{ "_id": "6a4fd1b2c30f0868bbf1eecb", "Package": "framrsquared", "Type": "Package", "Title": "FRAM Database Interface", "Version": "0.8.1.9000", "Authors@R": "c(\nperson(\"Ty\", \"Garber\",\nemail = \"tyler.garber@dfw.wa.gov\",\nrole = c(\"cre\",\"aut\")),\nperson(\"Collin\", \"Edwards\",\nemail = \"collin.edwards@dfw.wa.gov\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-4937-5159\")\n))", "Description": "A convenient tool for interfacing with FRAM access\ndatabases in R environments.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Roxygen": "list(markdown = TRUE)", "Remotes": [ "FRAMverse/framrosetta" ], "URL": "https://framverse.github.io/framrsquared/", "BugReports": "https://github.com/FRAMverse/framrsquared", "Config/pak/sysreqs": "make libicu-dev unixodbc-dev libx11-dev", "Repository": "https://framverse.r-universe.dev", "Date/Publication": "2026-04-09 20:39:30 UTC", "RemoteUrl": "https://github.com/FRAMverse/framrsquared", "RemoteRef": "HEAD", "RemoteSha": "728a067f4315b0c0998ea43c9272ef8de167edb9", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-09 16:48:07 UTC", "User": "root" }, "Author": "Ty Garber [cre, aut],\nCollin Edwards [aut] (ORCID: )", "Maintainer": "Ty Garber ", "_user": "framverse", "_type": "src", "_file": "framrsquared_0.8.1.9000.tar.gz", "_fileid": "https://r2.ropensci.org/e1f867a47bdf9e534bfe439396c576ee4eb8b32333c720ee1294b02fba848418", "_filesize": 770535, "_sha256": "e1f867a47bdf9e534bfe439396c576ee4eb8b32333c720ee1294b02fba848418", "_expires": "2026-10-17T16:52:00.000Z", "_created": "2026-07-09T16:48:07.000Z", "_published": "2026-07-09T16:52:02.980Z", "_jobs": [ { "job": 86176564846, "time": 155, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8205445579" }, { "job": 86176564812, "time": 158, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8205446744" }, { "job": 86176564794, 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"extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_cranurl": false, "_exports": [ "add_total_mortality", "addstock_check", "aeq_mortality", "bkfram_checks_coho", "calc_fram_scaling", "change_run_id", "coho_mark_rates", "cohort_abundance", "compare_databases", "compare_fishery_input_flags", "compare_fishery_inputs", "compare_inputs", "compare_inputs_chart", "compare_non_retention_input_flags", "compare_non_retention_inputs", "compare_recruits", "compare_runs", "compare_stock_fishery_rate_scalers", "connect_fram_db", "copy_fishery_scalers", "copy_run", "copy_tamms", "disconnect_all_fram_connections", "disconnect_fram_db", "fetch_quarto_templates", "fetch_table", "fetch_table_", "fetch_table_bkchin", "filter_ak", "filter_bc", "filter_ca", "filter_coast", "filter_commercial_wa_nt", "filter_flag", "filter_marine", "filter_net", "filter_or", "filter_puget_sound", "filter_sport", "filter_wa", "fishery_mortality", "fram_clean_tables", "fram_database_species", "fram_database_type", "get_fishery_ids", "get_run_ids", "get_stock_ids", "initialize_project", "label_fisheries", "label_fisheries_db", "label_flags", "label_stocks", "label_stocks_db", "list_extant_fram_connections", "make_batch_runs", "management_week", "modify_table", "mortality_scalers", "msf_encounters", "msf_encounters_chinook_", "msf_encounters_coho_", "msf_landed_catch", "msf_landed_catch_chinook_", "msf_landed_catch_coho_", "msf_mortalities", "msf_mortalities_chinook_", "msf_mortalities_coho_", "msp_mortality", "NR_flag_translate", "plot_impacts_per_catch_heatmap", "plot_stock_comp", "plot_stock_mortality", "plot_stock_mortality_time_step", "population_statistics", "post_season_abundance", "provide_table_names", "remove_run", "run_info", "scalers_flag_translate", "sensitivity_custom", "sensitivity_exact", "sensitivity_scaled", "statistical_week", "stock_fate", "stock_fate_chinook", "stock_fate_coho", "stock_mortality", "terminal_fisheries", "terminal_info", "terminal_stocks", "truns_fisheries", "truns_stocks" ], "_help": [ { "page": "add_total_mortality", "title": "Sum