This package is considered a duplicate. The official version of this package is found at:https://emvolz.r-universe.dev/treedater

Package: treedater 1.0.2

Erik Volz

treedater: Fast Molecular Clock Dating of Phylogenetic Trees with Rate Variation

Functions for estimating times of common ancestry and molecular clock rates of evolution using a variety of evolutionary models, parametric and nonparametric bootstrap confidence intervals, methods for detecting outlier lineages, root-to-tip regression, and a statistical test for selecting molecular clock models. For more details see Volz and Frost (2017) <doi:10.1093/ve/vex025>.

Authors:Erik Volz [aut, cre]

treedater_1.0.2.tar.gz
treedater_1.0.2.zip(r-4.7)treedater_1.0.2.zip(r-4.6)treedater_1.0.2.zip(r-4.5)
treedater_1.0.2.tgz(r-4.6-any)treedater_1.0.2.tgz(r-4.5-any)
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treedater_1.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
treedater/json (API)

# Install 'treedater' in R:

install.packages('treedater', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/emvolz/treedater/issues

On CRAN:

7.46 score 27 stars 71 scripts 215 downloads 16 mentions 10 exports 9 dependencies

Last updated from:0095be7e9b. Checks:9 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	OK	127
source / vignettes	OK	352
linux-release-x86_64	OK	120
macos-release-arm64	OK	89
macos-oldrel-arm64	OK	92
windows-devel	OK	89
windows-release	OK	86
windows-oldrel	OK	75
wasm-release	OK	97

Exports:boot dater gibbs_jitter goodnessOfFitPlot outlierLineages outlierTips parboot relaxedClockTest rootToTipRegressionPlot sampleYearsFromLabels

Dependencies:ape digest lattice limSolve lpSolve MASS nlme quadprog Rcpp

Molecular Clock Dating of Influenza H3N2

Rendered fromh3n2.Rmdusingknitr::rmarkdown

Last update: 2025-09-01
Started: 2018-04-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
treedater fits a molecular clock to a phylogenetic tree and estimates evolutionary rates and times of common ancestry.	treedater-package treedater
Estimate of confidence intervals of molecular clock parameters with user-supplied set of bootstrap trees	boot
Estimate a time-scaled tree and fit a molecular clock	dater
Sample node dates conditional on root time using Gibbs sampling and date prior	gibbs_jitter
Produce a goodness of fit plot	goodnessOfFitPlot
Detect lineages with unusually large evolutionary divergence under the fitted treedater model	outlierLineages
Detect terminal lineages with unusually large evolutionary divergence under the fitted treedater model	outlierTips
Estimate of confidence intervals using parametric bootstrap for molecular clock dating.	parboot
Plots lineages through time and confidence intervals estimated by bootstrap.	plot.bootTreedater
Use parametric bootstrap to test if relaxed clock offers improved fit to data.	relaxedClockTest
Plot evolutionary distance from root to sample times and estimated internal node times and regression lines	rootToTipRegressionPlot
Compute a vector of numeric sample times from labels in a sequence alignment or phylogeny	sampleYearsFromLabels