Package: EvoPhylo 0.3.3

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_0.3.3.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

Datasets:

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

On CRAN:

27 exports 4 stars 1.19 score 163 dependencies 7 scripts 265 downloads

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_reshape clockrate_dens_plot clockrate_reg_plot clockrate_summary cluster_to_nexus combine_log drop.dummy.beast drop.dummy.mb FBD_dens_plot FBD_normality_plot FBD_reshape FBD_summary FBD_tests1 FBD_tests2 get_clockrate_table_BEAST2 get_clockrate_table_MrBayes get_gower_dist get_pwt_rates_BEAST2 get_pwt_rates_MrBayes get_sil_widths make_clusters offset.to.dummy offset.to.dummy.metadata plot_back_rates plot_treerates_sgn write_partitioned_alignments write.beast.treedata

Dependencies:ape aplot askpass base64enc brew brio bslib cachem callr cli clipr cluster clusterGeneration coda codetools colorspace combinat commonmark cpp11 crayon credentials curl deeptime DEoptim desc devtools diffobj digest doParallel downlit dplyr ellipsis evaluate expm fansi farver fastmap fastmatch fontawesome foreach fs generics geomtextpath gert ggfittext ggforce ggfun ggnewscale ggplot2 ggplotify ggrepel ggseqlogo ggtree gh gitcreds glue gridExtra gridGraphics gridtext gtable highr htmltools htmlwidgets httpuv httr2 igraph ini isoband iterators jpeg jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr maps markdown MASS Matrix memoise mgcv mime miniUI mnormt munsell nlme numDeriv openssl optimParallel patchwork phangorn phytools pillar pkgbuild pkgconfig pkgdown pkgload png polyclip praise prettyunits processx profvis promises ps purrr quadprog R6 ragg rappdirs rcmdcheck RColorBrewer Rcpp RcppEigen rematch2 remotes rlang rmarkdown roxygen2 rprojroot rstudioapi Rtsne rversions sass scales scatterplot3d sessioninfo shades shiny sourcetools stringi stringr sys systemfonts testthat textshaping tibble tidyr tidyselect tidytree tinytex treeio tweenr unglue urlchecker usethis utf8 vctrs viridisLite waldo whisker withr xfun xml2 xopen xtable yaml yulab.utils zip

Analyzing FBD Parameters

Rendered fromfbd-params.Rmdusingknitr::rmarkdownon Aug 10 2024.

Last update: 2022-11-03
Started: 2022-05-04

Analyzing Trees With Offsets

Rendered fromoffset_handling.Rmdusingknitr::rmarkdownon Aug 10 2024.

Last update: 2022-10-31
Started: 2022-06-24

Character Partitioning

Rendered fromchar-part.Rmdusingknitr::rmarkdownon Aug 10 2024.

Last update: 2022-11-02
Started: 2022-05-04

Evolutionary Rates & Selection Mode (BEAST2)

Rendered fromrates-selection_BEAST2.Rmdusingknitr::rmarkdownon Aug 10 2024.

Last update: 2022-11-02
Started: 2022-10-28

Evolutionary Rates & Selection Mode (Mr.Bayes)

Rendered fromrates-selection_MrBayes.Rmdusingknitr::rmarkdownon Aug 10 2024.

Last update: 2023-07-21
Started: 2022-10-31

Theoretical background

Rendered fromdata_treatment.Rmdusingknitr::rmarkdownon Aug 10 2024.

Last update: 2022-09-29
Started: 2022-06-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A morphological phylogenetic data matrix	characters
Convert clock rate tables from wide to long format	clock_reshape
Plot clock rate distributions	clockrate_dens_plot
Plot regression lines between sets of rates	clockrate_reg_plot
Compute rate summary statistics across clades and clocks	clockrate_summary
Export character partitions to a Nexus file	cluster_to_nexus
Combine and filter (.p) log files from Mr.Bayes	combine_log
Remove dummy tip from beast summary trees, accounting for metadata on the tips	drop.dummy.beast
Remove dummy tip from Mr. Bayes summary trees, accounting for metadata on the tips	drop.dummy.mb
Density plots for each FBD parameter	FBD_dens_plot
Inspect FBD parameter distributions visually	FBD_normality_plot
Convert an FBD posterior parameter table from wide to long format	FBD_reshape
Summarize FBD posterior parameter estimates	FBD_summary
Test assumptions of normality and homoscedasticity for FBD posterior parameters	FBD_tests1
Test for differences in FBD parameter values	FBD_tests2
Extract evolutionary rates from Bayesian clock trees produced by BEAST2	get_clockrate_table_BEAST2
Extract evolutionary rates from a Bayesian clock tree produced by Mr. Bayes	get_clockrate_table_MrBayes
Compute Gower distances between characters	get_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 partitions	get_sil_widths plot.sil_width_df
Estimate and plot character partitions	make_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 mode	plot_treerates_sgn
Multiple phylogenetic clock trees	post_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 1	tree_clock1
BEAST2 phylogenetic tree with clock rates from partition 2	tree_clock2
Phylogenetic tree with a single clock partition	tree1p
Phylogenetic tree with 3 clock partitions	tree3p
Write character partitions as separate Nexus files (for use in BEAUti)	write_partitioned_alignments
Export multiple treedata objects (S4 class tree files) to BEAST NEXUS file	write.beast.treedata