputPathSpecies is the path to static data set EDAB_Datasets/SOE_species_list_24.rds.
  • inputPathSurvey is the path to the dynamically created survey data EDAB_Datasets/surveyNoLengths.rds.
  • outputPath is the path to folder where indicator data should be saved, EDAB_Indicators. The rds file name is hardcoded as species_dist.rds to match the ecodata package dataset

Commercial Landings Based Indicators

The commercial data will pulled from the Oracle database via a cron job (quarterly?) using R function

SOEworkflows::get_commercial_data(channel,outputPathDatasets)
  • channel is a connection object created using ROracle::dbConnect()
  • outputPathDatasets is the path to the folder where "raw" data is stored (EDAB_Datasets)
  • Currently the data sets created are:
    • commercial_comdat.rds - used in comdat
    • commercial_bennet.rds - used in bennet

Bennet

To run the "workflow" below, it is assumed that the commercial data has been pulled using the get_commercial_data function above.

Note: the following function resides in the folder data-raw and is NOT part of the package

workflow_bennet(inputPathBennet, inputPathSpecies, outputPath)
  • inputPathSpecies is the path to static data set EDAB_Datasets/SOE_species_list_24.rds.
  • inputPathBennet is the path to the dynamically created commercial data EDAB_Datasets/commercial_benent.rds.
  • outputPath is the path to folder where indicator data should be saved, EDAB_Indicators. The rds file name is hardcoded as bennet.rds to match the ecodata package dataset

comdat

To run the "workflow" below, it is assumed that the commercial data has been pulled using the get_commercial_data function above and that menhaden data have been pulled using the create_menhaden_input.R script in the folder data-raw. Note: the following function resides in the folder data-raw and is NOT part of the package

workflow_comdat(comdat_path, input_path_species, menhaden_path, outputPathDataSets)
  • comdat_path is the path to the raw, comprehensive commercial landings data file, e.g., EDAB_Datasets/commercial_comdat.rds.
  • input_path_species is the path to the species list used for grouping, e.g., EDAB_Datasets/SOE_species_list_24.rds.
  • menhaden_path is the path to the Menhaden landings data output by create_create_menhaden_input.R.
  • outputPathDataSets is the path to folder where indicator data should be saved, EDAB_Indicators. The rds file name is hardcoded as comdat.rds to match the ecodata package dataset

stocksmart Based Indicators

To run the "workflow" below, it is assumed that the stocksmart R package has been updated to include recent assessment data.

Note: the following function resides in the folder data-raw and is NOT part of the package

workflow_stock_status(inputPath, outputPath)
  • inputPath is the path to static data set EDAB_Datasets/decoder.csv.
  • outputPath is the path to folder where indicator data should be saved, EDAB_Indicators. The rds file name is hardcoded as stock_status.rds to match the ecodata package dataset

Oceanographic Indicators

Transition Dates (trans_dates)

To run the "workflow" below, it is assumed that the static input file from Kevin Friedland is present.

Note: the following function resides in the folder data-raw and is NOT part of the package

workflow_trans_dates(inputPath, outputPath)
  • inputPath is the path to static data set EDAB_Datasets/TS_SHP_adv rep MAB GOM GBK NES SCSPoly.csv.
  • outputPath is the path to folder where indicator data should be saved, EDAB_Indicators. The rds file name is hardcoded as trans_dates.rds to match the ecodata package dataset