C:\Rmisc>C:\R-2.9.0\bin\Rterm --vanilla 

R version 2.9.0 (2009-04-17)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> pdf("C:\\Rmisc\\graphs\\amoeba.pdf")
> 
> amoeba1 <- read.fwf("C:\\data\\amoeba.txt", width=c(8,8), col.names=c("Trt", "Yield"))
> 
> fTrt <- factor(amoeba1$Trt, levels=1:5)
> levels(fTrt) <- c("None", "H", "F", "HF", "FH")
> 
> amoeba <- data.frame(amoeba1, fTrt)
> attach(amoeba)

	The following object(s) are masked _by_ .GlobalEnv :

	 fTrt 

> 
> bonf <- function(y,trt,alpha) {
+ 
+ ybar <- mean(y)
+ print("Overall Mean")
+ print(ybar)
+ ybar.trt <- as.vector(tapply(y,trt,mean))
+ print("Treatment Means")
+ print(ybar.trt)
+ var.trt <- as.vector(tapply(y,trt,var))
+ print("Treatment Variances")
+ print(var.trt)
+ rep.trt <- as.vector(tapply(y,trt,length))
+ print("Treatment Replicates")
+ print(rep.trt)
+ num.trt <- length(ybar.trt)
+ print("Number of Treatments")
+ print(num.trt)
+ 
+ sse <- 0
+ num.pairs <- num.trt*(num.trt-1)/2
+ 
+ 
+ for (i1 in 1:num.trt) {
+ sse <- sse + (rep.trt[i1]-1)*var.trt[i1]
+ }
+ print("Error Sum of Squares")
+ print(sse)
+ 
+ mse=sse/(sum(rep.trt)-num.trt)
+ print("Mean Square Error")
+ print(mse)
+ 
+ 
+ 
+ print(c("Bonferroni Simultaneous CI's","Alpha=",alpha))
+ for(i1 in 1:(num.trt-1)) {
+ for (i2 in (i1+1):num.trt) {
+ bonf.msd <- qt(1-alpha/(2*num.pairs),(sum(rep.trt)-num.trt))*sqrt(mse*(1/rep.trt[i1]+1/rep.trt[i2]))
+ print(c("Bonferroni MSD","Alpha=",alpha))
+ print(c(round(c(i1,i2,bonf.msd),2)))
+ print(c(round(c(i1,i2),0),round(c((ybar.trt[i1]-ybar.trt[i2])-bonf.msd,(ybar.trt[i1]-ybar.trt[i2])+bonf.msd),2)))
+ }}
+ 
+ 
+ }
> 
> bonf(Yield,Trt,0.05)
[1] "Overall Mean"
[1] 210.72
[1] "Treatment Means"
[1] 246.4 203.5 196.9 216.5 190.3
[1] "Treatment Variances"
[1] 1330.2667  542.2778  256.9889 1596.9444 1146.6778
[1] "Treatment Replicates"
[1] 10 10 10 10 10
[1] "Number of Treatments"
[1] 5
[1] "Error Sum of Squares"
[1] 43858.4
[1] "Mean Square Error"
[1] 974.6311
[1] "Bonferroni Simultaneous CI's" "Alpha="                      
[3] "0.05"                        
[1] "Bonferroni MSD" "Alpha="         "0.05"          
[1]  1.00  2.00 41.22
[1]  1.00  2.00  1.68 84.12
[1] "Bonferroni MSD" "Alpha="         "0.05"          
[1]  1.00  3.00 41.22
[1]  1.00  3.00  8.28 90.72
[1] "Bonferroni MSD" "Alpha="         "0.05"          
[1]  1.00  4.00 41.22
[1]   1.00   4.00 -11.32  71.12
[1] "Bonferroni MSD" "Alpha="         "0.05"          
[1]  1.00  5.00 41.22
[1]  1.00  5.00 14.88 97.32
[1] "Bonferroni MSD" "Alpha="         "0.05"          
[1]  2.00  3.00 41.22
[1]   2.00   3.00 -34.62  47.82
[1] "Bonferroni MSD" "Alpha="         "0.05"          
[1]  2.00  4.00 41.22
[1]   2.00   4.00 -54.22  28.22
[1] "Bonferroni MSD" "Alpha="         "0.05"          
[1]  2.00  5.00 41.22
[1]   2.00   5.00 -28.02  54.42
[1] "Bonferroni MSD" "Alpha="         "0.05"          
[1]  3.00  4.00 41.22
[1]   3.00   4.00 -60.82  21.62
[1] "Bonferroni MSD" "Alpha="         "0.05"          
[1]  3.00  5.00 41.22
[1]   3.00   5.00 -34.62  47.82
[1] "Bonferroni MSD" "Alpha="         "0.05"          
[1]  4.00  5.00 41.22
[1]   4.00   5.00 -15.02  67.42
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>