R/llbt.design.R

########################################################################
# llbt.design.R                                                        #
#                                                                      #
# version 0.1   15.2.2008  based on OBTdesign051                       #
#                          input now through function call             #
#                          options for ctrl object, dataframe, filename#
#                          default values in call (to be overwritten   #
#                             either by pasing parameters or ctrl obj) #
#                           ctrl object unified with pcpatt0           #
#                          only REDUCECAT !!                           #
#                                                                      #
# ---------------------------------------------------------------------#

# changes 2010-12-21
### new: option objcovs (must be data.frame)
### value: object of class "llbtdes"

#llbt.design2<-function(obj, nitems=NULL, objnames="", obj.covs=NULL, blnCasewise=FALSE, cov.sel="",
#       blnGLIMcmds=FALSE, glimCmdFile="",outFile="")
#{
#llbt.design<-function(obj, nitems=NULL, objnames="", obj.covs=NULL, cov.sel="", casewise=FALSE,...)

llbt.design<-function(data, nitems=NULL, objnames="",
          objcovs=NULL, cat.scovs=NULL, num.scovs=NULL, casewise=FALSE,...)
{

#
# initialisations
#


### 2010-12-28 deprecated options, for backwards compatibility
dots<-as.list(substitute(list(...)))[-1]
nn<-names(dots)
for (i in seq(along=dots)) assign(nn[i],dots[[i]])

if(!exists("blnGLIMcmds")) blnGLIMcmds=FALSE
if(!exists("blnCasewise")) blnCasewise=casewise
if(!exists("glimCmdFile")) glimCmdFile=""
if(!exists("outFile")) outFile=""
if(!exists("cov.sel")) cov.sel=""

cov.sel<-eval(cov.sel)
blnGLIMcmds <- ifelse(blnGLIMcmds=="T",TRUE,FALSE)
blnCasewise <- ifelse((blnCasewise==TRUE) || (blnCasewise=="T") ,TRUE,FALSE)

if (blnGLIMcmds){
    stop("\nGLIMcmds deprecated. Please use preftest < 0.8-24!\n\n", call.=FALSE)
  }
###

  dfr<-NULL
  if(is.character(data)){          # argument obj changed to data 2010-12-30
          datafile<-data
          nobj         <- nitems
          objnames     <- objnames
          casewise     <- blnCasewise
          glimoutput   <- blnGLIMcmds
          glimoutFile  <- glimCmdFile
          outFile      <- outFile
  } else if(is.data.frame(data)){  # argument obj changed to data 2010-12-30
          dfr<-data
          nobj         <- nitems
          objnames     <- objnames
          cov.sel      <- cov.sel
          casewise     <- blnCasewise
          glimoutput   <- blnGLIMcmds
          glimoutFile  <- glimCmdFile
          outFile      <- outFile
  } else if (is.list(data)) {
          obj<-data                # argument obj changed to data 2010-12-30
          datafile     <- obj$datafile
          nobj         <- obj$nitems
          objnames     <- obj$objnames
          objcovs      <- obj$objcovs
          #reduce.cat   <- obj$blnReducecat
          casewise     <- obj$blnCasewise
          cov.sel      <- obj$cov.sel
          glimoutput   <- obj$blnGLIMcmds
          glimoutFile  <- obj$glimCmdFile
          outFile      <- obj$outFile
  } else {
          stop("first argument must be either ctrlobject, datafilename or dataframe")
  }

if (is.null(nobj)) stop("number of items not defined")



    reduce.cat <- TRUE # always TRUE until clarification

    if (length(objnames)!=nitems)
       objnames     <- paste("o",1:nobj,sep="")
    ncomp <- nobj * (nobj-1) / 2


###################only individual data for the time being
###if (aggreg) {                       # aggregated data
###
###   y<-scan(datafile)
###   if (reduce.cat) y <- red.cat.agg(y,nrespcat.data)
###
###} else {                            # individual data
####################################################

    if (is.null(dfr)) {
        if(file.access(datafile, mode=0) == 0){
           dat<-as.matrix(read.table(datafile,header=TRUE))  # datafile
        } else {
           stop("\ninput data file does not exist!\n")
        }
    } else {
        dat<-as.matrix(dfr)                                  # dataframe
        dat<-apply(dat,2,as.numeric)
    }

