compar.gee {ape} | R Documentation |
This function performs the comparative analysis using generalized estimating equations as described by Paradis and Claude (2002).
compar.gee(formula, data = NULL, family = "gaussian", phy, scale.fix = FALSE, scale.value = 1)
formula |
a formula giving the model to be fitted. |
data |
the name of the data frame where the variables in
formula are to be found; by default, the variables are looked
for in the global environment. |
family |
a character string specifying the distribution assumed
for the response; by default a Gaussian distribution (with link
identity) is assumed (see ?family for details on specifying
the distribution, and on changing the link function). |
phy |
an object of class "phylo" . |
scale.fix |
logical, indicates whether the scale parameter should be fixed (TRUE) or estimated (FALSE, the default). |
scale.value |
if scale.fix = TRUE , gives the value for the
scale (default: scale.value = 1 ). |
If a data frame is specified for the argument data
, then its
rownames are matched to the tip labels of phy
. The user must be
careful here since the function requires that both series of names
perfectly match, so this operation may fail if there is a typing or
syntax error. If both series of names do not match, the values in the
data frame are taken to be in the same order than the tip labels of
phy
, and a warning message is issued.
If data = NULL
, then it is assumed that the variables are in
the same order than the tip labels of phy
.
an object of class "compar.gee" with the following components:
call |
the function call, including the formula. |
nobs |
the number of observations. |
coefficients |
the estimated coefficients (or regression parameters). |
residuals |
the regression residuals. |
family |
a character string, the distribution assumed for the response. |
link |
a character string, the link function used for the mean function. |
scale |
the scale (or dispersion parameter). |
W |
the variance-covariance matrix of the estimated coefficients. |
dfP |
the phylogenetic degrees of freedom (see Paradis and Claude for details on this). |
Emmanuel Paradis paradis@isem.univ-montp2.fr
Paradis, E. and Claude J. (2002) Analysis of comparative data using generalized estimating equations. Journal of theoretical Biology, 218, 175–185.
### The example in Phylip 3.5c (originally from Lynch 1991) ### (the same analysis than in help(pic)...) cat("((((Homo:0.21,Pongo:0.21):0.28,", "Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);", file = "ex.tre", sep = "\n") tree.primates <- read.tree("ex.tre") X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259) ### Both regressions... the results are quite close to those obtained ### with pic(). compar.gee(X ~ Y, phy = tree.primates) compar.gee(Y ~ X, phy = tree.primates) ### Now do the GEE regressions through the origin: the results are quite ### different! compar.gee(X ~ Y - 1, phy = tree.primates) compar.gee(Y ~ X - 1, phy = tree.primates) unlink("ex.tre") # delete the file "ex.tre"