Package: RPANDA 2.3
![](https://r-universe.dev/static/nobody.jpg)
Hélène Morlon
RPANDA: Phylogenetic ANalyses of DiversificAtion
Implements macroevolutionary analyses on phylogenetic trees. See Morlon et al. (2010) <doi:10.1371/journal.pbio.1000493>, Morlon et al. (2011) <doi:10.1073/pnas.1102543108>, Condamine et al. (2013) <doi:10.1111/ele.12062>, Morlon et al. (2014) <doi:10.1111/ele.12251>, Manceau et al. (2015) <doi:10.1111/ele.12415>, Lewitus & Morlon (2016) <doi:10.1093/sysbio/syv116>, Drury et al. (2016) <doi:10.1093/sysbio/syw020>, Manceau et al. (2016) <doi:10.1093/sysbio/syw115>, Morlon et al. (2016) <doi:10.1111/2041-210X.12526>, Clavel & Morlon (2017) <doi:10.1073/pnas.1606868114>, Drury et al. (2017) <doi:10.1093/sysbio/syx079>, Lewitus & Morlon (2017) <doi:10.1093/sysbio/syx095>, Drury et al. (2018) <doi:10.1371/journal.pbio.2003563>, Clavel et al. (2019) <doi:10.1093/sysbio/syy045>, Maliet et al. (2019) <doi:10.1038/s41559-019-0908-0>, Billaud et al. (2019) <doi:10.1093/sysbio/syz057>, Lewitus et al. (2019) <doi:10.1093/sysbio/syz061>, Aristide & Morlon (2019) <doi:10.1111/ele.13385>, Maliet et al. (2020) <doi:10.1111/ele.13592>, Drury et al. (2021) <doi:10.1371/journal.pbio.3001270>, Perez-Lamarque & Morlon (2022) <doi:10.1111/mec.16478>, Perez-Lamarque et al. (2022) <doi:10.1101/2021.08.30.458192>, Mazet et al. (2023) <doi:10.1111/2041-210X.14195>, Drury et al. (2024) <doi:10.1016/j.cub.2023.12.055>.
Authors:
RPANDA_2.3.tar.gz
RPANDA_2.3.zip(r-4.5)RPANDA_2.3.zip(r-4.4)RPANDA_2.3.zip(r-4.3)
RPANDA_2.3.tgz(r-4.4-x86_64)RPANDA_2.3.tgz(r-4.4-arm64)RPANDA_2.3.tgz(r-4.3-x86_64)RPANDA_2.3.tgz(r-4.3-arm64)
RPANDA_2.3.tar.gz(r-4.5-noble)RPANDA_2.3.tar.gz(r-4.4-noble)
RPANDA_2.3.tgz(r-4.4-emscripten)RPANDA_2.3.tgz(r-4.3-emscripten)
RPANDA.pdf |RPANDA.html✨
RPANDA/json (API)
# Install 'RPANDA' in R: |
install.packages('RPANDA', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hmorlon/panda/issues
- Anolis.data - Anolis dataset
- BGB.examples - BioGeoBEARS stochastic maps
- Balaenopteridae - Balaenopteridae phylogeny
- Calomys - Calomys phylogeny
- Caprimulgidae - The _Caprimulgidae_ phylogeny.
- Caprimulgidae_ClaDS2 - An example run of ClaDS2.
- Cetacea - Cetacean phylogeny
- Cetacea_clades - Stochastic map of clade membership in Cetacean phylogeny
- ClaDS0_example - An example run of ClaDS0.