    # which variables are factors 2010-12-28 --- obsolete for time being
    # facs<-sapply(dfr,is.factor)

    nrespcat<-diff(range(dat[,1:ncomp],na.rm=TRUE))   # number of response categories categories
    raw.data <- dat[,1:ncomp]


# reduce categories
    if (min(raw.data,na.rm=TRUE)<0) raw.data<- -raw.data
    # data shifted to 0,...
    raw.data <- raw.data - min(raw.data,na.rm=TRUE)

    # check for cases with -1 1
    tab<-table(raw.data)
    levs<-as.numeric(names(tab))


      nlevs<-length(levs)
      mid<-median(levs)

       if(nlevs%%2==0) {                           # no undecided

             rawdata<-ifelse(raw.data<mid,0,1)
             nrespcat<-1
       } else {
             rawdata<-ifelse(raw.data<mid,0,ifelse(raw.data>mid,2,1))
             nrespcat<-2
       }



    nsubj<-nrow(dat)
    nrows <- ncomp * (nrespcat+1)        # number of rows for 1 design matrix (1 subject or no covs)

    ## treatment of subject covariates 201-12-30
    scovs <- c(num.scovs, cat.scovs)
    if (length(scovs)>0)
         cov.sel <- scovs
    if (length(num.scovs)>0) casewise <- TRUE
    blnSubjcov<-cov.sel[1]!=""             #    FALSE if ""

    if (blnSubjcov) {
       inpcovnames <- colnames(dat)[(ncomp+1):ncol(dat)]
       if (length(cov.sel)>1 && any(toupper(cov.sel[1])=="ALL"))  ## 2010-12-30
           stop("\n subject covariates incorrectly specified\n")
       if (toupper(cov.sel[1]) == "ALL"){   # all covariates included
          cov.sel <- inpcovnames
          cat.scovs <- cov.sel              # respecify cat.scovs for attribute in resulting data frame 2011-08-26
       } else if(length(setdiff(cov.sel,inpcovnames))>0) {
           stop("\n subject covariates incorrectly specified\n")
       }

       if (toupper("all") %in% toupper(num.scovs))
          stop("\n'all' is not allowed in num.scovs\n")
       for (var in cov.sel){
          if (var %in% num.scovs) next
          if((min(dat[,var])!=1)||(any(dat[,var]!=as.integer(dat[,var]))))
            stop("\ncategorical covariate '", var,"' incorrectly specified (perhaps numeric?)\n")
          if(max(dat[,var])>10)
            warning("\ncategorical covariate",var,"has > 10 categories (perhaps numeric?)\n")
       }

       ## 2010-12-30 --- obsolete for time being
       # check if casewise is specified for continuous covs
       # distinguish factors and variates
       # tst<-intersect(names(facs),cov.sel)
       # if (any(facs[tst]==FALSE)&&!casewise)
       #    stop("Not all selected subject covariates are factors, use casewise=TRUE.")


       cov.case<-as.matrix(dat[,c(cov.sel)])
       #if (any(is.na(cov.case)))
       #    stop("subject covariates with NAs not allowed")

       NAs<-which(!complete.cases(cov.case))                  # check for NA
       if (length(NAs)>0){

           warning("\tselected subject covariates have NAs in lines ",paste(NAs,collapse=",")," - removed from data\n")
           notNAs<-which(complete.cases(cov.case))
           dat<-dat[notNAs,]
           cov.case<-as.matrix(cov.case[notNAs,])
           nsubj<-nrow(dat)
       }


       colnames(cov.case)<-cov.sel
       covnames<-cov.sel
       covlevels<-apply(cov.case,2,max)
       ncov<-length(cov.sel)
       # if (any(apply(cov.case,2,min)<1))   # removed 2010-12-28
       #    warning("subject covariates with values < 1, if these are factors recode them")
    } else {
       cov.case=NULL
       covlevels=NULL
       covnames=NULL
       ncov<-0
    }


if (reduce.cat){                            #?????
   nrespcat <- 1 + (nrespcat+1)%%2
   nrows <- ncomp * (nrespcat+1)
}

