[R] desperate!

[KAREN KOTSCHY]

Dear R community

I sent a message out a while ago asking for help with multiple 
comparison tests for ANOVA's, but haven't had any response yet. 
I'm sending a final desperate plea. If I can't get this done in R I'm 
going to have to redo a whole lot of stuff in a commercial package, 
which I'm REALLY not keen to do!

My problem is how to implement these tests in R. Below is some 
code posted by Thomas Lumley which I might be able to use 
(sorry, I forgot to include the code in my last email). But I'm battling 
to follow what this code exactly does (especially the last bit). How 
would I link it to the ANOVA results? What sort of output would 
these functions give me - adjusted p values?  How would I then 
interpret these?

I'd really appreciate any help!!!

-----------------
Code for Bonferroni, Holm and Hochberg post hoc tests:

p.adjust.holm <- function(p, n=length(p)) {
   ##n <- length(p)
   r <- rank(p)
   index <- order(p)
   qi <- p*(n+1-r)
   for (i in 2:length(p)) {
        qi[index[i]] <- max(qi[index[i+1]])
        }
   list(adjp=pmin(qi, 1), p=p, method="Holm")
}

p.adjust.hochberg <- function(p) {
   n <- length(p)
   r <- rank(p)
   index <- order(p)
   qi <- p*(n+1-r)
   for (i in (n-1):1) {
        qi[index[i]] <- min(qi[index[i]], qi[index[i+1]])
        }
   list(adjp=qi, p=p, method="Hochberg")
}

p.adjust.bonferroni <- function(p, n=length(p)) {
   list(adjp=pmin(p*n, 1), p=p, method="Bonferroni")
   }
------------------
p.adjust <- function(p, method=c("hochberg", "holm",  
"bonferroni"),...) {
   how <- pmatch(method[1], c("hochberg", "holm",  "bonferroni"))
   if(is.na(how) stop(paste("Don't know method"))
   m <- match.call()
   m[[1]] <- as.name(paste("p.adjust", c("hochberg", "holm",            
          "bonferroni")[how], sep="."))
   m$method <- NULL
   eval(m, sys.parent())
}
---------------------

Karen Kotschy
Centre for Water in the Environment
Department of Animal, Plant and Environmental sciences
University of the Witwatersrand
Johannesburg
South Africa
Tel : +2911 716-2218

Postal address:
P/Bag 3
P.O Wits
2050
South Africa
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