Coordinated Assessments REST API R Interface

rCAX is an R client for the Coordinated Assessments API. Coordinated Assessments data eXchange (CAX) is developed by the Coordinated Assessments Partnership (CAP). CAP is a collaborative process to efficiently share and provide access to standardized derived information, such as fish population-scale high-level indicators (HLIs) and supporting metrics. Participants in CAP include state fish and wildlife management agencies, tribes, federal agencies such as National Oceanic and Atmospheric Administration Fisheries (NOAA Fisheries) and Bonneville Power Administration (BPA), and others. CAP is co-sponsored by StreamNet and Pacific Northwest Aquatic Monitoring Partnership (PNAMP). Make sure to review the StreamNet Terms of Use for these data, the StreamNet Data Policy and the citation information from StreamNet and PNAMP for database queries.

Version 1.0.3 changes are minor:

• Updating license to GPL-3
• Updating the url to nwfsc-cb after moving repo into the nwfsc-cb organization
• Some minor clean up of the Basic HLI queries vignette

Coordinated Assessments REST API R Interface

rCAX is an R client for the Coordinated Assessments API. Coordinated Assessments data eXchange (CAX) is developed by the Coordinated Assessments Partnership (CAP). CAP is a collaborative process to efficiently share and provide access to standardized derived information, such as fish population-scale high-level indicators (HLIs) and supporting metrics. Participants in CAP include state fish and wildlife management agencies, tribes, federal agencies such as National Oceanic and Atmospheric Administration Fisheries (NOAA Fisheries) and Bonneville Power Administration (BPA), and others. CAP is co-sponsored by StreamNet and Pacific Northwest Aquatic Monitoring Partnership (PNAMP). Make sure to review the StreamNet Terms of Use for these data, the StreamNet Data Policy and the citation information from StreamNet and PNAMP for database queries.

First production release

First production release.

beta version complete

This is version 1.0.0-beta ready for review before it becomes version 1.0.0 that we share.

• Removed API key info as rCAX now includes an internal read-only key
• Add plot to basics.Rmd
• Allow cols and sortcols in rcax_table_query() to be numbers, although the results might be non-intuitive for rcax_hli_xport() since the number will refer to the column order in the table before the columns are sorted into the order found in the downloaded Excel files.

v0.8.0 Condense the xport and base functions

• Condensed all the _xport functions into one function rcax_hli_xport() with argument hli to specify which HLI.
• Condensed all the individual HLI functions into one function rcax_hli() with argument hli to specify which HLI.
• Cleaned up the API vignette as it was out of date. Updated basics.Rmd given the changes to the functions.
• Added rcax_table_name() to look up the table based on XPort versus base and for a HLI short code.
• Added rcax_table_cols() and rcax_table_sortcols() to return these based on XPort versus base and for a HLI short code.
• Added 'hli' and 'hli_id' to the cax_column_definitions internal data.
• Added CITATION

version 0.7.0 added the column definitions table

• Added a setup vignette for how to download and install the package.
• Removed rcax_key(). Not needed. Cleaned up some {rredlist} refs.
• Added rcax_version() to print the installed versus GitHub version.
• Added cax_column_definitions from the definitions tab in the Excel files output by the HLI Tabular Query.
• type="colnames" now returns a data frame with a name and definition column.
• Added documentation for the internal data.
• Added RCMD check badge and workflow, did some minor cleanup to pass check.

v0.6.0 Completed the rest of the tables

• Added rcax_pni_xport(), rcax_rpers_xport(), rcax_juvout_xport(), rcax_presmolt_xport(), rcax_presmolt(), rcax_pni(), rcax_sar(), rcax_rpers(), rcax_presmolt()
• Added template roxygen for all xport and basetable functions. Now details and description elements are identical.
• Dynamically find a nmfs_id or popid for the examples so that the examples never return an empty table.
• in rcax_table_query() set rownames to NULL in returned tables
• Added ggplot2 to Suggests in DESCRIPTION file since I use it in some examples and will use in vignettes.
• removed {stringr} and |> dependency
• Added a check that all the flist names appear in the table. Requires an extra GET call but the call will fail otherwise if cols do not match.

version 0.5.0 added NOSA_XPort and SAR_XPort functions

• Added rcax_termsofuse() and a Terms of Use vignette. Add more links in Readme to StreamNet data use policies.
• Added rcax_nosa_xport() which is the data table available on https://www.streamnet.org/data/hli/ when one downloads a NOSA table
• Added rcax_sar_xport() which is the data table available on https://www.streamnet.org/data/hli/ when one downloads a SAR table
• Made rcax_table_query() more robust if the cols passed in do not match what is in the table. It will print a warning and only show cols that do appear. Also I added tolower(cols) and tolower(sortcols) so that these are case insensitive.
• Added nosa_xport_colnames to sysdata.rda. This is somewhat fragile since SteamNet might change the column names. The code to create the system data is in inst/docs.

version 0.4.0 Added filtering functionality

• added more sysdata: caxpops The Populations table. I had to download table from (StreamNet pop page)[https://www.streamnet.org/cap/current-hli/current-pop/] since the "Populations" table query is throwing an error), caxesus ESU_DPS names, caxsuperpops The SuperPopulations table.
• created rcax_table_query() as the base function for all the table query functions. That way I am not repeating the same code for each table.
• added info to rcax_table_query() documentation about the possible query params.
• added the rcax_filter() function to allow filtering the tables. Added examples in basics.Rmd.

version 0.2.0 added tables function

rCAX 0.2.0

• Cleaned up rcax_nosa() and figured out that you can pass in popid as a query param. Subset the columns.
• Make rcax_tables() to get the table ids that we need for queries.