# initialisations for covariates

if (ncov == 0 ) {         # no subject covariates
      totlev <- 1
      ones.totlev <- 1
      if (casewise){     # metric (and categorical subject covs)
        totlev<-nsubj
        ones.totlev <- rep(1,nsubj)
      }
} else if (casewise){     # metric (and categorical subject covs)
      totlev<-nsubj
      ones.totlev <- rep(1,nsubj)

} else {                  # categorical subject covariates
      totlev <- prod(covlevels)  # total number of covariate levels
      ones.totlev<-rep(1,totlev) # vector for kronecker products

      indx <- ncov:1
      if (ncov == 1) {
           baslev <- nrows
      } else {
           baslev <- c(covlevels[2:ncov],nrows)
      }
      levmult <- rev(cumprod(baslev[indx]))

# generate subject covariates

      cov<-NULL
      for (j in 1:ncov) {
          scov<-gl(covlevels[j],levmult[j],totlev*nrows)
          cov<-cbind(cov,scov)
      }
}

ones.ncomp<-rep(1,ncomp)         # vector for kronecker products
ones.nrows<-rep(1,nrows)         # vector for kronecker products



#
# design matrix for objects
#




obj <- objdesign(nrows,nobj,nrespcat)# /nrespcat  ## to make design -1 0 1 instead of -2 0 2 in case of undecided
obj<- ones.totlev %x% obj        # stack object design matrix totlev times


#
# mu - factor for comparisons
#
mu<-rep.int(1:ncomp, rep.int((nrespcat+1),ncomp))
mu<-factor(rep(mu,totlev))           # stack mu totlev times


#
# design matrix for gammas (category parameters)
#

g <- ones.ncomp %x% diag(nrespcat+1)  # stack gamma matrix ncomp times for 1 subject
#print(g)
g <- ones.totlev %x% g              # stack gammas totlev times
#print(g)

gamnames<-paste("g", 0:nrespcat, sep = "")



# case: no subject covariates
#
if (ncov == 0 && !casewise) {

      y<-rep(0,nrows)
      for (i in 1:nsubj) {
        k<-1
        for (j in 1:ncomp) {
           t<-rawdata[i,j]
           if (!is.na(t)) {
              y[k+t]=y[k+t]+1
           }
           k <- k + nrespcat + 1
        }
      }


# case: categorical subject covariates
#
} else if (ncov>0 && !casewise) {

      y<-rep(0,totlev * nrows)
      for (i in 1:nsubj) {
          y.address <- sum((cov.case[i,]-1)*levmult)
          for (j in 1:ncomp) {
             t<-rawdata[i,j]
           if (!is.na(t)) {
                y[y.address+t+1]=y[y.address+t+1]+1
             }
          y.address <- y.address + nrespcat+1
          }
      }

# case: metric (and categorical) subject covariates
#
} else {

   if(ncov==0){
      cov<-NULL
   } else {
      cov<-cov.case %x% ones.nrows  # expand covariates for all response categories
      cov<-data.frame(cov)
   }
      case<-rep.int(1:nsubj, rep.int(nrows,nsubj))
      case<-factor(case)                            # factor for cases
      cov<-cbind(cov,case)
      cov<-data.frame(cov)
      cov$case<-factor(cov$case)
      covnames<-c(covnames,"CASE")
      covlevels<-c(covlevels,nsubj)
      k<-1
      y<-rep(0,nrows * totlev)

      for (i in 1:nsubj) {
        for (j in 1:ncomp) {
           t<-rawdata[i,j]
           if (!is.na(t)) {
              y[k+t]=y[k+t]+1
           }
           k <- k + nrespcat + 1
        }
      }