separate mortality columns into new \"total_mortality\" column", "topics": [ "add_total_mortality" ] }, { "page": "addstock_check", "title": "Check FRAM database after adding new stock", "topics": [ "addstock_check" ] }, { "page": "aeq_mortality", "title": "Extract AEQ mortality from Chinook FRAM database. Refactored and stripped down from the framr package written by Dan Auerbach. https://github.com/FRAMverse/framr/", "topics": [ "aeq_mortality" ] }, { "page": "bkfram_checks_coho", "title": "Performs error checks of a backwards FRAM run Returns nested tibble with diagnostics", "topics": [ "bkfram_checks_coho" ] }, { "page": "calc_fram_scaling", "title": "*[Experimental]* Calculate match/replace df based on scaling", "topics": [ "calc_fram_scaling" ] }, { "page": "change_run_id", "title": "Changes a run's ID number in a FRAM database", "topics": [ "change_run_id" ] }, { "page": "check_demo_coverage", "title": "Check if exported functions are documented in a file", "topics": [ "check_demo_coverage" ] }, { "page": "coho_mark_rates", "title": "*[Experimental]* Returns a tibble displaying predicted FRAMencounter mark rates by fishery, fishery type, and time-step.", "topics": [ "coho_mark_rates" ] }, { "page": "cohort_abundance", "title": "*[Experimental]* Calculate starting cohort abundance", "topics": [ "cohort_abundance" ] }, { "page": "compare_databases", "title": "*[Experimental]* Compare tables in two equivalent FRAM databases", "topics": [ "compare_databases" ] }, { "page": "compare_fishery_input_flags", "title": "Compares the fishery flags of two runs", "topics": [ "compare_fishery_input_flags" ] }, { "page": "compare_fishery_inputs", "title": "Compares the fishery inputs of two runs", "topics": [ "compare_fishery_inputs" ] }, { "page": "compare_inputs", "title": "Generates a dataframe that compares fishery scalers table for two runs identified by run_id's", "topics": [ "compare_inputs" ] }, { "page": "compare_inputs_chart", "title": "Generate heat map of changed values between two run inputs.", "topics": [ "compare_inputs_chart" ] }, { "page": "compare_non_retention_input_flags", "title": "Compares the non retention flags of two runs", "topics": [ "compare_non_retention_input_flags" ] }, { "page": "compare_non_retention_inputs", "title": "Compares the non retention inputs of two runs", "topics": [ "compare_non_retention_inputs" ] }, { "page": "compare_recruits", "title": "Compares the recruit scalers of two runs", "topics": [ "compare_recruits" ] }, { "page": "compare_runs", "title": "Generates a report to the console of changes to inputs between two runs", "topics": [ "compare_runs" ] }, { "page": "compare_stock_fishery_rate_scalers", "title": "Compares the stock fishery rate scalers of two runs", "topics": [ "compare_stock_fishery_rate_scalers" ] }, { "page": "connect_fram_db", "title": "Connect to FRAM database", "topics": [ "connect_fram_db" ] }, { "page": "copy_fishery_scalers", "title": "Experimental copying scaler inputs from one run to another DANGEROUS", "topics": [ "copy_fishery_scalers" ] }, { "page": "copy_run", "title": "*[Experimental]* Copies a run a number of times", "topics": [ "copy_run" ] }, { "page": "copy_tamms", "title": "*[Experimental]* Copy TAMM for FRAM batch runs", "topics": [ "copy_tamms" ] }, { "page": "disconnect_all_fram_connections", "title": "Clear all connections", "topics": [ "disconnect_all_fram_connections" ] }, { "page": "disconnect_fram_db", "title": "Safely disconnect from FRAM database", "topics": [ "disconnect_fram_db" ] }, { "page": "fetch_quarto_templates", "title": "Creates quarto template files", "topics": [ "fetch_quarto_templates" ] }, { "page": "fetch_table", "title": "Fetch a complete table from a FRAM database.", "topics": [ "fetch_table", "fetch_table_" ] }, { "page": "fetch_table_bkchin", "title": "Safely fetch Chinook BackwardsFRAM table", "topics": [ "fetch_table_bkchin" ] }, { "page": "filter_ak", "title": "Filters a dataframe to