Package: EvoPhylo 0.3.3
EvoPhylo: Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics
Performs automated morphological character partitioning for phylogenetic analyses and analyze macroevolutionary parameter outputs from clock (time-calibrated) Bayesian inference analyses, following concepts introduced by Simões and Pierce (2021) <doi:10.1038/s41559-021-01532-x>.
Authors:
EvoPhylo_0.3.3.tar.gz
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EvoPhylo.pdf |EvoPhylo.html✨
EvoPhylo/json (API)
NEWS
# Install 'EvoPhylo' in R: |
install.packages('EvoPhylo', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tiago-simoes/evophylo/issues
- RateTable_Means_1p_Clades - Mean clock rates by node and clade
- RateTable_Means_3p_Clades - Mean clock rates by node and clade
- characters - A morphological phylogenetic data matrix
- post_trees - Multiple phylogenetic clock trees
- posterior1p - Posterior parameter samples
- posterior3p - Posterior parameter samples
- tree1p - Phylogenetic tree with a single clock partition
- tree3p - Phylogenetic tree with 3 clock partitions
- tree_clock1 - BEAST2 phylogenetic tree with clock rates from partition 1
- tree_clock2 - BEAST2 phylogenetic tree with clock rates from partition 2
Last updated 1 years agofrom:2cb8d612a8. Checks:OK: 1 NOTE: 6. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 10 2024 |
R-4.5-win | NOTE | Aug 10 2024 |
R-4.5-linux | NOTE | Aug 10 2024 |
R-4.4-win | NOTE | Aug 10 2024 |
R-4.4-mac | NOTE | Aug 10 2024 |
R-4.3-win | NOTE | Aug 10 2024 |
R-4.3-mac | NOTE | Aug 10 2024 |
Exports:clock_reshapeclockrate_dens_plotclockrate_reg_plotclockrate_summarycluster_to_nexuscombine_logdrop.dummy.beastdrop.dummy.mbFBD_dens_plotFBD_normality_plotFBD_reshapeFBD_summaryFBD_tests1FBD_tests2get_clockrate_table_BEAST2get_clockrate_table_MrBayesget_gower_distget_pwt_rates_BEAST2get_pwt_rates_MrBayesget_sil_widthsmake_clustersoffset.to.dummyoffset.to.dummy.metadataplot_back_ratesplot_treerates_sgnwrite_partitioned_alignmentswrite.beast.treedata
Dependencies:apeaplotaskpassbase64encbrewbriobslibcachemcallrclicliprclusterclusterGenerationcodacodetoolscolorspacecombinatcommonmarkcpp11crayoncredentialscurldeeptimeDEoptimdescdevtoolsdiffobjdigestdoParalleldownlitdplyrellipsisevaluateexpmfansifarverfastmapfastmatchfontawesomeforeachfsgenericsgeomtextpathgertggfittextggforceggfunggnewscaleggplot2ggplotifyggrepelggseqlogoggtreeghgitcredsgluegridExtragridGraphicsgridtextgtablehighrhtmltoolshtmlwidgetshttpuvhttr2igraphiniisobanditeratorsjpegjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrmapsmarkdownMASSMatrixmemoisemgcvmimeminiUImnormtmunsellnlmenumDerivopenssloptimParallelpatchworkphangornphytoolspillarpkgbuildpkgconfigpkgdownpkgloadpngpolyclippraiseprettyunitsprocessxprofvispromisespspurrrquadprogR6raggrappdirsrcmdcheckRColorBrewerRcppRcppEigenrematch2remotesrlangrmarkdownroxygen2rprojrootrstudioapiRtsnerversionssassscalesscatterplot3dsessioninfoshadesshinysourcetoolsstringistringrsyssystemfontstestthattextshapingtibbletidyrtidyselecttidytreetinytextreeiotweenrunglueurlcheckerusethisutf8vctrsviridisLitewaldowhiskerwithrxfunxml2xopenxtableyamlyulab.utilszip
Analyzing FBD Parameters
Rendered fromfbd-params.Rmd
usingknitr::rmarkdown
on Aug 10 2024.Last update: 2022-11-03
Started: 2022-05-04
Analyzing Trees With Offsets
Rendered fromoffset_handling.Rmd
usingknitr::rmarkdown
on Aug 10 2024.Last update: 2022-10-31
Started: 2022-06-24
Character Partitioning
Rendered fromchar-part.Rmd
usingknitr::rmarkdown
on Aug 10 2024.Last update: 2022-11-02
Started: 2022-05-04
Evolutionary Rates & Selection Mode (BEAST2)
Rendered fromrates-selection_BEAST2.Rmd
usingknitr::rmarkdown
on Aug 10 2024.Last update: 2022-11-02
Started: 2022-10-28
Evolutionary Rates & Selection Mode (Mr.Bayes)
Rendered fromrates-selection_MrBayes.Rmd
usingknitr::rmarkdown
on Aug 10 2024.Last update: 2023-07-21
Started: 2022-10-31
Theoretical background
Rendered fromdata_treatment.Rmd
usingknitr::rmarkdown
on Aug 10 2024.Last update: 2022-09-29
Started: 2022-06-27