Nothing
# Changes:
# 03-07-2013: Added the keepPM option, DF
# 06-07-2013: Made the output consistent with other tests, DF
# 19-09-2013: Fixed a naming issue with the innerLoop functions, DF
kw.gmw <- function(X,g,cluster,goi,type,nper,mc,PARAMETERS,output, keepPM){
res <- list()
diffTests <- t(as.matrix(sort(goi)))
METHOD <- c("********* Kruskal-Wallis Test *********")
DNAME <- PARAMETERS[[1]]
TEST <- PARAMETERS[[2]]
TYPE <- PARAMETERS[[3]]
ALTERNATIVE <- PARAMETERS[[4]]
STATISTIC <- PARAMETERS[[5]]
PVAL <- PARAMETERS[[6]]
dimX <- PARAMETERS[[7]]
XisVector <- PARAMETERS[[8]]
#totalObs <- length(group)
## Case: X is vector
if(XisVector){
##---------------------------------------------------------------------------------------------------------------------------------------
if(type=="permutation"){
#----------------------------------------------------------------------------------------------------------------------------------------
# Case: permutation, two sided, X is vector
for(testRun in 1:nrow(diffTests))
{
obsValue <- kwObs(X,g,goi)
# if a cluster object is given, then we permute cluster internal
if(is.null(cluster)==T)
{
nullDist <- kwNullDist(X,g,goi,nper)
} else {
nullDist <- kwNullDistCluster(X,g,cluster,goi,nper)
}
PVAL <- sum(nullDist>obsValue)/nper
names(PVAL) <- "p.value"
STATISTIC <- obsValue
names(STATISTIC) <- "obs.value"
ALTERNATIVE <- "two.sided"
resTemp<-c(list(method=METHOD,data.name=DNAME,alternative=ALTERNATIVE,statistic=STATISTIC,test=TEST,p.value=PVAL,type=TYPE))
class(resTemp)<-"htest"
res[[testRun]] <- resTemp
#names(res)[testRun] <- paste(diffTests[testRun,],collapse="")
names(res)[testRun] <- paste("H1: P_tt' != 0.5 for some t,t'")
}
if(output=="min")
{
resMin <- matrix(NA,ncol=1,nrow=length(res))
colnames(resMin) <- "pValues"
rownames(resMin) <- names(res)
for(i in 1:length(res))
{
resMin[i,1] <- res[[i]]$p.value
}
res <- resMin
}
} else if(type=="asymptotic"){
#----------------------------------------------------------------------------------------------------------------------------------------
# Case: asymptotic, two sided, X is vector
res <- c()
stop("We do not have a two-sided version for the Kruskal-Wallis test, sorry!!!")
} else if(type=="external"){
#----------------------------------------------------------------------------------------------------------------------------------------
# Case: KW from base system, two sided, X is vector
for(testRun in 1:nrow(diffTests))
{
testResult <- kruskal.test(X[is.element(g,goi)],g[is.element(g,goi)])
PVAL <- testResult$p.value
names(PVAL) <- "p.value"
STATISTIC <- testResult$statistic
names(STATISTIC) <- "obs.value"
ALTERNATIVE <- "two.sided"
resTemp<-c(list(method=METHOD,data.name=DNAME,alternative=ALTERNATIVE,statistic=STATISTIC,test=TEST,p.value=PVAL,type=TYPE))
class(resTemp)<-"htest"
res[[testRun]] <- resTemp
#names(res)[testRun] <- paste(diffTests[testRun,],collapse="")
names(res)[testRun] <- paste("H1: P_tt' != 0.5 for some t,t'")
}
if(output=="min")
{
resMin <- matrix(NA,ncol=1,nrow=length(res))
colnames(resMin) <- "pValues"
rownames(resMin) <- names(res)
for(i in 1:length(res))
{
resMin[i,1] <- res[[i]]$p.value
}
res <- resMin
}
} else {
#----------------------------------------------------------------------------------------------------------------------------------------
# Case: other options, two sided, X is vector
res <- c()
stop("We do not have this kind of type for the Kruskal-Wallis test!")
