R/wwwmcp.R

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

wwwmcp <-
function(J,K,L, x,tr=.2,alpha=.05,dif=TRUE,op=FALSE,grp=NA){
#
# MULTIPLE COMPARISONS FOR A 3-WAY within-by-within-by within ANOVA
# Do all multiple comparisons associated with
# main effects for Factor A and B and C and all interactions
# based on trimmed means
#
        #   The data are assumed to be stored in x in list mode or in a matrix.
        #  If grp is unspecified, it is assumed 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 factor: level 1,2
        #  x[[j+1]] is the data for level 2,1, etc.
        #  If the data are in wrong order, grp can be used to rearrange the
        #  groups. For example, for a two by two design, grp<-c(2,4,3,1)
        #  indicates that the second group corresponds to level 1,1;
        #  group 4 corresponds to level 1,2; group 3 is level 2,1;
        #  and group 1 is level 2,2.
        #
        #   Missing values are automatically removed.
        #
if(is.data.frame(x))x=as.matrix(x)
        JKL <- J*K*L
        if(is.matrix(x))
                x <- listm(x)
        if(!is.na(grp[1])) {
                yy <- x
                x<-list()
                for(j in 1:length(grp))
                        x[[j]] <- yy[[grp[j]]]
        }
        if(!is.list(x))
                stop("Data must be stored in list mode or a matrix.")
        for(j in 1:JKL) {
                xx <- x[[j]]
                x[[j]] <- xx[!is.na(xx)] # Remove missing values
        }
        #

        if(JKL != length(x))
                warning("The number of groups does not match the number of contrast coefficients.")
for(j in 1:JKL){
temp<-x[[j]]
temp<-temp[!is.na(temp)] # Remove missing values.
x[[j]]<-temp
}
        # Create the three contrast matrices
temp<-con3way(J,K,L)
conA<-temp$conA
conB<-temp$conB
conC<-temp$conC
conAB<-temp$conAB
conAC<-temp$conAC
conBC<-temp$conBC
conABC<-temp$conABC
Factor.A<-rmmcp(x,con=conA,tr=tr,alpha=alpha,dif=dif)
Factor.B<-rmmcp(x,con=conB,tr=tr,alpha=alpha,dif=dif)
Factor.C<-rmmcp(x,con=conC,tr=tr,alpha=alpha,dif=dif)
Factor.AB<-rmmcp(x,con=conAB,tr=tr,alpha=alpha,dif=dif)
Factor.AC<-rmmcp(x,con=conAC,tr=tr,alpha=alpha,dif=dif)
Factor.BC<-rmmcp(x,con=conBC,tr=tr,alpha=alpha,dif=dif)
Factor.ABC<-rmmcp(x,con=conABC,tr=tr,alpha=alpha,dif=dif)
list(Factor.A=Factor.A,Factor.B=Factor.B,Factor.C=Factor.C,
Factor.AB=Factor.AB,Factor.AC=Factor.AC,Factor.BC=Factor.BC,
Factor.ABC=Factor.ABC,conA=conA,conB=conB,conC=conC,
conAB=conAB,conAC=conAC,conBC=conBC,conABC=conABC)
}