R: Functions for Phylogenetically Based Statistical Analyses

# Functions for Phylogenetically Based Statistical Analyses

## Documentation for package ‘PHYLOGR’ version 1.0.11

- DESCRIPTION file.
- Package NEWS.

## Help Pages

cancor.phylog | Canonical Correlation Analysis from Simulated Data Sets
cor.origin | Correlation Through the Origin
GarlandJanis.IC | Independet contrasts for Garland & Janis data set
GarlandJanis.Original | Garland & Janis's 1993 data on mammalian running speed and limb length
GarlandJanis.varcov | Phylogenetic variance-covariance matrix for Garland & Janis (1993).
Lacertid.IC | Independet contrasts for Bauwens and Diaz-Uriarte (1997) lacertid data set
Lacertid.Original | Bauwens and Diaz-Uriarte (1997) lacertid data
Lacertid.varcov | Variance-covariance matrix for lacertids from Bauwens and Diaz-uriarte (1997)
lm.phylog | Linear Models from Simulated Data Sets
matrix.D | Produce the Matrix D of Garland and Ives (2000) for GLS
num.sim.tips | Helper functions
number.of.simulations | Helper functions
number.of.tips.inp | Helper functions
number.of.tips.pdi | Helper functions
number.of.tips.sim | Helper functions
phylog.gls.fit | Phylogenetically-Based GLS Model Fitting
plot.phylog.cancor | Plot a phylog.cancor object
plot.phylog.lm | Plot a phylog.lm object
plot.phylog.prcomp | Plot a phylog.prcomp object
prcomp.phylog | Principal Components Analysis from Simulated Data Sets
print.summary.phylog.cancor | Printing summaries of PHYLOGR statistical functions
print.summary.phylog.lm | Printing summaries of PHYLOGR statistical functions
print.summary.phylog.prcomp | Printing summaries of PHYLOGR statistical functions
read.inp.data | Read Inp Data Files
read.pdi.data | Read Pdi Data Files
read.phylip.data | Read Phylip Infile Data Files
read.phylog.matrix | Read a Phylogenetic Covariance Matrix
read.sim.data | Read Sim Files From PDSIMUL
scan.inp.file | Helper functions
scan.pdi.file | Helper functions
scan.simulation.file | Helper functions
SimulExample | A simulated data set
summary.phylog.cancor | Summarize a phylog.cancor object
summary.phylog.lm | Summarize a phylog.lm object
summary.phylog.prcomp | Summarize a phylog.prcomp object
tips.names.inp | Helper functions
tips.names.pdi | Helper functions