}
## Case: X is a matrix
} else{
##----------------------------------------------------------------------------------------------------------------------------------------
#Preparational things for the case that X is a matrix
# First, restrict the cores to maximum of possible tests
if(mc>detectCores()){
mc <- detectCores()
warning("You do not have so many cores on this machine! I automatically reduced it to your maximum number ",mc)
}
mc <- min(dimX[2],mc)
if(type=="permutation"){
#----------------------------------------------------------------------------------------------------------------------------------------
# Case: permutation, two sided, X is matrix
innerLoop <- function(i,testRun,nper){
nullDist <- kwNullDist(X[,i],g,goi,nper)
obsValue <- kwObs(X[,i],g,goi)
pValue <- sum(nullDist>obsValue)/nper
return(list(pValue=pValue,obsValue=obsValue))
}
innerLoopPM <- function(i,testRun,nper){
nullDist <- kwNullDist(X[,i],g,goi,nper)
obsValue <- kwObs(X[,i],g,goi)
pValue <- sum(nullDist>obsValue)/nper
return(list(pValue=pValue,obsValue=obsValue, nullDist=nullDist))
}
if(keepPM){
nullDistRES <- list()
STATISTIC <- list()
for(i in 1:nrow(diffTests)){
nullDistRES[[i]] <- matrix(0, ncol=dimX[2],nrow=nper)
STATISTIC[[i]] <- c(rep(-1,dimX[2]))
}
}
for(testRun in 1:nrow(diffTests))
{
resTemp <- list()
if(keepPM==TRUE){
resInner <- unlist(mclapply(c(1:dimX[2]),innerLoopPM,testRun=testRun, nper=nper,mc.cores=mc))
#nullDistRES <- matrix(0, ncol=dimX[2],nrow=nper)
} else {
resInner <- unlist(mclapply(c(1:dimX[2]),innerLoop,testRun=testRun, nper=nper,mc.cores=mc))
}
for(i in 1:dimX[2])
{
if(keepPM==TRUE){
PVAL <- resInner[nper*(i-1) + 2*(i) - 1]
STATISTIC[[testRun]][i] <- resInner[nper*(i-1) + 2*i]
nullDistRES[[testRun]][,i] <- resInner[(nper*(i-1) + 2*i + 1):(nper*i + 2*i)]
} else {
PVAL <- resInner[2*i-1]
STATISTIC <- resInner[2*i]
}
obsValue <- STATISTIC
names(PVAL) <- "p.value"
ALTERNATIVE <- "two.sided"
names(STATISTIC) <- "obs.value"
resTemp[[i]]<-c(list(method=METHOD,data.name=DNAME,alternative=ALTERNATIVE,statistic=STATISTIC,test=TEST,p.value=PVAL,type=TYPE))
class(resTemp[[i]])<-"htest"
}
res[[testRun]] <- resTemp
#names(res)[testRun] <- paste(diffTests[testRun,],collapse="")
names(res)[testRun] <- paste("H1: P_tt' != 0.5 for some t,t'")
}
if(output=="min")
{
resMin <- matrix(NA,ncol=dimX[2],nrow=length(res))
colnames(resMin) <- colnames(X)
rownames(resMin) <- names(res)
for(i in 1:length(res))
{
for(j in 1:dimX[2])
{
resMin[i,j] <- res[[i]][[j]]$p.value
}
}
res <- resMin
}
} else if(type=="asymptotic"){
#----------------------------------------------------------------------------------------------------------------------------------------
# Case: asymptotic, two sided, X is matrix
res <- c()
stop("We do not have a asymptotic version, sorry!!!")
} else if(type=="external"){
#----------------------------------------------------------------------------------------------------------------------------------------
# Case: KW from base system, two sided, X is matrix
innerLoopEX <- function(i,testRun){
testResult <- kruskal.test(X[is.element(g,goi),i],g[is.element(g,goi)])
obsValue <- testResult$statistic
pValue <- testResult$p.value
return(list(pValue=pValue,obsValue=obsValue))
}
for(testRun in 1:nrow(diffTests))
{
resTemp <- list()
resInner <- unlist(mclapply(c(1:dimX[2]),innerLoopEX,testRun=testRun,mc.cores=mc))
for(i in 1:dimX[2])
{
PVAL <- resInner[2*i-1]
STATISTIC <- resInner[2*i]
names(PVAL) <- "p.value"
ALTERNATIVE <- "two.sided"
#DNAME <- paste("Data:",deparse(substitute(X)),", Groups:",deparse(substitute(g)),", Order: max(P",diffTests[testRun,1],diffTests[testRun,3],",P",diffTests[testRun,2],diffTests[testRun,3],")",sep="")
names(STATISTIC) <- "obs.value"
resTemp[[i]]<-c(list(method=METHOD,data.name=DNAME,alternative=ALTERNATIVE,statistic=STATISTIC,test=TEST,p.value=PVAL,type=TYPE))
class(resTemp[[i]])<-"htest"
}
res[[testRun]] <- resTemp
#names(res)[testRun] <- paste(diffTests[testRun,],collapse="")
names(res)[testRun] <- paste("H1: P_tt' != 0.5 for some t,t'")
}
if(output=="min")
{
resMin <- matrix(NA,ncol=dimX[2],nrow=length(res))
colnames(resMin) <- colnames(X)
rownames(resMin) <- names(res)
for(i in 1:length(res))
{
for(j in 1:dimX[2])
{
resMin[i,j] <- res[[i]][[j]]$p.value
}
}
res <- resMin
}
} else {
#----------------------------------------------------------------------------------------------------------------------------------------
# Case: other options, two sided, X is vector
res <- c()
stop("We do not have this kind of type for the triple test!,O,T,M")
}
}
if(type=="permutation"){
ifelse(keepPM,res <- list(p.values=res, nullDist=nullDistRES, obsValue=obsValue), res <- list(p.values=res))
} else {
res <- list(p.values=res)
}
res
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.