[R] Help in using multcomp.

[A Ezhil]

Hi Chuck,

Thank you very much for this is help. It is fantastic
and the code works perfectly.

Thanks again, Chuck.

Kind regards,
Ezhil
  
--- Chuck Cleland <ccleland at optonline.net> wrote:

> 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
> >>> 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.
> >>
> >> -- 
> >> 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
> 



 
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