R/stutil.R

In stepp: Subpopulation Treatment Effect Pattern Plot (STEPP)

#################################################################
#
# stutil.R
#
#################
# stepp utility #
#################
setGeneric("estimate", function(.Object, ...)
  standardGeneric("estimate"))

setGeneric("test", function(.Object, ...)
  standardGeneric("test"))  

# setGeneric("subset1", function(.Object, ...)
#  standardGeneric("subset1"))

#
# internal routine to generate covariance matrix, pvalue
#
ssigma <- function(imatrix) {
  sigma <- var(imatrix)
  sigmainv <- matrix(nrow=dim(sigma)[1], ncol=dim(sigma)[1])  # inverse matrix all NAs by default

#  catch the error if we encounter a singularity problem when inverting the matrix sigma
#
  tryCatch({
    sigmainv <- solve(sigma)
    }, error = function(ex) {
      #cat(geterrmessage())
      #cat("\n")
      #set.seed<-4593432
      #stop("STEPP has encountered an unexpected problem. Please retry. If problem persists, try different values of minpatspop(r1) and patspop(r2).")
    }
  )
     
  return (list(sigma=sigma, sigmainv=sigmainv))
}

#
# internal routine to generate the permutation pvalue
# compute the chisq or homogeneous association statistics and generate the pvalue
#
ppv <- function(imatrix, sigmainv, estarray, est, noPerms) {
  perm <- rep(NA,noPerms)
  for (i in 1:noPerms){
    temp <- matrix(imatrix[i,],ncol=1)
    perm[i] <- t(temp)%*%sigmainv%*%temp
  }
  obs <- matrix(estarray - est, ncol=1)
  obs1 <- c(t(obs)%*%sigmainv%*%obs)
  pvalue <- sum(ifelse(perm > obs1, 1, 0))/noPerms
  signif(pvalue, 6)

  return(pvalue)
}

# compute the supremum statistics and generate the pvalue
#
ppv2 <- function(imatrix, estarray, est, noPerms) {
  sigma <- sqrt(diag(var(imatrix)))
  stdDifferences <- t(apply(imatrix, 1, function(x) x/sigma))
  tPerm <- apply(abs(stdDifferences), 1, max)

  obsDifferences <- t(matrix(estarray - est, ncol=1))
  stdObsDifferences <- apply(obsDifferences, 1, function(x) x/sigma)
  tObs <- apply(abs(stdObsDifferences), 2, max)
  pvalue <- sum(ifelse(tPerm > tObs, 1, 0))/noPerms
  signif(pvalue, 6)

  return(pvalue)
}