Package: PHYLOGR 1.0.11

Ramon Diaz-Uriarte

PHYLOGR: Functions for Phylogenetically Based Statistical Analyses

Manipulation and analysis of phylogenetically simulated data sets and phylogenetically based analyses using GLS.

Authors:Ramon Diaz-Uriarte <[email protected]> and Theodore Garland, Jr <[email protected]>

PHYLOGR_1.0.11.tar.gz
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PHYLOGR.pdf |PHYLOGR.html✨
PHYLOGR/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/rdiaz02/phylogr/issues

Datasets:

On CRAN:

11 exports 1.59 score 0 dependencies 4 mentions 26 scripts 282 downloads

Last updated 4 years agofrom:973387e086. Checks:OK: 1 NOTE: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKAug 31 2024
R-4.5-winNOTEAug 31 2024
R-4.5-linuxNOTEAug 31 2024
R-4.4-winNOTEAug 31 2024
R-4.4-macNOTEAug 31 2024
R-4.3-winNOTEAug 31 2024
R-4.3-macNOTEAug 31 2024

Exports:cancor.phylogcor.originlm.phylogmatrix.Dphylog.gls.fitprcomp.phylogread.inp.dataread.pdi.dataread.phylip.dataread.phylog.matrixread.sim.data

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Canonical Correlation Analysis from Simulated Data Setscancor.phylog
Correlation Through the Origincor.origin
Independet contrasts for Garland \& Janis data setGarlandJanis.IC
Garland \& Janis's 1993 data on mammalian running speed and limb lengthGarlandJanis.Original
Phylogenetic variance-covariance matrix for Garland \& Janis (1993).GarlandJanis.varcov
Helper functionsnum.sim.tips number.of.simulations number.of.tips.inp number.of.tips.pdi number.of.tips.sim scan.inp.file scan.pdi.file scan.simulation.file tips.names.inp tips.names.pdi
Independet contrasts for Bauwens and Diaz-Uriarte (1997) lacertid data setLacertid.IC
Bauwens and Diaz-Uriarte (1997) lacertid dataLacertid.Original
Variance-covariance matrix for lacertids from Bauwens and Diaz-uriarte (1997)Lacertid.varcov
Linear Models from Simulated Data Setslm.phylog
Produce the Matrix D of Garland and Ives (2000) for GLSmatrix.D
Phylogenetically-Based GLS Model Fittingphylog.gls.fit
Plot a phylog.cancor objectplot.phylog.cancor
Plot a phylog.lm objectplot.phylog.lm
Plot a phylog.prcomp objectplot.phylog.prcomp
Principal Components Analysis from Simulated Data Setsprcomp.phylog
Printing summaries of PHYLOGR statistical functionsprint.summary.phylog.cancor print.summary.phylog.lm print.summary.phylog.prcomp
Read Inp Data Filesread.inp.data
Read Pdi Data Filesread.pdi.data
Read Phylip Infile Data Filesread.phylip.data
Read a Phylogenetic Covariance Matrixread.phylog.matrix
Read Sim Files From PDSIMULread.sim.data
A simulated data setSimulExample
Summarize a phylog.cancor objectsummary.phylog.cancor
Summarize a phylog.lm objectsummary.phylog.lm
Summarize a phylog.prcomp objectsummary.phylog.prcomp