R/bwmedbmcp.R

In musto101/wilcox_R: What the package does (short line)

bwmedbmcp <-
function(J,K,x,JK=J*K,grp=c(1:JK),con=0,alpha=.05,dif=FALSE,pool=FALSE,bop=FALSE,nboot=100,SEED=TRUE){
#
# All pairwise comparisons among levels of Factor B
# in a split-plot design using trimmed means.
#
# Data are pooled for each level
# of Factor B.
# bop=T, use bootstrap estimates of standard errors.
# FWE controlled with Rom's method
#
#  The R variable x is assumed to contain the raw
#  data stored in list mode or in a matrix.
#  If in list mode, x[[1]] contains the data
#  for the first level of both factors: level 1,1.
#  x[[2]] is assumed to contain the data for level 1 of the
#  first factor and level 2 of the second: level 1,2
#  x[[K]] is the data for level 1,K
#  x[[K+1]] is the data for level 2,1, x[[2K]] is level 2,K, etc.
#
#  If the data are in a matrix, column 1 is assumed to
#  correspond to x[[1]], column 2 to x[[2]], etc.
#
#  When in list mode x is assumed to have length JK, the total number of
#  groups being tested, but a subset of the data can be analyzed
#  using grp
#
       if(is.matrix(x)) {
                y <- list()
                for(j in 1:ncol(x))
                        y[[j]] <- x[, j]
                x <- y
}
JK<-J*K
data<-list()
for(j in 1:length(x)){
data[[j]]<-x[[grp[j]]] # Now have the groups in proper order.
}
x<-data
if(pool){
data<-list()
m1<-matrix(c(1:JK),J,K,byrow=T)
for(k in 1:K){
for(j in 1:J){
flag<-m1[j,k]
if(j==1)temp<-x[[flag]]
if(j>1){
temp<-c(temp,x[[flag]])
}}
data[[k]]<-temp
}
print("Group numbers refer to levels of Factor B")
if(!dif)temp<-lincdm(data,con=con,alpha=alpha,nboot=nboot,mop=bop)
if(dif)temp<-qdmcpdif(data,con=con,alpha=alpha)
return(temp)
}
if(!pool){
mat<-matrix(c(1:JK),ncol=K,byrow=T)
for(j in 1:J){
data<-list()
ic<-0
for(k in 1:K){
ic<-ic+1
data[[ic]]<-x[[mat[j,k]]]
}
print(paste("For level ", j, " of Factor A:"))
if(!dif)temp<-lincdm(data,con=con,alpha=alpha,nboot=nboot,mop=bop)
if(dif)temp<-qdmcpdif(data,con=con,alpha=alpha)
print(temp$test)
print(temp$psihat)
}}
}