Package: pdindicatoR 0.0.2
Lissa Breugelmans
pdindicatoR: Calculate and visualize a phylogenetic diversity indicators based on species occurence data cubes
A package to calculate and produce a map of phylogenetic diversity scores for each grid cell in the input species occurences 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_0.0.2.tar.gz
pdindicatoR_0.0.2.zip(r-4.5)pdindicatoR_0.0.2.zip(r-4.4)pdindicatoR_0.0.2.zip(r-4.3)
pdindicatoR_0.0.2.tgz(r-4.5-any)pdindicatoR_0.0.2.tgz(r-4.4-any)pdindicatoR_0.0.2.tgz(r-4.3-any)
pdindicatoR_0.0.2.tar.gz(r-4.5-noble)pdindicatoR_0.0.2.tar.gz(r-4.4-noble)
pdindicatoR_0.0.2.tgz(r-4.4-emscripten)pdindicatoR_0.0.2.tgz(r-4.3-emscripten)
pdindicatoR.pdf |pdindicatoR.html✨
pdindicatoR/json (API)
NEWS
| # 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 site:https://b-cubed-eu.github.io
biodiversityconservationdatacubeindicatorphylogenetic-diversity
Last updated 3 months agofrom:8e86f2c121. Checks:1 OK, 7 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 17 2025 |
| R-4.5-win | NOTE | Feb 17 2025 |
| R-4.5-mac | NOTE | Feb 17 2025 |
| R-4.5-linux | NOTE | Feb 17 2025 |
| R-4.4-win | NOTE | Feb 17 2025 |
| R-4.4-mac | NOTE | Feb 17 2025 |
| R-4.3-win | NOTE | Feb 17 2025 |
| R-4.3-mac | NOTE | Feb 17 2025 |
Exports:aggregate_cubeappend_ott_idcalculate_faithpdcheck_completenessconvert_multipolygonsgenerate_map_and_indicatorget_pd_cubemake_shiny_mapsretrieve_example_datataxonmatch
Dependencies:apeaskpassbase64encbslibcachemclassclassIntclicolorspacecommonmarkcrayoncurlDBIdigestdplyre1071fansifarverfastmapfontawesomefsgdalUtilitiesgenericsggplot2gluegtablehmshtmltoolshttpuvhttrisobandjquerylibjsonliteKernSmoothlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigprettyunitsprogresspromisesproxyR6rappdirsRColorBrewerRcpprentrezrlangrnaturalearthrnaturalearthdatarnclrotls2sassscalessfshinysourcetoolsstringistringrsysterratibbletidyselectunitsutf8vctrsviridisLitewithrwkXMLxtable
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 |
