Package: POUMM 2.1.7

POUMM: The Phylogenetic Ornstein-Uhlenbeck Mixed Model

The Phylogenetic Ornstein-Uhlenbeck Mixed Model (POUMM) allows to estimate the phylogenetic heritability of continuous traits, to test hypotheses of neutral evolution versus stabilizing selection, to quantify the strength of stabilizing selection, to estimate measurement error and to make predictions about the evolution of a phenotype and phenotypic variation in a population. The package implements combined maximum likelihood and Bayesian inference of the univariate Phylogenetic Ornstein-Uhlenbeck Mixed Model, fast parallel likelihood calculation, maximum likelihood inference of the genotypic values at the tips, functions for summarizing and plotting traces and posterior samples, functions for simulation of a univariate continuous trait evolution model along a phylogenetic tree. So far, the package has been used for estimating the heritability of quantitative traits in macroevolutionary and epidemiological studies, see e.g. Bertels et al. (2017) <doi:10.1093/molbev/msx246> and Mitov and Stadler (2018) <doi:10.1093/molbev/msx328>. The algorithm for parallel POUMM likelihood calculation has been published in Mitov and Stadler (2019) <doi:10.1111/2041-210X.13136>.

Authors:Venelin Mitov [aut, cre, cph], Matt Dowle [ctb]

POUMM_2.1.7.tar.gz
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POUMM.pdf |POUMM.html
POUMM/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/venelin/poumm/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

4.94 score 4 stars 22 scripts 286 downloads 1 mentions 37 exports 41 dependencies

Last updated 4 years agofrom:e55e66ab71. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 26 2024
R-4.5-win-x86_64NOTEOct 26 2024
R-4.5-linux-x86_64NOTEOct 26 2024
R-4.4-win-x86_64NOTEOct 26 2024
R-4.4-mac-x86_64NOTEOct 26 2024
R-4.4-mac-aarch64NOTEOct 26 2024
R-4.3-win-x86_64NOTEOct 26 2024
R-4.3-mac-x86_64NOTEOct 26 2024
R-4.3-mac-aarch64NOTEOct 26 2024

Exports:alphacovFunPOUMMcovHPDFunPOUMMcovPOUMMcovVTipsGivenTreePOUMMdOUdVNodesGivenTreePOUMMH2H2elikPOUMMGivenTreeVTipslikPOUMMGivenTreeVTipsCmeanOUnodeTimesPOUMMPOUMMIsADevReleasepruneTreerOUrTrajectoryOUrVNodesGivenTreePOUMMsdOUsigmaesigmaOUsimulatePOUMMLikelihoodMainLoopsimulateTraitspecifyPMMspecifyPMM_H2tMeanSespecifyPMM_H2tMeanSeG0specifyPMM_SSeG0specifyPOUMMspecifyPOUMM_ATH2tMeanSespecifyPOUMM_ATH2tMeanSeG0specifyPOUMM_ATSspecifyPOUMM_ATSG0specifyPOUMM_ATSSeG0statisticsvalidateSpecPOUMMvarOU

Dependencies:adaptMCMCapeclicodacodetoolscolorspacedata.tabledigestfansifarverforeachggplot2gluegtableisobanditeratorslabelinglamWlatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6ramcmcRColorBrewerRcppRcppArmadilloRcppParallelrlangscalestibbleutf8vctrsviridisLitewithr

A User Guide to the POUMM R-package

Rendered fromUserGuide.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2019-04-08
Started: 2017-03-09

Interpreting the POUMM

Rendered fromInterpretingPOUMM.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2019-12-07
Started: 2018-01-04

