Package: phyr 1.1.0
phyr: Model Based Phylogenetic Analysis
A collection of functions to do model-based phylogenetic analysis. It includes functions to calculate community phylogenetic diversity, to estimate correlations among functional traits while accounting for phylogenetic relationships, and to fit phylogenetic generalized linear mixed models. The Bayesian phylogenetic generalized linear mixed models are fitted with the 'INLA' package (<https://www.r-inla.org>).
Authors:
phyr_1.1.0.tar.gz
phyr_1.1.0.tar.gz(r-4.5-noble)phyr_1.1.0.tar.gz(r-4.4-noble)
phyr_1.1.0.tgz(r-4.4-emscripten)phyr_1.1.0.tgz(r-4.3-emscripten)
phyr.pdf |phyr.html✨
phyr/json (API)
NEWS
# Install 'phyr' in R: |
install.packages('phyr', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/daijiang/phyr/issues
Pkgdown:https://daijiang.github.io
Last updated 4 years agofrom:a4cc0a4ca9. Checks:OK: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 22 2024 |
R-4.5-linux-x86_64 | OK | Nov 22 2024 |
Exports:%nin%align_comm_Vboot_cicommunityPGLMMcommunityPGLMM.matrix.structurecommunityPGLMM.plot.recommunityPGLMM.predicted.valuescommunityPGLMM.profile.LRTcommunityPGLMM.show.recor_phylofixefget_design_matrixmatch_comm_treepcdpcd_predpglmmpglmm_comparepglmm_matrix_structurepglmm_plot_ranefpglmm_plot_repglmm_predicted_valuespglmm_profile_LRTplot_bayesplot_dataprep_dat_pglmmpscpsdpsepsrpsvpsv.sppranefrefit_bootsrm_site_noobsrm_sp_noobsvcv2
Dependencies:apebootclicpp11deldirdigestdplyrfansigenericsgluegridExtragtableinterpjpeglatticelatticeExtralifecyclelme4magrittrMASSMatrixminqamvtnormnlmenloptrpillarpkgconfigpngpurrrR6RColorBrewerRcppRcppArmadilloRcppEigenrlangstringistringrtibbletidyrtidyselectutf8vctrswithr
Performance benchmark
Rendered frombenchmarks.Rmd
usingknitr::rmarkdown
on Nov 22 2024.Last update: 2019-10-24
Started: 2019-10-24
Plot random terms of communityPGLMM
Rendered fromplot-re.Rmd
usingknitr::rmarkdown
on Nov 22 2024.Last update: 2020-12-18
Started: 2019-10-24
Usage of pglmm()
Rendered frompglmm.Rmd
usingknitr::rmarkdown
on Nov 22 2024.Last update: 2020-12-18
Started: 2019-10-24