}


#
# prepare dataframe and export
#

if (nrespcat%%2==0) obj<-obj/2   ### just as long as ordinal model not clarified
                                 ### converts -2 0 2 to -1 0 1
if (ncov == 0 && !casewise) {
      dm<-data.frame(y,mu,g,obj)
      varnames<-c("mu",gamnames,objnames)
} else {
      dm<-data.frame(y,mu,g,obj,cov)
      varnames<-c("mu",gamnames,objnames,covnames)
}

### new: object specific covariates
if(!is.null(objcovs)){
   if(!is.data.frame(objcovs)) stop("object specific covariates must be specified as a data frame")
   if(any(sapply(objcovs,is.factor))) stop("object specific covariates must not be factors (use model.matrix first)")
   dm<-data.frame(dm, obj %*% as.matrix(objcovs)) # add obj covs to design data frame
   objcovnames <- colnames(objcovs)
   varnames <- c(varnames, objcovnames)
   rownames(objcovs) <- objnames
   attr(dm, which="objcovs")<-as.matrix(objcovs, drop=FALSE)
}

### new: attributes in design data frame, gamnames added 2011-08-13
attr(dm, which="objnames")<-objnames
names(dm)<-c("y",varnames)
if(!is.null(cat.scovs)) attr(dm, which="cat.scovs")<-cat.scovs  # rh 2011-03-27 wieder: 2011-08-26
##if(!is.null(cat.scovs)) attr(dm, which="cat.scovs")<-covnames  # rh 2011-08-13
if(!is.null(num.scovs)) attr(dm, which="num.scovs")<-num.scovs
attr(dm, which="categories")<-gamnames

# define factors according cat.scovs 2010-12-30
if (length(cat.scovs)>0){
   if("ALL" %in% toupper(cat.scovs)) facnam<-cov.sel else facnam<-cat.scovs
   dmnam<-intersect(facnam,colnames(dm))
   dm[dmnam]<-lapply(dm[dmnam],factor)
}

class(dm)<-c("data.frame","llbtdes")

return(dm)


# ################################################################
# #
# # GLIM commands output deprecated from 0.8-24 onwards
# #
#
# if (glimoutput) {
#
#     names(dm[,1])<-"!y"
#     write.table(dm,outFile,quote=F,row.names=F)  #
#
#     txt<-paste("$SL ",length(y),sep="")
#     write(txt,file=glimoutFile)
#
#     txt<-paste("$DATA y ",paste(varnames,collapse=" "),sep="")
#     write(txt,file=glimoutFile,append=T)
#
#     txt<-paste("$DINP '",outFile,"' 132",sep="")
#     write(txt,file=glimoutFile,append=T)
#
#     txt<-paste("$FAC mu ",ncomp," ",sep="")
#     if (ncov>0) {
#          facs<-na.omit(data.frame(covnames,covlevels))
#          txt<-paste(txt, paste(facs[,1],facs[,2],sep = " ",collapse=" "),sep="")
#     }
#     write(txt,file=glimoutFile,append=T)
#
#     if (ncov==0) {
#          txt<-"$ELIM mu"
#     } else if(casewise) {
#          txt<-"$ELIM mu*case"
#     } else {
#          txt<-paste("$ELIM mu*",paste(covnames,collapse="*"),sep="")
#     }
#     write(txt,file=glimoutFile,append=T)
#
#     write("$ERR P $YV y",file=glimoutFile,append=T)
#
#     txt<-paste("$FIT",paste(objnames,collapse="+"),sep=" ")
#     write(txt,file=glimoutFile,append=T)
#
#     write("$DISP E",file=glimoutFile,append=T)
#
#     write("$RETURN",file=glimoutFile,append=T)
# }
#
# define factors according to input data frame 2010-12-28 obsolete for the time being
# facnam<-names(facs[facs])


# if (glimoutput) {
#   invisible(dm)
# } else {
#   return(dm)
# }
}

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prefmod documentation built on May 2, 2019, 4:59 p.m.