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. Q Stat. Value Prob.
>>> RABINT / SPAN r -0.0478943 0.038 *
>>> RABINT / TREE r 0 1.000
>>> RABINT / SHRU r 0 1.000
>>> RABINT / HERB r 0.0261879 0.340
>>> RABINT / SEDG r -0.0320345 0.316
>>> RABINT / GRAS r 0.0124263 0.399
>>>
>>> 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
>>>
>>> ---------------------------------------------------------------------------------------------------
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> 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<http://www.r-project.org/posting-guide.html>
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>>
>
>
> --
> 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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