Hi Christoph,
Thank you soo much, this is great!
All the very best,
Cristina
On Wed, Oct 12, 2011 at 4:52 PM, Christoph Molnar
christoph.mol...@googlemail.com wrote:
Hi,
the function fourthcorners() returns a list. You can access the pvalues
shown in the summary by four1[[tabGProb]]. This is a matrix containing the
pvalues in the summary.
I did some copy and paste from the summary.4thcorners() function (which is
called, by using summary on your four1 object). And I changed it a little
bit, so that it doesn't print the summary, but returns you the result as a
data.frame. So you can access the Pvalues in the same way you are used to.
summary_fourth - function(object){
res - matrix(0, nrow(object$tabG) * ncol(object$tabG), 6)
res - as.data.frame(res)
res[, 1] = format(colnames(object$tabG)[col(as.matrix(object$tabG))],
justify = right)
res[, 2] = format(rownames(object$tabG)[row(as.matrix(object$tabG))])
res[, 3] = as.vector(outer(object$indexQ, object$indexR))
if (!inherits(object, 4thcorner.rlq)) {
res[res[, 4] == 1, 4] = r
res[res[, 4] == 2, 4] = F
res[res[, 4] == 4, 4] = Chi2
}
else {
res[res[, 4] == 1, 4] = r^2
res[res[, 4] == 2, 4] = Eta^2
res[res[, 4] == 4, 4] = Chi2/sum(L)
}
res[, 4] = as.vector(signif(as.matrix(object$tabG)))
res[, 5] = as.vector(as.matrix(object$tabGProb))
signifpval - symnum(as.numeric(res[, 5]), corr = FALSE,
na = FALSE, cutpoints = c(0, 0.001, 0.01, 0.05, 0.1,
1), symbols = c(***, **, *, ., ))
res[, 6] = signifpval
colnames(res) = c(Var. R, Var. Q, Stat., Value,
Prob., )
res
}
fourth - summary_fourth(four1)
p.adjust(fourth$Prob, method=holm)
Christoph
2011/10/12 Cristina Ramalho cristina.rama...@grs.uwa.edu.au
Hi, probably I didnt formulate my question correctly. I know that to aply
Holm correction I have to do something like:
woody=read.table(woody.txt, sep=\t, head=T, row.names = 1)
woodyadj = p.adjust(woody$p, method = holm)
My question is how to do the correction directly on the results of
4thcorner? Or, another way, how can I convert the 4th corner results in a
data matrix where I can run the p.adjust function?
Thank you so much. Cheers,
C.
On Wed, Oct 12, 2011 at 3:20 PM, Christoph Molnar
christoph.mol...@googlemail.com wrote:
Hi,
?p.adjust
Christoph
2011/10/12 Cristina Ramalho cristina.rama...@grs.uwa.edu.au
Hi all,
This is probably a very simple question but I cannot figure out how to
do
it. I run the fourthcorner method with my data and would like to adjust
the
p values for multiple comparisons using Holm correction. When I run the
fourthcorner I obtain the results in yellow. What do I need to do to be
able
to aply the Holm correction to those p values?
library(ade4)
four1 - fourthcorner(tabR, tabL, tabQ, modeltype = 1, nrepet = 999,
tr01
= FALSE)
summary(four1)
Fourth-corner Statistics
Permutation method 1 ( 999 permutations)
---
Var. R Var. QStat. ValueProb.
RABINT / SPAN r -0.0478943 0.038 *
RABINT / TREEr 0 1.000
RABINT / SHRU r 0 1.000
RABINT / HERB r 0.02618790.340
RABINT / SEDG r -0.0320345 0.316
RABINT / GRAS r 0.01242630.399
Thank you in advance for your help,
Regards,
C.
--
Cristina E. Ramalho
PhD Candidate
MSc in GIS
Ecosystem Restoration Intervention Ecology Research Group
School of Plant Biology (M090)
The University of Western Australia
35 Stirling Highway, Crawley WA 6009 Perth, Australia
Phone: +61 (08) 6488 4655; Fax: +61 (08) 6488 7461
www.plants.uwa.edu.au/research/ecosystem_restoration
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--
Cristina E. Ramalho
PhD Candidate
MSc in GIS
Ecosystem Restoration Intervention Ecology Research Group
School of Plant Biology (M090)
The University of Western Australia
35 Stirling Highway, Crawley WA 6009 Perth, Australia
Phone: +61 (08) 6488 4655; Fax: +61 (08) 6488 7461
www.plants.uwa.edu.au/research/ecosystem_restoration
---
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R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
