Package: EvoPhylo 0.3.5

Tiago Simoes

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:Tiago Simoes [cre, aut], Noah Greifer [aut], Joelle Barido-Sottani [aut], Stephanie Pierce [aut]

EvoPhylo_0.3.5.tar.gz
EvoPhylo_0.3.5.zip(r-4.7)EvoPhylo_0.3.5.zip(r-4.6)EvoPhylo_0.3.5.zip(r-4.5)
EvoPhylo_0.3.5.tgz(r-4.6-any)EvoPhylo_0.3.5.tgz(r-4.5-any)
EvoPhylo_0.3.5.tar.gz(r-4.7-any)EvoPhylo_0.3.5.tar.gz(r-4.6-any)
EvoPhylo_0.3.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
EvoPhylo/json (API)

# 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

Pkgdown/docs site:https://tiago-simoes.github.io

Datasets:

On CRAN:

Conda:

5.81 score 4 stars 27 scripts 212 downloads 29 exports 109 dependencies

Last updated from:17d07eb2d4. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK203
source / vignettesOK327
linux-release-x86_64OK239
macos-release-arm64OK149
macos-oldrel-arm64OK151
windows-develOK156
windows-releaseOK150
windows-oldrelOK129
wasm-releaseOK172

Exports:clade_membershipclock_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_partitioned_alignments2write.beast.treedata

Dependencies:apeaplotbackportsbase64encbslibcachemcheckmatecliclustercodetoolscommonmarkcpp11curldeeptimedeeptimedatadigestdplyrevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverfsfuturefuture.applygdtoolsgenericsggfittextggforceggfunggh4xggiraphggplot2ggplotifyggrepelggtreeglobalsgluegridExtragridGraphicsgridtextgrImport2gtablehighrhtmltoolshtmlwidgetsigraphisobandjpegjquerylibjsonliteknitrlabelinglatticelazyevallifecyclelistenvlitedownmagrittrmarkdownMASSMatrixmemoisemimenlmeosqpparallellypatchworkphangornpillarpkgconfigpngpolyclipprogressrpurrrR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownRtsneS7sassscalesshadesstringistringrsystemfontstibbletidyrtidyselecttidytreetinytextreeiotweenrunglueutf8vctrsviridisLitewithrxfunXMLxml2yamlyulab.utils

Analyzing FBD Parameters
FBD Parameters Statistics and Plots (Mr. Bayes) | 1. Import combined log file from all runs. | 2. Summarize FBD parameters by time bin | 3. Plot the distribution of each FBD parameter | 4. Test for assumptions | 5. Test for significant FBD shifts between time bins | FBD Parameters Statistics and Plots (BEAST2) | References
Rendered fromfbd-params.Rmdusingknitr::rmarkdown

Last update: 2025-08-27
Started: 2022-05-04

Analyzing Trees With Offsets
Analyzing Trees With Offset ages (BEAST2) | 1. Import the posterior tree distribution. | 2. Summarize the modified tree distribution | 3. Restore the final summary tree | Analyzing Trees With Offset ages (Mr.Bayes) | References
Rendered fromoffset_handling.Rmdusingknitr::rmarkdown

Last update: 2025-08-27
Started: 2022-06-24

Character Partitioning
Character Partitioning (Case 1) | 1. Generate distance matrix | 2. Estimate the optimal number of partitions | 3. Simple Workflow | 4. Complete Workflow | Character Partitioning (Case 2) | 3. Complete Workflow | References
Rendered fromchar-part.Rmdusingknitr::rmarkdown

Last update: 2025-08-27
Started: 2022-05-04

Evolutionary Rates & Selection Mode (BEAST2)
Evolutionary Rates Statistics and Plots | 0. Set your BEAST2 analysis to log multiple clocks | 1. Get rates from the clock tree and create a rate table | 2. Export the rate table and plot tree with node values | Plot tree node labels to customize clade names | 3. Import rate table with custom clade memberships | 4. Get summary stats for each clade/clock partition | 5. Plot rates by clock partition and clade | 6. Rate linear models | Selection Mode | 1. Import posterior log file | 3. Plot selection gradient on the summary tree | 4. Pairwise t-tests of rate values among clades | References
Rendered fromrates-selection_BEAST2.Rmdusingknitr::rmarkdown

