Package: pdindicatoR 0.1.0
Lissa Breugelmans
pdindicatoR: Calculate and visualize a phylogenetic diversity indicators based on species occurrence data cubes
A package to calculate and produce a map of phylogenetic diversity scores for each grid cell in the input species occurrences data cube, and calculate the percentage of high PD cells within currently protected areas. You provide a phylogenetic tree, the datacube for the corresponding species is downloaded from GBIF (or user-uploaded), and the package does the rest.
Authors:
pdindicatoR_0.1.0.tar.gz
pdindicatoR_0.1.0.zip(r-4.7)pdindicatoR_0.1.0.zip(r-4.6)pdindicatoR_0.1.0.zip(r-4.5)
pdindicatoR_0.1.0.tgz(r-4.6-any)pdindicatoR_0.1.0.tgz(r-4.5-any)
pdindicatoR_0.1.0.tar.gz(r-4.7-any)pdindicatoR_0.1.0.tar.gz(r-4.6-any)
pdindicatoR_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
pdindicatoR/json (API)
| # Install 'pdindicatoR' in R: |
| install.packages('pdindicatoR', repos = c('https://b-cubed-eu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/b-cubed-eu/pdindicator/issues
Pkgdown/docs site:https://b-cubed-eu.github.io
biodiversityconservationdatacubeindicatorphylogenetic-diversity
Last updated from:5bbd91d038. Checks:7 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | ERROR | 177 | ||
| source / vignettes | OK | 206 | ||
| linux-release-x86_64 | ERROR | 172 | ||
| macos-release-arm64 | ERROR | 100 | ||
| macos-oldrel-arm64 | ERROR | 92 | ||
| windows-devel | ERROR | 123 | ||
| windows-release | ERROR | 116 | ||
| windows-oldrel | ERROR | 140 | ||
| wasm-release | OK | 129 |
Exports:aggregate_cubeappend_ott_idcalculate_faithpdcheck_completenessconvert_multipolygonsgenerate_map_and_indicatorget_pd_cubemake_shiny_mapsretrieve_example_datataxonmatch
Dependencies:apeaskpassassertthatbase64encbslibcachemclassclassIntclicommonmarkcpp11crayoncurlDBIdigestdplyre1071farverfastmapfontawesomefsgdalUtilitiesgenericsggplot2gluegtablehmshtmltoolshttpuvhttrisobandjquerylibjsonliteKernSmoothlabelinglaterlatticelifecyclemagrittrMASSmemoisemimenlmeopensslotelpillarpkgconfigprettyunitsprogresspromisesproxyR6rappdirsRColorBrewerRcpprentrezrlangrnaturalearthrnaturalearthdatarnclrotls2S7sassscalessfshinysourcetoolsstringistringrsysterratibbletidyselectunitsutf8vctrsviridisLitewithrwkXMLxtable
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Aggregate datacube over grid cell to create new dataframe with species list per grid | aggregate_cube |
| Append ott id's to cube | append_ott_id |
| Calculation of Faith's PD | calculate_faithpd |
| Check if provided phylogenetic tree is complete and covers all species in occurrence cube | check_completeness |
| Convert multisurface object to multipolygon object | convert_multipolygons |
| Mapping PD and calculating indicator | generate_map_and_indicator |
| Find MRCA for data cube and call function to calculate PD metrics | get_pd_cube |
| Visualizing PD maps for time periods in tabs | make_shiny_maps |
| Retrieve example data | retrieve_example_data |
| Taxon matching | taxonmatch |