Readme and manuals

Help Manual

Help pageTopics
Extract data from an MCMC chain This is an internal function.analyseMCMCs
Node indices of the direct descendants of n in the phylogeny.chld
Extract maximum likelihood fitted parameters (coefficients) from a fitted POUMM model.coef.POUMM
A vectorized expected covariance function for a given tree and a fitted POUMM modelcovFunPOUMM
A vectorized function returning HPD intervals of the expected covariance for a given tree and a fitted POUMM modelcovHPDFunPOUMM
Expected covariance of two tips at given root-tip time and phylogenetic distancecovPOUMM
Variance covariance matrix of the values at the tips of a tree under an OU processcovVTipsGivenTreePOUMM
Multivariate density of observed values along a tree given an OU process of evolution and root-valuedVNodesGivenTreePOUMM
Edge indices of the edges in tree starting from nedgesFrom
Extract maximum likelihood expected genotypic values at the tips of a tree, to which a POUMM model has been previously fittedfitted.POUMM
Distribution of the genotypic values under a POUMM fitgPOUMM
Phylogenetic heritability estimated at time tH2
Density of observed tip-values given a tree, assuming Ornstein-Uhlenbeck process for the genetic contributions along the tree and normally distributed environmental deviations.dVTipsGivenTreePOUMM likPOUMMGivenTreeVTips
Fast (parallel) POUMM likelihood calculation using the SPLITT librarylikPOUMMGivenTreeVTipsC
Processing of the root value and calculation of the maximum log-likelihood for the given coefficients abc, and parameters theta, g0 and g0Prior. This is an internal function.loglik_abc_g0_g0Prior
Extract maximum likelihood and degrees of freedom from a fitted POUMM modellogLik.POUMM
Find a maximum likelihood fit of the POUMM modelmaxLikPOUMMGivenTreeVTips
MCMC-sampling from a posterior distribution of a P(OU)MM model given tree, values at the tips and a prior distributionmcmc.poumm mcmcPOUMMGivenPriorTreeVTips
Number of tips in a phylogenetic tree, POUMM has been fit on.nobs.POUMM
Calculate the time from the root to each node of the treenodeTimes
Distribution of an Ornstein-Uhlenbeck Process at Time t, Given Initial State at Time 0dOU meanOU OU rOU sdOU varOU
Phylogenetic Heritabilityalpha H2e PhylogeneticH2 sigmae sigmaOU
Plots of a POUMM-fitplot.POUMM
Plot a summary of a POUMM fitplot.summary.POUMM
The Phylogenetic (Ornstein-Uhlenbeck) Mixed ModelPOUMM
Check if the POUMM version correpsonds to a dev releasePOUMMIsADevRelease
Extract information for fast likelihood calculation using the breadth-first pruning algorithm.pruneTree
Extract maximum likelihood environmental contributions (residuals) at the tips of a tree, to which a POUMM model has been fitted.residuals.POUMM
Generation of a random trajectory of an OU process starting from a given initial staterTrajectoryOU
Generation of a random trajectory of an OU process starting from a given initial state (only for test purpose)rTrajectoryOUDef
Random generation of values along a phylogenetic tree following a branching OU processrVNodesGivenTreePOUMM
Writes verbose messages of the order of tree traversal during likelihood calculationsimulatePOUMMLikelihoodMainLoop
Simulate a trait on a tree under a ML fit of the POUMM modelsimulateTrait
Specifying a POUMM fitspecifyPMM specifyPMM_H2tMeanSe specifyPMM_H2tMeanSeG0 specifyPMM_SSeG0 specifyPOUMM specifyPOUMM_ATH2tMeanSe specifyPOUMM_ATH2tMeanSeG0 specifyPOUMM_ATS specifyPOUMM_ATSG0 specifyPOUMM_ATSSeG0 specPOUMM
Extract statistics from sampled or inferred parameters of a POUMM fitstatistics statistics.POUMM
Summarize the results of a POUMM-fitsummary.POUMM
Validate a POUMM specificationvalidateSpecPOUMM
Validate phenotypic values and phylogenetic treevalidateZTree
Cached objects for the POUMM vignettes and examplesvignetteCachedResults