Skip to contents

Changelog

Source: NEWS.md

expowo 3.2

Major changes

  • The mining functions powoFam(), powoGenera(), powoSpecies(), powoSpDist(), megaGen() and topGen() gain a new argument source. The default source = "wcvp" reads the bulk data of the World Checklist of Vascular Plants (WCVP), the taxonomic backbone of POWO, instead of mining the source HTML page of each taxon at the POWO website. This was needed because POWO now blocks automated requests, which made every search fail with HTTP status was '403 Forbidden'.

  • The WCVP file (about 90 MB) is downloaded from Kew only once and cached at tools::R_user_dir("expowo", "cache"). It is downloaded again only when Kew releases a new WCVP version, and the cached copy is used when offline. Any search after the first one runs in seconds, even for the largest families.

  • The output tables keep exactly the same columns as in previous versions. The botanical countries keep the WGSRPD level-3 names used by POWO (e.g. “Zaire”, “Turkey”, “Yugoslavia”), so that powoMap() and the botregions country lookup work as before.

  • The previous mining of POWO source pages is still available with source = "powo".

New functions

  • endemicMap() maps the number of species endemic to each botanical country (WGSRPD level 3), i.e. the species native to a single botanical country. While powoMap() maps where species occur, endemicMap() maps where they are restricted to. The classes of the map are set with breaks.

  • discoveryGraph() plots, in two panels, the number of species described and of synonyms published in each decade (or any period set with bin). A species is counted in the year of its basionym, i.e. the year it was discovered. It complements the cumulative curves of accGraph(), showing when taxonomic work was most intense.

  • introGraph() plots a heatmap with the number of species native to each continent (or WGSRPD region, with level = "region") that are introduced in each other one.

  • The three functions take the output of powoSpecies(), return a ggplot object and save the graphic with save, dir, filename, format and dpi, like powoMap() and accGraph(). The TDWG map of botanical countries used by endemicMap() (about 4 MB) is downloaded only once and cached with the WCVP data.

  • A small internal table of the 368 WGSRPD level-3 areas, with their names as returned by expowo and their region and continent, is built by data-raw/build_wgsrpd_l3.R. It lets introGraph() work without any download and endemicMap() match the map by area code, so that botanical countries with accented names in the TDWG map (e.g. “Réunion”, “Zaïre”) are not missed.

How the output is built from WCVP

  • Only two WCVP tables are used: wcvp_names.csv and wcvp_distribution.csv. They are downloaded together in wcvp.zip from https://sftp.kew.org/pub/data-repositories/WCVP/ and kept as a slim RDS file in the cache.

  • Genera (powoGenera(), powoFam(), megaGen(), topGen()) are the names with taxon_rank “Genus” and taxon_status “Accepted” in each family, in alphabetical order. Families are searched in the same order as POWOcodes.

  • Species (powoSpecies(), powoSpDist()) are the names with taxon_rank “Species” and taxon_status “Accepted” whose parent is one of the searched genera, in alphabetical order within each genus. Infraspecific taxa are not listed, as in the POWO genus pages.

  • species_number is the number of accepted species in each genus, including hybrid species. powoFam() sums it over the genera of each family. A genus with no accepted species gets 0, where the POWO search returned NA.

  • hybrid: a genus or species is a hybrid when its name contains “×” or “+”, as in the POWO search.

  • authors and scientific_name come from taxon_authors and taxon_name.

  • publication joins publication_author, place_of_publication, volume_and_page and first_published, e.g. “H.G.A.Engler (ed.), Pflanzenr., IV, 219a: 31 (1939)”.

  • native_to_botanical_countries and introduced_to_botanical_countries list the WGSRPD level-3 areas of each taxon, in alphabetical order. Extinct and doubtful records are left out. An area where the taxon is native is not also listed as introduced. “unknown” is used when there is no record, as before.

  • native_to_country and introduced_to_country convert those areas to political countries with the botregions dataset, as in the POWO search. Areas missing from botregions keep their own name.

  • The WCVP area names that changed after the POWO names (e.g. “DR Congo”, “Türkiye”, “Eswatini”, “Czechia-Slovakia”, “NW. Balkan Pen.”, “Réunion”) are translated back by their level-3 code to the names used by POWO and by the TDWG level-3 shapefile read in powoMap().

  • synonyms = TRUE lists the non-accepted names whose accepted name is one of the returned species, right after that species. Misapplied names are left out. Homotypic synonyms come first and then heterotypic ones, each in alphabetical order. The status is “Homotypic Synonym” or “Heterotypic Synonym”. The accepted_name is the scientific name of the accepted species, and the publication is “unknown publication” when WCVP has none. As in the POWO search, the species, authors and distribution columns of synonyms are NA.

  • kew_id is the WCVP powo_id (the IPNI id when powo_id is empty), and powo_uri is built from it with the same URL as before.

  • country, genus, hybrid, rerun and save behave as before; the country filter is the same function used by the POWO search, so a taxon is kept when it is native or introduced in any of the given countries.

Minor changes

  • With source = "wcvp", the botanical country names are no longer truncated at 20 characters, the publications keep their original accents and the & HTML entities are replaced by &.

  • The distribution of each genus in powoGenera() also includes the distribution of all its accepted species, as in the POWO genus pages.

  • powoSpDist() no longer fails when none of the given species is accepted.

  • The powoSpDist() example and the species distribution vignette now use Bertholletia excelsa, because Lecythis pisonis is currently treated as a synonym of Pachylecythis pisonis.

  • expowo now requires R >= 4.0.0.

  • Added a README.Rmd from which README.md is generated.

  • Added three vignettes showing how to make the new graphics: mapping endemic species, plotting species discovery over time and plotting species introductions.

  • The test suite now covers about 98% of the code, including the POWO mining (tested offline with copies of POWO pages), the WCVP download and cache, the maps and the graphics. A GitHub Actions workflow reports the coverage to Codecov.

expowo 3.1

CRAN release: 2026-07-24

  • Released on CRAN on 14 July 2026.