PHYLOGR (version 1.0.11)

GarlandJanis.IC: Independet contrasts for Garland \& Janis data set

Description

Independent contrast for Garland \& Janis (1993) data set; they are based on the data in the file GarlandJanis.Original using the phylogeny in Garland et al. (1993) --- see GarlandJanis.varcov

Format

The data frame contains seven columns. The first four columns are the (standardized) independent contrasts for the respective variables ---see detailed explanation in GarlandJanis.Original. The rest of the columns are:

branch.lengths

Standard Deviation of Contrast = square root of sum of corrected branch lengths.

names.contr

the names of the contrasts, as the names of the two nodes that form the contrast

clade.contr

A factor with levels Carnivore, Herbivore, root, that indicates whether the contrast is a contrast within the carnivore lineage, within the ungulates, or the root contrast ---between the carnivore and the ungulate clades.

See Also

GarlandJanis.Original, GarlandJanis.varcov

Examples

# NOT RUN {
# Multiple regression with independent contrasts
# excluding the polar bear - grizzly bear contrast
data(GarlandJanis.IC)
lm(running.speed ~ body.mass + hind.l.length - 1,
subset=names.contr!="Tm-Ur", data= GarlandJanis.IC)



# }
# NOT RUN {
# This data set can be obtained from the original files as:

garland.janis.ic <- cbind(read.table("49ms.fic")[,c(3,4)],
                          read.table("49hmt.fic")[,c(3,4)])

branch.lengths <- read.table("49ms.fic")[,5]
garland.janis.ic <- garland.janis.ic/branch.lengths
names(garland.janis.ic) <- c("body.mass", "running.speed",
                             "hind.l.length", "mtf.ratio")
garland.janis.ic[garland.janis.ic$body.mass<0,] <-
        -1 * garland.janis.ic[ garland.janis.ic$body.mass<0, ]
garland.janis.ic$branch.lengths <- branch.lengths
garland.janis.ic$names.contr <-
                       as.factor(read.table("49ms.fic")[,1])
garland.janis.ic$clade.contr <-
    as.factor( c("root",rep("Carnivore",18), rep("Herbivore",29))) 
# }
# NOT RUN {

# }