Package: Rphylopars 0.3.9

Eric W. Goolsby

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
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Rphylopars_0.3.9.tgz(r-4.4-x86_64)Rphylopars_0.3.9.tgz(r-4.4-arm64)Rphylopars_0.3.9.tgz(r-4.3-x86_64)Rphylopars_0.3.9.tgz(r-4.3-arm64)
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Rphylopars.pdf |Rphylopars.html✨
Rphylopars/json (API)

# Install 'Rphylopars' in R:

install.packages('Rphylopars', repos = c('https://phylotastic.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:

14 exports 28 stars 3.39 score 74 dependencies 11 mentions 71 scripts 546 downloads

Last updated 2 years agofrom:284efae471. Checks:OK: 4 NOTE: 5. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Sep 06 2024
R-4.5-win-x86_64	NOTE	Sep 06 2024
R-4.5-linux-x86_64	NOTE	Sep 06 2024
R-4.4-win-x86_64	NOTE	Sep 06 2024
R-4.4-mac-x86_64	NOTE	Sep 06 2024
R-4.4-mac-aarch64	NOTE	Sep 06 2024
R-4.3-win-x86_64	OK	Sep 06 2024
R-4.3-mac-x86_64	OK	Sep 06 2024
R-4.3-mac-aarch64	OK	Sep 06 2024

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 fansi farver fastmatch foreach future future.apply generics ggplot2 ggseqlogo globals glue gtable igraph isoband iterators labeling lattice lifecycle listenv magrittr maps MASS Matrix mgcv microbenchmark mnormt modelr munsell nlme numDeriv optimParallel parallelly phangorn phylolm phytools pillar pkgconfig purrr quadprog R6 RColorBrewer Rcpp RcppArmadillo rlang scales scatterplot3d stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

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