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varCompPhylip(x, phy, exec = NULL)varA and varE with the phylogenetic
(additive) and phenotypic (environmental) variance-covariance
matrices. If a single trait is analyzed, these contains its variances.x can be in several forms: (i) a numeric vector if
there is single trait and one observation per species; (ii) a
matrix or data frame if there are several traits (as columns) and a
single observation of each trait for each species; (iii) a list of
vectors if there is a single trait and several observations per
species; (iv) a list of matrices or data frames: same than (ii) but
with several traits and the rows are individuals. If x has names, its values are matched to the tip labels of
phy, otherwise its values are taken to be in the same order
than the tip labels of phy.
Phylip (version 3.68 or higher) must be accessible on your computer. If
you have a Unix-like operating system, the executable name is assumed
to be "phylip contrast" (as in Debian); otherwise it is set
to "contrast". If this doesn't suit your system, use the
option exec accordingly. If the executable is not in the path, you
may need to specify it, e.g., exec = "C:/Program Files/Phylip/contrast".
Felsenstein, J. (2008) Comparative methods with sampling error and within-species variation: Contrasts revisited and revised. American Naturalist, 171, 713--725.
pic, pic.ortho, compar.lynchtr <- rcoal(30)
### Five traits, one observation per species:
x <- replicate(5, rTraitCont(tr, sigma = 1))
varCompPhylip(x, tr) # varE is small
x <- replicate(5, rnorm(30))
varCompPhylip(x, tr) # varE is large
### Five traits, ten observations per species:
x <- replicate(30, replicate(5, rnorm(10)), simplify = FALSE)
varCompPhylip(x, tr)Run the code above in your browser using DataLab