NEWS.md
BeeBDC::taxadbToBeeBDC() now prompts users to install taxadb when it’s not already installed.BeeBDC::continentOutlieRs(), which is conceptually the same as BeeBDC::countryOutlieRs() except on a continental level. This function recognises that sometimes knowledge (including data) are insufficient for country-level analyses. A continent-level function might actually see greater use for taxa beyond bees where country-level checklists may not exist but a continent-level checklist could be created.BeeBDC::beesTaxonomy() and BeeBDC::beesChecklist() to allow the new function to be used properly. It will also include new tests and added sections to the vignette. I have also added a warning for use of this function with older versions of beesChecklist and added compatibility with BeeBDC::plotFlagSummary().BeeBDC::summaryFun() to allow users to specify “onlyFilterThese” instead of “dontFilterThese”.BeeBDC::taxadbToBeeBDC(), that can use the taxadb package to download taxonomic data for any taxa. The function will transform the taxadb format into the BeeBDC format that can be put directly into BeeBDC::harmoniseR(). Users may choose their data source (e.g., “gbif” or “itis”), but some formats may be better than others. Comments and issues are welcome in regards to how well the function works, or not, for your taxon.
BeeBDC::interactiveMapR() function were inverted from what they should have been. Thanks to Neil Cobb for pointing this out.BeeBDC::dateFindR() to identify more dates and exceptions on the advice of Elsa Youngsteadt.BeeBDC::dupeSummary() to update igraph::clusters to igraph::components(); a simple renaming.Suggestions by Elsa Youngsteadt (North Carolina State University) to allow functionality in harmoniseR to search for name matches in the verbatimScientificName column. This functionality has been optionally added with the checkVerbatim argument (default = FALSE) whereby if TRUE the function will make all checks on the normal name columns and then, only for those rows that failed, it will check the verbatimScientificName column for matches.
Exception found by Elsa Youngsteadt where repoMerge and attr_builder would fail to complete when multiple families were included in a single GBIF, iDigBio, or SCAN download. This has been updated whereby these functions can now work together in order to identify a multi-family download and label the dataSource column accordingly. This will also be reflected in the metadata and EML data to show the different sources, while maintaining the metadata for each download (doi, link, …).
Minor exception found by Elsa Youngsteadt where some synonyms would fail to be matched due to double brackets (e.g., “Lasioglossum (leucocomum) (Lovell)”). This has been fixed by letting harmoniseR stringr::str_replace instead of stringr::str_replace_all when finding matches without subgenus. Additionally, harmoniseR now ignores “non-ambiguous…” flags as these are more notes than actual issues.
Update to rnaturalearthdata 1.0.0 breaks BeeBDC::countryOutliers(). This function now uses the column “iso_a3_eh” instead of “iso_a3”. Thanks to @PMassicotte for identifying the issue and the solution.
Minor update to plotFlagSummary to allow individual species maps to get updated.
Update to atlasDownloader from mjwestgate to work with galah version 2.0.0
Minor update to the bee taxonomy file (29th November 2023), especially in regards to a few species that were getting associated with genus-only identifications. In particular, users who have downloaded version 1 of the dataset should be careful with the following species: Coelioxys texanus, Lasioglossum albipenne, Megachile brevis, and Xylocopa virginica. Likely the verbatimScientificName column could be filtered to remove these issues with something like: beeData %>% dplyr::filter(verbatimScientificName %in% c(“Coelioxys”, “Lasioglossum”, “Megachile”, “Xylocopa”)). Thanks to Angela Nava-Bolaños for identifying this issue.
ComplexHeatmap has been moved from imports to suggests and chordDiagramR will now ask a user if they want to install BiocManager and ComplexHeatmap (only if each is not already installed) before completing the function. This will simplify the installation process greatly.
A new readr function has been added (readr_VicWam), which reads data from the combined Victorian and Western Australian Museums in Australia.
A typo and potential pitfall has been fixed in countryOutliers where sometimes .sea records were not flagged and where NA record counts for .countryOutlier were not stated in the text output.
How users access the taxonomy and checklist files were slightly modified to include better warnings to help with troubleshooting as well as specific file-path operations for Windows machines.
jbd_coordCountryInconsistent was updated to better capture mismatched countries by using more columns to match.
Tests and workflows were updated in accordingly.