Package: OUwie 2.13

OUwie: Analysis of Evolutionary Rates in an OU Framework

Estimates rates for continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck based Hansen models that allow both the strength of the pull and stochastic motion to vary across selective regimes. Beaulieu et al (2012).

Authors:Jeremy M. Beaulieu <[email protected]>, Brian O'Meara <[email protected]>

OUwie_2.13.tar.gz
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OUwie.pdf |OUwie.html✨
OUwie/json (API)

# Install 'OUwie' in R:
install.packages('OUwie', repos = c('https://thej022214.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/thej022214/ouwie/issues

Datasets:
  • trait - An example dataset
  • trait - An example dataset
  • tree - An example dataset
  • tree - An example dataset

On CRAN:

8.12 score 9 stars 148 scripts 748 downloads 22 mentions 19 exports 86 dependencies

Last updated 2 months agofrom:892d71dacf. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-winOKSep 27 2024
R-4.5-linuxOKOct 27 2024
R-4.4-winOKOct 27 2024
R-4.4-macOKOct 27 2024
R-4.3-winOKOct 27 2024
R-4.3-macOKOct 27 2024

Exports:check.identifyfix.kappagetModelAvgParamsgetModelTablegetOUParamStructurehOUwiehOUwie.fixedhOUwie.reconhOUwie.simhOUwie.thoroughhOUwie.walkOUwieOUwie.ancOUwie.bootOUwie.contourOUwie.dredgeOUwie.fixedOUwie.formatOUwie.sim

Dependencies:apebitopscliclusterGenerationcodacodetoolscolorspacecombinatcorHMMcorpcorcpp11data.tabledeldirDEoptimdeSolvedigestdoParallelexpmfansifarverfastmatchforeachfuturefuture.applygeigergenericsGenSAggplot2globalsgluegmpgridExtragtableigraphinterpisobanditeratorsjsonlitelabelinglatticelhslifecyclelistenvmagrittrmapsMASSMatrixmgcvmnormtmunsellmvtnormncbitnlmenloptrnnetnumDerivoptimParallelpaleotreeparallellyphangornphylolmphytoolspillarpkgconfigplyrpngquadprogR6RColorBrewerRcppRcppEigenRCurlreshape2rlangRmpfrscalesscatterplot3dstringistringrsubplextibbleutf8vctrsviridisviridisLitewithr

hOUwie User Guide

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Rendered fromhOUwieStarterGuide.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2023-01-19
Started: 2023-01-18

New additions as of OUwie 2.1

Jeremy M. Beaulieu and Brian C. O'Meara

Rendered fromOUwie_2.1_adds.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2024-08-27
Started: 2020-05-12

Readme and manuals

Help Manual

Help pageTopics
A test of regime identifiabilitycheck.identify
Propose new values This proposes new values using a normal distribution centered on the original parameter values, with desired standard deviation. If any proposed values are outside the bounds, it will propose again.dent_propose
Sample points from along a ridgedent_walk
An example datasettrait tree
Adjust tree for matrix conditionfix.kappa
Model average the parameter estimates over severl hOUwie fits.getModelAvgParams
Generate a table from a set of hOUwie models describing their relative fit to data.getModelTable
Generate a continuous model parameter structuregetOUParamStructure
Fit a joint model of discrete and continuous characters via maximum-likelihood.hOUwie
Fit a joint model of discrete and continuous characters via maximum-likelihood with fixed regimes.hOUwie.fixed
Reconstruct the marginal probability of discrete node states under the hOUwie model.hOUwie.recon
Simulate a discrete and continuous character following a Markov and Ornstein-Uhlenbeck model.hOUwie.sim
Rerun a set of hOUwie models with the best mappings of the set.hOUwie.thorough
Sample points from along a ridge for a hOUwie modelhOUwie.walk
Generalized Hansen modelsOUwie
Estimate ancestral states given a fitted OUwie modelOUwie.anc
Parametric bootstrap functionOUwie.boot
Generates data for contour plot of likelihood surfaceOUwie.contour
Generalized Detection of shifts in OU processOUwie.dredge
Generalized Hansen model likelihood calculatorOUwie.fixed
Format data and tree for OUwieOUwie.format
Generalized Hansen model simulatorOUwie.sim
Plot the dented samples This will show the univariate plots of the parameter values versus the likelihood as well as bivariate plots of pairs of parameters to look for ridges.plot.dentist
Contour plotplot.OUwie.contour
Print dentist print summary of output from dent_walkprint.dentist
Summarize dentist Display summary of output from dent_walksummary.dentist