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:Joel H. Nitta [aut, cre], Shawn W. Laffan [ctb, dtc], Brent D. Mishler [ctb, dtc], Wataru Iwasaki [ctb], Klaus Schliep [rev]

canaper_1.0.1.9000.tar.gz
canaper_1.0.1.9000.zip(r-4.7-any)canaper_1.0.1.9000.zip(r-4.6-any)canaper_1.0.1.9000.zip(r-4.5-any)
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:

On CRAN:

Conda:

biodiversitycanape

5.72 score 8 stars 44 scripts 350 downloads 6 exports 77 dependencies

Last updated from:ea3c4cb9f3 (on main). Checks:10 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK192
pkgdown docsOK266
source / vignettesOK197
linux-releaseOK233
macos-releaseOK149
macos-oldrelOK122
windows-develOK159
windows-releaseOK139
windows-oldrelOK151
wasm-releaseOK182

Exports:cpr_classify_endemcpr_classify_signifcpr_iter_simcpr_make_palcpr_rand_commcpr_rand_test

Dependencies:abindapeassertrassertthatbetapartclassclassIntcliclusterclustMixTypecodetoolscolorspacecombinatcpp11DBIdigestdoSNOWdplyre1071fastmatchforeachfuturefuture.applygenericsgeometryglobalsglueigraphiteratorsitertoolsKernSmoothlatticelifecyclelinproglistenvlpSolvemagicmagrittrmaptpxMASSMatrixmclustmgcvminpack.lmnlmeparallellypermutephangornphyloregionpicantepillarpkgconfigpredictsprogressrproxypurrrquadprogR6rcddRColorBrewerRcppRcppProgressrlangs2sfslamsmoothrsnowterratibbletidyselectunitsutf8vctrsveganwithrwk

CANAPE example
Setup | Dataset | Randomization test | Classify endemism | Classify significance | Visualize results | References
Rendered fromcanape.Rmdusingknitr::rmarkdown

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
Rendered fromhow-many-rand.Rmdusingknitr::rmarkdown

Last update: 2023-04-05
Started: 2021-10-18

Parallel computing
How to parallelize | Sequential mode | Parallel mode | When to parallelize? | Progress bars | Conclusion
Rendered fromparallel.Rmdusingknitr::rmarkdown

Last update: 2023-04-05
Started: 2021-10-20