Rphylopars: Phylogenetic Comparative Tools for Missing Data and Within-Species Variation

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Tools for performing phylogenetic comparative methods for datasets with with multiple observations per species (intraspecific variation or measurement error) and/or missing data. Performs ancestral state reconstruction and missing data imputation on the estimated evolutionary model, which can be specified as Brownian Motion, Ornstein-Uhlenbeck, Early-Burst, Pagel's lambda, kappa, or delta, or a star phylogeny.

Author
Eric W. Goolsby, Jorn Bruggeman, Cecile Ane
Date of publication
2016-06-16 18:26:19
Maintainer
Eric W. Goolsby <eric.goolsby.evolution@gmail.com>
License
GPL (>= 2)
Version
0.2.9
URLs

View on CRAN

Man pages

anc.recon
Ultra-fast maximum likelihood ancestral state reconstruction
anova.phylopars.lm
Phylopars regression ANOVA
fast.SSC
Fast Phylogenetic Signal Using Sum of Squared Changes (SSC)
logLik.phylopars
Extract Log_likelihood
logLik.phylopars.lm
Extract Log_likelihood
phylopars
Estimation of phylogenetic and phenotypic covariance...
phylopars.lm
Rphylopars regression
print.phylopars
Print phylopars
print.phylopars.lm
Print phylopars.lm
print.SSC
Print SSC
Rphylopars-package
Phylogenetic Comparative Tools for Missing Data and...
simtraits
Simulate traits for phylopars estimation
summary.phylopars
Phylopars summary
summary.phylopars.lm
phylopars.lm summary
write.phylopars
Write data and tree files for Python phylopars compatability.

Files in this package

Rphylopars
Rphylopars/src
Rphylopars/src/Makevars
Rphylopars/src/phylopars_rcpp.cpp
Rphylopars/src/Makevars.win
Rphylopars/src/RcppExports.cpp
Rphylopars/NAMESPACE
Rphylopars/R
Rphylopars/R/phylopars_main.R
Rphylopars/R/RcppExports.R
Rphylopars/R/phylopars_update.R
Rphylopars/README.md
Rphylopars/MD5
Rphylopars/DESCRIPTION
Rphylopars/man
Rphylopars/man/write.phylopars.Rd
Rphylopars/man/fast.SSC.Rd
Rphylopars/man/anova.phylopars.lm.Rd
Rphylopars/man/logLik.phylopars.Rd
Rphylopars/man/phylopars.lm.Rd
Rphylopars/man/phylopars.Rd
Rphylopars/man/logLik.phylopars.lm.Rd
Rphylopars/man/print.phylopars.Rd
Rphylopars/man/Rphylopars-package.Rd
Rphylopars/man/summary.phylopars.Rd
Rphylopars/man/simtraits.Rd
Rphylopars/man/anc.recon.Rd
Rphylopars/man/print.SSC.Rd
Rphylopars/man/print.phylopars.lm.Rd
Rphylopars/man/summary.phylopars.lm.Rd