R/gptk_cmpndKernExtractParam.R

In robin: ROBustness in Network

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# YEAR: 2013
# COPYRIGHT HOLDER: Alfredo Kalaitzis
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.cmpndKernExtractParam <-
function (kern, only.values=TRUE,
                                   untransformed.values=FALSE) {

  startVal <- 1
  endVal <- 0
  
  if ( only.values ) {
    params <- c()

    for ( i in seq(along=kern$comp) ) 
      params <- c(params, .kernExtractParam(kern$comp[[i]],
                                           untransformed.values=untransformed.values))

  } else {
    storedTypes <- c()
    params <- c()
    paramNames <- c()
    origNames <- c()
    for ( i in seq(along=kern$comp) ) {
      paramsList <- .kernExtractParam(kern$comp[[i]], only.values=only.values,
                                     untransformed.values=untransformed.values)
      params <- c(params, paramsList)
      kernName <- paste(kern$comp[[i]]$type, length(grep(kern$comp[[i]]$type, storedTypes))+1, sep="")
      paramName <- paste(kernName, names(paramsList), sep="_")
      origNames <- c(origNames, paramName)
      storedTypes <- c(storedTypes, kern$comp[[i]]$type)
    }
  }

  paramNames <- array()
  if ( "paramGroups" %in% names(kern) ) {
    paramGroups <- kern$paramGroups
    for ( i in seq(length.out=dim(paramGroups)[2]) ) {
      ind <- grep(1, paramGroups[,i])
      if ( !only.values ) {
        paramNames[i] <- origNames[ind[1]]
        for ( j in seq(2, length.out=length(ind)-1) )
          paramNames[i] <- paste(paramNames[i], origNames[ind[j]],sep="/")
      }
   
      paramGroups[ind[seq(2,length(ind),length=length(ind)-1)], i] <- 0
    }
  }

  params <- params%*%paramGroups
  if ( !only.values )
    names(params) <- paramNames

  return (params)
}