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PHYLOGR (version 1.0.11)

Functions for Phylogenetically Based Statistical Analyses

Description

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

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Version

Install

install.packages('PHYLOGR')

Monthly Downloads

223

Version

1.0.11

License

GPL (>= 2)

Maintainer

Ramon Diaz-Uriarte

Last Published

April 14th, 2020

Functions in PHYLOGR (1.0.11)

print.summary.phylog

Printing summaries of PHYLOGR statistical functions
prcomp.phylog

Principal Components Analysis from Simulated Data Sets
cancor.phylog

Canonical Correlation Analysis from Simulated Data Sets
Lacertid.varcov

Variance-covariance matrix for lacertids from Bauwens and Diaz-uriarte (1997)
read.phylip.data

Read Phylip Infile Data Files
cor.origin

Correlation Through the Origin
GarlandJanis.Original

Garland \& Janis's 1993 data on mammalian running speed and limb length
GarlandJanis.IC

Independet contrasts for Garland \& Janis data set
matrix.D

Produce the Matrix D of Garland and Ives (2000) for GLS
Lacertid.Original

Bauwens and Diaz-Uriarte (1997) lacertid data
Lacertid.IC

Independet contrasts for Bauwens and Diaz-Uriarte (1997) lacertid data set
read.phylog.matrix

Read a Phylogenetic Covariance Matrix
SimulExample

A simulated data set
plot.phylog.cancor

Plot a phylog.cancor object
summary.phylog.cancor

Summarize a phylog.cancor object
lm.phylog

Linear Models from Simulated Data Sets
read.pdi.data

Read Pdi Data Files
summary.phylog.prcomp

Summarize a phylog.prcomp object
summary.phylog.lm

Summarize a phylog.lm object
phylog.gls.fit

Phylogenetically-Based GLS Model Fitting
plot.phylog.lm

Plot a phylog.lm object
plot.phylog.prcomp

Plot a phylog.prcomp object
read.sim.data

Read Sim Files From PDSIMUL
read.inp.data

Read Inp Data Files
GarlandJanis.varcov

Phylogenetic variance-covariance matrix for Garland \& Janis (1993).
Helper.functions

Helper functions