Last update: 2025-08-27
Started: 2022-10-28

Evolutionary Rates & Selection Mode (Mr.Bayes)
Evolutionary Rates Statistics and Plots | 1. Get rates from the clock tree and create a rate table | 2. Export the rate table and plot tree with node values | Plot tree node labels to customize clade names | 3. Import rate table with custom clade memberships | 4. Get summary stats for each clade/clock partition | 5. Plot rates by clock partition and clade | 6. Rate linear models | ADDENDUM: Example using rates from single clock analysis (no partitioning) | Selection Mode | 1. Import combined log file from all runs. | 3. Plot selection gradient on the summary tree | 4. Pairwise t-tests of rate values among clades | References
Rendered fromrates-selection_MrBayes.Rmdusingknitr::rmarkdown

Last update: 2025-08-27
Started: 2022-10-31

Theoretical background
Creating Inter-character Distance Matrices | Types of morphological data | Treatment of inapplicable and missing data
Rendered fromdata_treatment.Rmdusingknitr::rmarkdown

Last update: 2025-08-27
Started: 2022-06-27

Readme and manuals

Help Manual

Help pageTopics
A morphological phylogenetic data matrixcharacters
Designate clade membership for each tip for downstream analyses summarizing rates for each cladeclade_membership
Convert clock rate tables from wide to long formatclock_reshape
Plot clock rate distributionsclockrate_dens_plot
Plot regression lines between sets of ratesclockrate_reg_plot
Compute rate summary statistics across clades and clocksclockrate_summary
Export character partitions to a Nexus filecluster_to_nexus
Combine and filter (.p) log files from Mr.Bayes, BEAST2 and MCMCTREEcombine_log
Remove dummy tip from beast summary trees, accounting for metadata on the tipsdrop.dummy.beast
Remove dummy tip from Mr. Bayes summary trees, accounting for metadata on the tipsdrop.dummy.mb
Density plots for each FBD parameterFBD_dens_plot
Inspect FBD parameter distributions visuallyFBD_normality_plot
Convert an FBD posterior parameter table from wide to long formatFBD_reshape
Summarize FBD posterior parameter estimatesFBD_summary
Test assumptions of normality and homoscedasticity for FBD posterior parametersFBD_tests1
Test for differences in FBD parameter valuesFBD_tests2
Extract evolutionary rates from Bayesian clock trees produced by BEAST2get_clockrate_table_BEAST2
Extract evolutionary rates from a Bayesian clock tree produced by Mr. Bayesget_clockrate_table_MrBayes
Compute Gower distances between charactersget_gower_dist
Conduct pairwise t-tests between node rates and clock base rates from a BEAST2 output.get_pwt_rates_BEAST2
Conduct pairwise t-tests between node rates and clock base rate from a Mr.Bayes output.get_pwt_rates_MrBayes
Calculate silhouette widths index for various numbers of partitionsget_sil_widths plot.sil_width_df
Estimate and plot character partitionsmake_clusters plot.cluster_df
Convert trees produced by a BEAST2 FBD analysis with offset to trees with correct ages.offset.to.dummy
Convert trees produced by a BEAST2 FBD analysis with offset to trees with correct ages, accounting for possible metadata on the tips.offset.to.dummy.metadata
Plots distribution of background rates extracted from posterior log files.plot_back_rates
Plot Bayesian evolutionary tree with rate thresholds for selection modeplot_treerates_sgn
Multiple phylogenetic clock treespost_trees
Posterior parameter samples (single clock)posterior1p
Posterior parameter samples (3 clock partions)posterior3p
Mean clock rates by node and clade (single clock)RateTable_Means_1p_Clades
Mean clock rates by node and clade (3 clock partitions)RateTable_Means_3p_Clades
BEAST2 phylogenetic tree with clock rates from partition 1tree_clock1
BEAST2 phylogenetic tree with clock rates from partition 2tree_clock2
Phylogenetic tree with a single clock partitiontree1p
Phylogenetic tree with 3 clock partitionstree3p
Write character partitions as separate Nexus files (for use in BEAUti)write_partitioned_alignments
Write alignment partitions as separate alignment files for various data typeswrite_partitioned_alignments2
Export multiple treedata objects (S4 class tree files) to BEAST NEXUS filewrite.beast.treedata