- InfTemp - Paleotemperature data across the Cenozoic
- Phocoenidae - Phocoenidae phylogeny
- Phyllostomidae - Phyllostomidae phylogeny
- Phyllostomidae_genera - Phylogenies of Phyllostomidae genera
- co2 - Co2 data since the Jurassic
- co2 - Co2 data since the Jurassic
- coccolithophore - Coccolithophore diversity since the Jurassic
- d13c - D13c data since the Jurassic
- foraminifera - Foraminifera diversity since the Jurassic
- greenalgae - Green algae diversity since the Jurassic
- landplant - Land plant diversity since the Jurassic
- mycorrhizal_network - Mycorrhizal network from La Réunion island
- ostracoda - Ostracod diversity since the Jurassic
- radiolaria - Radiolaria diversity since the Jurassic
- redalgae - Red algae diversity since the Jurassic
- sealevel - Sea level data since the Jurassic
- shifts_cetacea - Cetacean shift.estimates results
- silica - Silica data across the Cenozoic
- taxo_cetacea - Cetacean taxonomy
Last updated 2 months agofrom:5d02681797. Checks:OK: 1 WARNING: 8. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 09 2024 |
R-4.5-win-x86_64 | WARNING | Aug 09 2024 |
R-4.5-linux-x86_64 | WARNING | Aug 09 2024 |
R-4.4-win-x86_64 | WARNING | Aug 09 2024 |
R-4.4-mac-x86_64 | WARNING | Aug 09 2024 |
R-4.4-mac-aarch64 | WARNING | Aug 09 2024 |
R-4.3-win-x86_64 | WARNING | Aug 09 2024 |
R-4.3-mac-x86_64 | WARNING | Aug 09 2024 |
R-4.3-mac-aarch64 | WARNING | Aug 09 2024 |
Exports:add.gtsancestralapply_prob_dttBIComparebuild_network.BipartiteEvolCreateClassObjectCreateGeobyClassObjectCreateGeoObjectCreateGeoObject_BioGeoBEARScreateModelcreateModelCoevolutiondefine_species.BipartiteEvoldelineate_phylotypesdiv.modelsdiv.ratesfit_bdfit_bd_backbonefit_bd_backbone_cfit_bd_in_pastfit_ClaDSfit_ClaDS0fit_coal_cstfit_coal_varfit_envfit_env_in_pastfit_sgdfit_t_compfit_t_comp_subgroupfit_t_envfit_t_env_oufit_t_plfit_t_standardfitTipDataget.comb.shiftget.sampling.fractionsgetDataLikelihoodgetMAPS_ClaDSgetMAPS_ClaDS0getTipDistributiongic_criterionJSDt_clusterJSDtreeJSDtree_clusterlikelihood_bdlikelihood_bd_backbonelikelihood_coal_cstlikelihood_coal_varlikelihood_sgdlikelihood_subgroup_modellikelihood_t_DDlikelihood_t_DD_geoglikelihood_t_envlikelihood_t_MClikelihood_t_MC_geoglines.fit_t.envlines.fit_t.env.oumake_gen.BipartiteEvolmantel_testmantel_test_nbpartnersmodelSelectionpaleodivphyl.pca_plphylosignal_networkphylosignal_sub_networkpi_estimatorplot_BICompareplot_ClaDS_chainsplot_ClaDS_phyloplot_ClaDS0_chainsplot_div.BipartiteEvolplot_dttplot_fit_bdplot_fit_envplot_net.BipartiteEvolplot_phylo_combplot_phylosignal_sub_networkplot_prob_dttplot_spectRplot.fit_t.envplot.fit_t.env.ouPosdefprintprob_dttremove.modelshift.estimatesshowsim_ClaDSsim_env_bdsim_MCBDsim_sgdsim_t_compsim_t_envsim_t_env_ousim_t_tworegimesim.BipartiteEvolsim.convergence.geosim.divergence.geosimul.comb.shiftsimulateTipDataspectRspectR_ttheta_estimator
Dependencies:apeBBbipartiteclasscliclueclusterclusterGenerationcodacodetoolscolorspacecombinatcorpcorcpp11DEoptimDEoptimRdeSolvedigestdiptestdirmultdoParalleldotCall64expmfansifarverfastmatchfBasicsfieldsflexmixforeachfpcgeigergenericsggplot2ggrepelggseqlogoglassoFastgluegmpgssgtableGUniFracigraphinlineisobanditeratorsjsonlitekernlablabelinglatticelifecyclemagrittrmapsMASSMatrixmatrixStatsmclustmgcvmnormtmodeestmodeltoolsmunsellmvMORPHmvtnormncbitnetworknlmennetnumDerivoptimParallelParallelLoggerpbmcapplypermutephangornphytoolspicantepillarpkgconfigprabcluspracmapsplinepvclustquadprogR.methodsS3R.ooR.utilsR6rasterRColorBrewerRcpprlangRmpfrrmutilrobustbaserpartscalesscatterplot3dsnasnowspspamspatialstablestablediststatipstatmodstatnet.commonsubplexterraTESStibbletimeDatetimeSeriesutf8vctrsveganviridisLitewithrxml2