Alaska fisheries. Will automatically detect whether it's working with a Chinook or Coho dataset if the tables were generated within this package. '.data' must have a 'fishery_id' column name.", "concept": [ "fishery_filters" ], "topics": [ "filter_ak" ] }, { "page": "filter_bc", "title": "Filters a dataframe to Canadian (BC) fisheries. Will automatically detect whether it's working with a Chinook or Coho dataset if the tables were generated within this package. '.data' must have a 'fishery_id' column name.", "concept": [ "fishery_filters" ], "topics": [ "filter_bc" ] }, { "page": "filter_ca", "title": "Filters a dataframe to California fisheries. Will automatically detect whether it's working with a Chinook or Coho dataset if the tables were generated within this package. '.data' must have a 'fishery_id' column name.", "concept": [ "fishery_filters" ], "topics": [ "filter_ca" ] }, { "page": "filter_coast", "title": "Filters a dataframe to Coastal fisheries. Will automatically detect whether it's working with a Chinook or Coho dataset if the tables were generated within this package. '.data' must have a 'fishery_id' column name.", "concept": [ "fishery_filters" ], "topics": [ "filter_coast" ] }, { "page": "filter_commercial_wa_nt", "title": "Filters a dataframe to WA non-treaty commercial fisheries.", "concept": [ "fishery_filters" ], "topics": [ "filter_commercial_wa_nt" ] }, { "page": "filter_flag", "title": "NA's all the information in the FisheryScalers that's not being used e.g Flag 1 only NS Scalers will be returned", "topics": [ "filter_flag" ] }, { "page": "filter_marine", "title": "Filters a dataframe to marine fisheries. Will automatically detect whether it's working with a Chinook or Coho dataset if the tables were generated within this package. '.data' must have a 'fishery_id' column name.", "concept": [ "fishery_filters" ], "topics": [ "filter_marine" ] }, { "page": "filter_net", "title": "Filters a dataframe to net fisheries. Will automatically detect whether it's working with a Chinook or Coho dataset if the tables were generated within this package. '.data' must have a 'fishery_id' column name.", "concept": [ "fishery_filters" ], "topics": [ "filter_net" ] }, { "page": "filter_or", "title": "Filters a dataframe to Oregon fisheries. Will automatically detect whether it's working with a Chinook or Coho dataset if the tables were generated within this package. '.data' must have a 'fishery_id' column name.", "concept": [ "fishery_filters" ], "topics": [ "filter_or" ] }, { "page": "filter_puget_sound", "title": "Filters a dataframe to Puget Sound fisheries. Will automatically detect whether it's working with a Chinook or Coho dataset if the tables were generated within this package. '.data' must have a 'fishery_id' column name.", "concept": [ "fishery_filters" ], "topics": [ "filter_puget_sound" ] }, { "page": "filter_sport", "title": "Filters a dataframe to sport fisheries. Will automatically detect whether it's working with a Chinook or Coho dataset if the tables were generated within this package. '.data' must have a 'fishery_id' column name.", "concept": [ "fishery_filters" ], "topics": [ "filter_sport" ] }, { "page": "filter_wa", "title": "Filters a dataframe to Washington State fisheries. Will automatically detect whether it's working with a Chinook or Coho dataset if the tables were generated within this package. '.data' must have a 'fishery_id' column name.", "concept": [ "fishery_filters" ], "topics": [ "filter_wa" ] }, { "page": "find_tables_by_column_", "title": "Finds tables that contain a specific column name", "topics": [ "find_tables_by_column_" ] }, { "page": "fishery_mortality", "title": "Returns a tibble matching the Fishery Mortality screen.", "topics": [ "fishery_mortality" ] }, { "page": "fram_clean_tables", "title": "Cleans the names of FRAM tables and coverts to a tibble", "topics": [ "fram_clean_tables" ] }, { "page": "fram_database_species", "title": "Identifies