Package: Rphylopars 0.3.9

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

Tools for performing phylogenetic comparative methods for datasets with with multiple observations per species (intraspecific variation or measurement error) and/or missing data (Goolsby et al. 2017). 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.

Authors:Eric W. Goolsby [aut, cre], Jorn Bruggeman [aut], Cecile Ane [aut]

Rphylopars_0.3.9.tar.gz
Rphylopars_0.3.9.zip(r-4.7)Rphylopars_0.3.9.zip(r-4.6)Rphylopars_0.3.9.zip(r-4.5)
Rphylopars_0.3.9.tgz(r-4.6-x86_64)Rphylopars_0.3.9.tgz(r-4.6-arm64)Rphylopars_0.3.9.tgz(r-4.5-x86_64)Rphylopars_0.3.9.tgz(r-4.5-arm64)
Rphylopars_0.3.9.tar.gz(r-4.7-arm64)Rphylopars_0.3.9.tar.gz(r-4.7-x86_64)Rphylopars_0.3.9.tar.gz(r-4.6-arm64)Rphylopars_0.3.9.tar.gz(r-4.6-x86_64)
Rphylopars_0.3.9.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Rphylopars/json (API)

# Install 'Rphylopars' in R:

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

Bug tracker:https://github.com/ericgoolsby/rphylopars/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

On CRAN:

openblas cpp

7.08 score 32 stars 1 packages 126 scripts 633 downloads 11 mentions 14 exports 78 dependencies

Last updated from:284efae471. Checks:11 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	WARNING	220
linux-devel-x86_64	WARNING	193
source / vignettes	OK	247
linux-release-arm64	WARNING	183
linux-release-x86_64	WARNING	251
macos-release-arm64	WARNING	162
macos-release-x86_64	WARNING	291
macos-oldrel-arm64	WARNING	169
macos-oldrel-x86_64	WARNING	262
windows-devel	WARNING	179
windows-release	WARNING	173
windows-oldrel	WARNING	277
wasm-release	OK	136

Exports:anc.recon anova.phylopars.lm fast.SSC logLik.phylopars logLik.phylopars.lm phylopars phylopars.lm print.phylopars print.phylopars.lm print.SSC simtraits summary.phylopars summary.phylopars.lm write.phylopars

Dependencies:ape backports boot broom cli clusterGeneration coda codetools colorspace combinat cowplot cpp11 DEoptim Deriv digest doBy doParallel dplyr expm farver fastmatch foreach forecast fracdiff future future.apply generics ggplot2 globals glue gtable igraph isoband iterators labeling lattice lifecycle listenv lmtest magrittr maps MASS Matrix microbenchmark mnormt modelr nlme nnet numDeriv optimParallel parallelly phangorn phylolm phytools pillar pkgconfig purrr quadprog R6 RColorBrewer Rcpp RcppArmadillo rlang S7 scales scatterplot3d stringi stringr tibble tidyr tidyselect timeDate urca utf8 vctrs viridisLite withr zoo

Citation

Development and contributors

Readme and manuals

Help Manual

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