Setup | Dataset | Randomization test | Classify endemism | Classify significance | Visualize results | References
Package: canaper 1.0.1.9000
Joel H. Nitta
canaper: Categorical Analysis of Neo- And Paleo-Endemism
Provides functions to analyze the spatial distribution of biodiversity, in particular categorical analysis of neo- and paleo-endemism (CANAPE) as described in Mishler et al (2014) <doi:10.1038/ncomms5473>. 'canaper' conducts statistical tests to determine the types of endemism that occur in a study area while accounting for the evolutionary relationships of species.
Authors:
canaper_1.0.1.9000.tar.gz
canaper_1.0.1.9000.zip(r-4.7)canaper_1.0.1.9000.zip(r-4.6)canaper_1.0.1.9000.zip(r-4.5)
canaper_1.0.1.9000.tgz(r-4.6-any)canaper_1.0.1.9000.tgz(r-4.5-any)
canaper_1.0.1.9000.tar.gz(r-4.7-any)canaper_1.0.1.9000.tar.gz(r-4.6-any)
canaper_1.0.1.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
canaper/json (API)
| # Install 'canaper' in R: |
| install.packages('canaper', repos = c('https://packages.ropensci.org', 'https://cloud.r-project.org')) |
Reviews:rOpenSci Software Review #475
Bug tracker:https://github.com/ropensci/canaper/issues
Pkgdown/docs site:https://docs.ropensci.org
Datasets:
- acacia - _Acacia_ example data
- biod_example - Biodiverse example data
- biod_results - Output from Biodiverse
- cpr_endem_cols - CVD-friendly color palette for plotting results of CANAPE
- cpr_endem_cols_2 - CVD-friendly color palette for plotting results of CANAPE, version 2
- cpr_endem_cols_3 - CVD-friendly color palette for plotting results of CANAPE, version 3
- cpr_endem_cols_4 - CVD-friendly color palette for plotting results of CANAPE, version 4
- cpr_signif_cols - CVD-friendly color palette for plotting results of randomization test
- cpr_signif_cols_2 - CVD-friendly color palette for plotting results of randomization test, version 2
- mishler_endem_cols - Original color palette for plotting results of CANAPE
- mishler_signif_cols - Original color palette for plotting results of CANAPE
- phylocom - Phylocom example data
Last updated from:ea3c4cb9f3 (on main). Checks:10 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 231 | ||
| pkgdown docs | OK | 183 | ||
| source / vignettes | OK | 222 | ||
| linux-release-x86_64 | OK | 212 | ||
| macos-release-arm64 | OK | 132 | ||
| macos-oldrel-arm64 | OK | 154 | ||
| windows-devel | OK | 173 | ||
| windows-release | OK | 168 | ||
| windows-oldrel | OK | 139 | ||
| wasm-release | OK | 190 |
Exports:cpr_classify_endemcpr_classify_signifcpr_iter_simcpr_make_palcpr_rand_commcpr_rand_test
Dependencies:abindapeassertrassertthatbetapartclassclassIntcliclusterclustMixTypecodetoolscolorspacecombinatcpp11DBIdigestdoSNOWdplyre1071fastmatchforeachfuturefuture.applygenericsgeometryglobalsglueigraphiteratorsitertoolsKernSmoothlatticelifecyclelinproglistenvlpSolvemagicmagrittrmaptpxMASSMatrixmclustmgcvminpack.lmnlmeparallellypermutephangornphyloregionpicantepillarpkgconfigpredictsprogressrproxypurrrquadprogR6rcddRColorBrewerRcppRcppProgressrlangs2sfslamsmoothrsnowterratibbletidyselectunitsutf8vctrsveganwithrwk
CANAPE example
Last update: 2023-04-05
Started: 2021-06-27
How many randomizations?
A word about randomization algorithms | Replicates vs. iterations | Effect of n_iterations | Effect of n_reps | Conclusion | References
Last update: 2023-04-05
Started: 2021-10-18
Parallel computing
How to parallelize | Sequential mode | Parallel mode | When to parallelize? | Progress bars | Conclusion
Last update: 2023-04-05
Started: 2021-10-20
