[R] Help in using multcomp.

[Chuck Cleland]

A Ezhil wrote:
> Hi Chuck,
> 
> Thank you very for this help. I am able to store the
> results. Now, I am facing the following problems:
> 
> 1. I am trying to extract only the p-values from 
> 
> dunres <- lapply(amod, function(x){summary(glht(x,
> linfct=mcp(f = contr)))})
> 
> but I am stuck. If I use dunres[[1]], it displays the
> results. But I don't know how to extract the p value
> from this. 

Ezhil:

str(summary(glht(amod[[1]], linfct=mcp(f = contr)))) suggests a way to
extract just the p values.  Try this:

library(multcomp)

dat <- matrix(rnorm(45), nrow=5, ncol=9)
f <- gl(3,3,9, label=c("C", "Tl", "T2"))

aof <- function(x) {
        m <- data.frame(f, x);
        aov(x ~ f, m)
}

amod <- apply(dat,1,aof)

my.pvals <- sapply(amod, function(x){summary(glht(x, linfct=mcp(f =
contr)))$test$pvalues})

rownames(my.pvals) <- rownames(contr)
colnames(my.pvals) <- paste("amod", 1:5, sep="")

my.pvals
               amod1     amod2     amod3     amod4     amod5
C - T1    0.03348242 0.3581771 0.9873633 0.9764219 0.9225445
C - T2    0.67794496 0.7138491 0.2183949 0.9962458 0.8439224
C - All T 0.10621039 0.4344881 0.4913578 0.9970689 0.8519888

> 2. If I want to get raw pvalues instead of adjusted
> ones, what should I do in summary(glht)? 

  See the test argument of summary.glht().  You could do something like
this:

my.pvals <- sapply(amod, function(x){summary(glht(x, linfct=mcp(f =
contr)), test = adjusted("none"))$test$pvalues})

rownames(my.pvals) <- rownames(contr)
colnames(my.pvals) <- paste("amod", 1:5, sep="")

my.pvals
               amod1     amod2     amod3     amod4     amod5
C - T1    0.01770489 0.2197886 0.8985143 0.8611198 0.7466660
C - T2    0.46651736 0.4994115 0.1278132 0.9448342 0.6364631
C - All T 0.05953715 0.2733017 0.3149223 0.9512189 0.6464735

hope this helps,

Chuck Cleland

> Thanks again for your help. I look forward to your
> reply.
> 
> Kind regards,
> Ezhil
> 
> 
> --- Chuck Cleland <ccleland at optonline.net> wrote:
> 
>> A Ezhil wrote:
>>> Hi All,
>>>
>>> I am trying use 'multcomp' for multiple
>> comparisons
>>> after my ANOVA analysis. I have used the following
>>> code to do ANOVA:
>>>
>>> dat <- matrix(rnorm(45), nrow=5, ncol=9)
>>> f <- gl(3,3,9, label=c("C", "Tl", "T2"))
>>>
>>> aof <- function(x) {
>>>         m <- data.frame(f, x);
>>>         aov(x ~ f, m)
>>> }
>>> amod <- apply(dat,1,aof)
>>>
>>> Now, how can I use 'glht' for the above amod. I
>> know
>>> that I cannot use simply 
>>>
>>> glht(amod, linfct = mcp(f = "Dunnett")). 
>>   Since amod is a list of models rather than one
>> model, do you want
>> something like this?
>>
>> lapply(amod, function(x){summary(glht(x, linfct =
>> mcp(f = "Dunnett")))})
>>
>>> Also, if I want to use Dunnett for comparing C vs
>> (T1
>>> and T2), how can I specify this in the glht
>> function.
>>
>>   How about doing it with user-defined contrasts?
>>
>> contr <- rbind("C - T1   " = c(-1, 1, 0),
>>                "C - T2   " = c(-1, 0, 1),
>>                "C - All T" = c(-1,.5,.5))
>>
>> lapply(amod, function(x){summary(glht(x, linfct =
>> mcp(f = contr)))})
>>
>>> Thanks in advance. 
>>> Regards,
>>> Ezhil
>>>
>>> ______________________________________________
>>> R-help at stat.math.ethz.ch mailing list
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>>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained,
>> reproducible code.
>>
>> -- 
>> Chuck Cleland, Ph.D.
>> NDRI, Inc.
>> 71 West 23rd Street, 8th floor
>> New York, NY 10010
>> tel: (212) 845-4495 (Tu, Th)
>> tel: (732) 512-0171 (M, W, F)
>> fax: (917) 438-0894
>>
> 
> 
> 
>  
> ____________________________________________________________________________________
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-- 
Chuck Cleland, Ph.D.
NDRI, Inc.
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 512-0171 (M, W, F)
fax: (917) 438-0894