Re: [R-sig-phylo] compar.gee: how to extract SE, t, and P from output?

[Emmanuel Paradis]

Hi Nina,

You cannot do it directly: you have to get the code from 
print.compar.gee; from R:

> print.compar.gee

From this you can create a function, eg:

foo <- function(x)
{
    nas <- is.na(x$coef)
    coef <- x$coef[!nas]
    cnames <- names(coef)
    coef <- matrix(rep(coef, 4), ncol = 4)
    dimnames(coef) <- list(cnames,
                           c("Estimate", "S.E.", "t", "Pr(T > |t|)"))
    df <- x$dfP - dim(coef)[1]
    coef[, 2] <- sqrt(diag(x$W))
    coef[, 3] <- coef[, 1]/coef[, 2]
    coef
}

Then do:

foo(GEE)

HTH.

Best,

Emmanuel

Nina Hobbhahn wrote on 08/05/2012 18:55:
Dear fellow list users,

I would like to extract the values for SE, t, and Pr from the compar.gee 
output, but seem to unable to do so. The command lines

GEE<-­�compar.gee(trait~reward-­�1, phy=phy2, data=DF.Disa, 
family=gaussian)

GEE

return the following output:

Beginning Cgee S-­�function, @(#) geeformula.q 4.13 98/01/27 running glm to 
get initial regression estimate

rewardN rewardY
2.689142 3.421509
Beginning Cgee S-­�function, @(#) geeformula.q 4.13 98/01/27 running glm to 
get initial regression estimate

rewardN rewardY
2.689142 3.421509
Call: compar.gee(formula = trait ~ reward -­� 1, data = DF.Disa,

family = gaussian, phy = phy2) Number of observations: 31

Model:
Link: identity

Variance to Mean Relation: gaussian


QIC: 165.2011

Summary of Residuals:
Min 1Q Median 3Q Max

3.1462585 0.2560335 1.5256031 2.2012787 4.6689764

Coefficients:
Estimate S.E. t Pr(T>  |t|)

rewardN 1.959375 1.091801 1.794626 0.1016430 rewardY 1.908384 1.117150 1.708261 
0.1170666

Estimated Scale Parameter: 4.862036 "Phylogenetic" df (dfP): 12.45332

When typing

GEE$coefficients

I get


rewardN rewardY

1.959375 1.908384


but I'm unable to access SE, t, and Pr(T>  |t|). Please can any of you help? 
Thank you very much,


Nina




Dr. Nina Hobbhahn
Post-doctoral fellow
Lab of Prof. S. D. Johnson
School of Life Sciences
University of KwaZulu-Natal
Private Bag X01
Scottsville, Pietermaritzburg, 3201
South Africa
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--
Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/

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