the FRAM database species focus - Chinook or Coho", "topics": [ "fram_database_species" ] }, { "page": "fram_database_type", "title": "Identifies the FRAM database type - Full or Transfer", "topics": [ "fram_database_type" ] }, { "page": "get_fishery_ids", "title": "Gets all fishery_ids of FRAM database", "topics": [ "get_fishery_ids" ] }, { "page": "get_run_ids", "title": "Gets all run_ids of FRAM database", "topics": [ "get_run_ids" ] }, { "page": "get_stock_ids", "title": "Gets all stock_id of FRAM database", "topics": [ "get_stock_ids" ] }, { "page": "initialize_project", "title": "*[Experimental]* Initializes a FRAM project", "topics": [ "initialize_project" ] }, { "page": "input_summary_", "title": "Generates an input summary based on a FisheryScalers dataframe. Probably end up streamlining / revising this.", "topics": [ "input_summary_" ] }, { "page": "label_fisheries_db", "title": "Label fisheries based on FRAM database", "topics": [ "label_fisheries_db" ] }, { "page": "label_flags", "title": "Adds a column with a text version of flags for either non-retention or fishery scalers", "topics": [ "label_flags" ] }, { "page": "label_stocks_db", "title": "Label stocks based on FRAM database", "topics": [ "label_stocks_db" ] }, { "page": "list_extant_fram_connections", "title": "Describe existing fram connections (including orphans)", "topics": [ "list_extant_fram_connections" ] }, { "page": "make_batch_runs", "title": "Make batch runs", "topics": [ "make_batch_runs" ] }, { "page": "management_week", "title": "Vectorized approach to calculating the management week, returns an integer", "topics": [ "management_week" ] }, { "page": "modify_table", "title": "*[Experimental]* Modify FRAM database based on match/replace dataframe", "topics": [ "modify_table" ] }, { "page": "mortality_scalers", "title": "Quantify the proportion of fishery mortalities associated with stock(s) of interest", "topics": [ "mortality_scalers" ] }, { "page": "msf_encounters", "title": "Reproduce MSF encounters screen", "topics": [ "msf_encounters" ] }, { "page": "msf_encounters_chinook_", "title": "Replicate MSF screen report encounters for Chinook", "topics": [ "msf_encounters_chinook_" ] }, { "page": "msf_encounters_coho_", "title": "Replicate MSF screen report encounters for COHO", "topics": [ "msf_encounters_coho_" ] }, { "page": "msf_landed_catch", "title": "Reproduce MSF landed catch screen", "topics": [ "msf_landed_catch" ] }, { "page": "msf_landed_catch_chinook_", "title": "Replicate MSF screen report landed catch for Chinook", "topics": [ "msf_landed_catch_chinook_" ] }, { "page": "msf_landed_catch_coho_", "title": "Replicate MSF screen report landed catch for COHO", "topics": [ "msf_landed_catch_coho_" ] }, { "page": "msf_mortalities", "title": "Reproduce MSF mortalities screen", "topics": [ "msf_mortalities" ] }, { "page": "msf_mortalities_chinook_", "title": "Replicate MSF screen report mortalities for Chinook", "topics": [ "msf_mortalities_chinook_" ] }, { "page": "msf_mortalities_coho_", "title": "Replicate MSF screen report mortalities for COHO", "topics": [ "msf_mortalities_coho_" ] }, { "page": "msp_mortality", "title": "Expand Chinook mortality table using Model-Stock Proportion", "topics": [ "msp_mortality" ] }, { "page": "NR_flag_translate", "title": "Provides English translation of numeric non-retention flags", "topics": [ "NR_flag_translate" ] }, { "page": "plot_impacts_per_catch_heatmap", "title": "Make plots to show the amount of landed catch_per_impact", "topics": [ "plot_impacts_per_catch_heatmap" ] }, { "page": "plot_stock_comp", "title": "Plot stock composition", "topics": [ "plot_stock_comp" ] }, { "page": "plot_stock_mortality", "title": "Plot total mortalities by fishery", "topics": [ "plot_stock_mortality" ] }, { "page": "plot_stock_mortality_time_step", "title": "Creates an ordered bar chart with the top number of mortalities per fishery and time step.", "topics": [ "plot_stock_mortality_time_step" ] }, { "page": "population_statistics", "title": "Replicate Population Statistics screen", "topics": [ "population_statistics" ] }, { "page": "post_season_abundance", "title": "Generates post-season January age 3 abundances by stock from post-season databases. Used for forecasting.", "topics": [ "post_season_abundance" ] }, { "page": "provide_table_names", "title": "List names of FRAM table", "topics": [ "provide_table_names" ] }, { "page": "remove_run", "title": "Removes a run in a FRAM database", "topics": [ "remove_run" ] }, { "page": "run_info", "title": "Provides a print out of Run ID information", "topics": [ "run_info" ] }, { "page": "scalers_flag_translate", "title": "Provides English translation of numeric scalers flags", "topics": [ "scalers_flag_translate" ] }, { "page": "sensitivity_custom", "title": "*[Experimental]* Generate sensitivity analyses runs based on a list of match/replace dataframes", "topics": [ "sensitivity_custom" ] }, { "page": "sensitivity_exact", "title": "*[Experimental]* Generate sensitivity analyses runs based on exact values", "topics": [ "sensitivity_exact" ] }, { "page": "sensitivity_scaled", "title": "*[Experimental]* Generate sensitivity analyses runs scaled by template values", "topics": [ "sensitivity_scaled" ] }, { "page": "statistical_week", "title": "Vectorized approach to calculating the statistical week, returns an integer", "topics": [ "statistical_week" ] }, { "page": "stock_age_checker", "title": "Helper function to check that all stock x age combinations are present", "topics": [ "stock_age_checker" ] }, { "page": "stock_check_helper", "title": "Helper function to check that stock id make sense", "topics": [ "stock_check_helper" ] }, { "page": "stock_fate", "title": "*[Experimental]* Summarizes the three true outcomes of a stocks abundance, where it dies to fishery related mortality, natural mortality, or reaches some sort of escapement. When run against the coho database spawning escapement will be displayed, when run against the Chinook database escapement to the river will be dislpayed along with recruits to the next year 'age_up'", "topics": [ "stock_fate" ] }, { "page": "stock_fate_chinook", "title": "*[Experimental]* Chinook flavor of the stock fate function", "topics": [ "stock_fate_chinook" ] }, { "page": "stock_fate_coho", "title": "*[Experimental]* Coho flavor of the stock fate function", "topics": [ "stock_fate_coho" ] }, { "page": "stock_id_comp", "title": "Helper function to check that stock id exist in the Stock database", "topics": [ "stock_id_comp" ] }, { "page": "stock_mortality", "title": "Replicate Stock Mortality screen", "topics": [ "stock_mortality" ] }, { "page": "styleguide", "title": "Framrsquared style guide", "topics": [ "frs_stylecheck_assignment", "frs_stylecheck_snakecase", "styleguide" ] }, { "page": "terminal_fisheries", "title": "*[Experimental]* List terminal stock information", "topics": [ "terminal_fisheries" ] }, { "page": "terminal_info", "title": "*[Experimental]* Parse TAAETRS table", "topics": [ "terminal_info" ] }, { "page": "terminal_stocks", "title": "*[Experimental]* List terminal stock information", "topics": [ "terminal_stocks" ] }, { "page": "truns_fisheries", "title": "Returns a dataframe with fisheries defined by the TRuns report driver", "topics": [ "truns_fisheries" ] }, { "page": "truns_stocks", "title": "Returns a dataframe with stocks defined by the TRuns report driver", "topics": [ "truns_stocks" ] }, { "page": "validate_fishery_ids", "title": "Convenience function to check fishery input", "topics": [ "validate_fishery_ids" ] }, { "page": "validate_fram_db", "title": "Convenience function to check fram_db input", "topics": [ "validate_fram_db" ] }, { "page": "validate_run_id", "title": "Convenience function to check run_id input", "topics": [ "validate_run_id" ] }, { "page": "validate_stock_ids", "title": "Convenience function to check 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