Nothing
# Get the data, either in case order or sorted by the
# sequence variable order. Use only variables, and in the
# order, of those on the MRSP command line.
#Make sure this deals with missing values correctly l_DoScreen4MsngVals
#l_HasSPVar if spvar name was supplied this was true then the data is sorted based on this
#so if a sequencing variable is provided, make sure to sort based on it
#Find default number of permutations for mrsp
sp<-function(data, expon=1,commens=TRUE,
number.perms,exact=FALSE,save.test,sequence,variables){
# deriving some required input from the data matrix
Call<-match.call()
if(missing(data)) {if(missing(sequence)) {data <- variables
colnames(data)<-Call$variables
} else {data <- cbind(variables,sequence)
colnames(data)<-cbind(Call$variables,Call$sequence)
}
}
if(!is.null(Call$variables)) x<-data[,match(eval(Call$variables),names(data))]
else x<-data
x<-as.matrix(x)
ifelse((missing(number.perms)),{do.resample<-FALSE;number.perms<-0},do.resample<-TRUE)
if(!is.null(Call$sequence)){
if(is.character(eval(Call$sequence))) sequen<-order(data[,match(eval(Call$sequence),names(data))])
else sequen<-order(eval(Call$sequence))
x<-as.matrix(x[sequen,])
}
i_NumObs=nrow(x)
i_NumVars=ncol(x)
#remove incomplete cases and issue a warning
x<-as.matrix(x[complete.cases(x),])
comp.cases<-nrow(x)
if(comp.cases/i_NumObs!=1) {warning(paste(i_NumObs-comp.cases,ifelse(i_NumObs-comp.cases==1," case was removed because of a missing value ",
" cases were removed because of missing values."),sep=""))
i_NumObs<-nrow(x)
}
if(missing(save.test)) save.test<-FALSE
da_STV<-rep(0,times=number.perms)
if(i_NumObs>200 && do.resample==TRUE){
cat("This may take a while")
}
if(i_NumObs<6 & !exact) stop(paste("There are only", i_NumObs, "cases. There must be at least 6 to do MRSP"))
if(i_NumObs<2 & exact) stop(paste("There are only", i_NumObs, "cases. There must be at least 2 to do an EMRSP"))
if(i_NumObs>2147483647) stop("Number of cases (observations) should not exceed 2147483647 for MRSP")
if(i_NumVars>65536) stop("Number of variables should not exceed 65536 for MRSP")
# output is initilized here
d_TestStat=0
d_ObsDelta=0
d_ExpDelta=0
d_VarDelta=0
d_SkwDelta=0
d_RhoAgreement=0
d_PValue=0
iEr=0
CommAvgDist=rep(0,times=i_NumVars)
storage.mode(x) <- "double"
storage.mode(da_STV)<-"double"
storage.mode(CommAvgDist)="double"
mrspOut=.Fortran("wrapmrsp",
as.integer(i_NumObs),
as.integer(i_NumVars),
as.double(expon),
as.integer(number.perms),
as.logical(do.resample),
as.logical(exact),
as.logical(commens),
x,
as.double(d_TestStat),
as.double(d_ObsDelta),
as.double(d_ExpDelta),
as.double(d_VarDelta),
as.double(d_SkwDelta),
as.double(d_RhoAgreement),
as.double(d_PValue),
as.integer(iEr),
as.logical(save.test),
da_STV,
CommAvgDist
)
mrspOut<-new("MRSPObj",NumObs=mrspOut[[1]],NumVars=mrspOut[[2]],
DistExp=mrspOut[[3]],NumPerm=mrspOut[[4]],DoResamp=mrspOut[[5]],Exact=mrspOut[[6]],Commens=mrspOut[[7]],inputData=mrspOut[[8]],
TestStat=mrspOut[[9]],ObsDelta=mrspOut[[10]],ExpectDelta=mrspOut[[11]],DeltaVar=mrspOut[[12]],
DeltaSkew=mrspOut[[13]],RhoAgreement=mrspOut[[14]],P_value=mrspOut[[15]],
Call=deparse(Call,width.cutoff=200L),SaveTest=mrspOut[[17]],PermVals=mrspOut[[18]],CommAvgDist=mrspOut[[19]])
mrspOut
}
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