PHYLOGR: Functions for Phylogenetically Based Statistical Analyses

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

Author
Ramon Diaz-Uriarte <rdiaz@cnio.es> and Theodore Garland, Jr <theodore.garland@ucr.edu>
Date of publication
2014-11-10 01:39:39
Maintainer
Ramon Diaz-Uriarte <rdiaz02@gmail.com>
License
GPL (>= 2)
Version
1.0.8
URLs

View on CRAN

Man 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...
GarlandJanis.varcov
Phylogenetic variance-covariance matrix for Garland & Janis...
Helper.functions
Helper functions
Lacertid.IC
Independet contrasts for Bauwens and Diaz-Uriarte (1997)...
Lacertid.Original
Bauwens and Diaz-Uriarte (1997) lacertid data
Lacertid.varcov
Variance-covariance matrix for lacertids from Bauwens and...
lm.phylog
Linear Models from Simulated Data Sets
matrix.D
Produce the Matrix D of Garland and Ives (2000) for GLS
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
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
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

Files in this package

PHYLOGR
PHYLOGR/COPYING
PHYLOGR/inst
PHYLOGR/inst/Examples
PHYLOGR/inst/Examples/iclag.pdi
PHYLOGR/inst/Examples/49hmt.sim
PHYLOGR/inst/Examples/49hmt.inp
PHYLOGR/inst/Examples/49ms.sim
PHYLOGR/inst/Examples/ifsmi.pdi
PHYLOGR/inst/Examples/icfxx.sim
PHYLOGR/inst/Examples/ihshw.sim
PHYLOGR/inst/Examples/ihshw.fic
PHYLOGR/inst/Examples/49ms.fic
PHYLOGR/inst/Examples/49lbr.pdi
PHYLOGR/inst/Examples/ihshw.pdi
PHYLOGR/inst/Examples/49hmt.pdi
PHYLOGR/inst/Examples/ifsmi.sim
PHYLOGR/inst/Examples/49hmt.fic
PHYLOGR/inst/Examples/49lbr.inp
PHYLOGR/inst/Examples/Rplots.ps
PHYLOGR/inst/Examples/iclag.sim
PHYLOGR/inst/Examples/49ms.dsc
PHYLOGR/inst/Examples/LacertidData.PhylipIntree
PHYLOGR/inst/Examples/49ms.pdi
PHYLOGR/inst/Examples/Examples-code.R
PHYLOGR/inst/Examples/LacertidData.PhylipInfile
PHYLOGR/inst/Examples/Index
PHYLOGR/inst/Examples/iclag.fic
PHYLOGR/inst/Examples/ifsmi.fic
PHYLOGR/inst/Examples/icfxx.pdi
PHYLOGR/inst/Examples/ifsmi.dsc
PHYLOGR/inst/Examples/Examples.pdf
PHYLOGR/inst/Examples/49lbr.sim
PHYLOGR/inst/Examples/icfxx.fic
PHYLOGR/NAMESPACE
PHYLOGR/data
PHYLOGR/data/GarlandJanis.Original.txt.gz
PHYLOGR/data/Lacertid.varcov.txt.gz
PHYLOGR/data/GarlandJanis.varcov.txt.gz
PHYLOGR/data/SimulExample.txt.gz
PHYLOGR/data/Lacertid.IC.txt.gz
PHYLOGR/data/GarlandJanis.IC.txt.gz
PHYLOGR/data/Lacertid.Original.txt.gz
PHYLOGR/R
PHYLOGR/R/PHYLOGR.R
PHYLOGR/MD5
PHYLOGR/DESCRIPTION
PHYLOGR/man
PHYLOGR/man/plot.phylog.lm.Rd
PHYLOGR/man/read.pdi.data.Rd
PHYLOGR/man/summary.phylog.lm.Rd
PHYLOGR/man/cor.origin.Rd
PHYLOGR/man/read.sim.data.Rd
PHYLOGR/man/Lacertid.varcov.Rd
PHYLOGR/man/matrix.D.Rd
PHYLOGR/man/Lacertid.IC.Rd
PHYLOGR/man/cancor.phylog.Rd
PHYLOGR/man/Helper.functions.Rd
PHYLOGR/man/summary.phylog.prcomp.Rd
PHYLOGR/man/SimulExample.Rd
PHYLOGR/man/phylog.gls.fit.Rd
PHYLOGR/man/GarlandJanis.IC.Rd
PHYLOGR/man/GarlandJanis.varcov.Rd
PHYLOGR/man/GarlandJanis.Original.Rd
PHYLOGR/man/prcomp.phylog.Rd
PHYLOGR/man/read.phylog.matrix.Rd
PHYLOGR/man/lm.phylog.Rd
PHYLOGR/man/plot.phylog.prcomp.Rd
PHYLOGR/man/print.summary.phylog.Rd
PHYLOGR/man/plot.phylog.cancor.Rd
PHYLOGR/man/read.phylip.data.Rd
PHYLOGR/man/Lacertid.Original.Rd
PHYLOGR/man/summary.phylog.cancor.Rd
PHYLOGR/man/read.inp.data.Rd
PHYLOGR/INDEX
PHYLOGR/CHANGES