R/methods.R

Defines functions confint.hdi plot.clusterGroupTest plot.clusterGroupBound print.hdi

Documented in plot.clusterGroupBound

print.hdi <- function(x, ...)
{
  ## Purpose:
  ## ----------------------------------------------------------------------
  ## Arguments:
  ## ----------------------------------------------------------------------
  ## Author: Lukas Meier, Date:  3 Apr 2013, 15:12

  method <- if(is.list(x)) x$method else ""

  #####################
  ## Multi-Splitting ##
  #####################

  if(method == "multi.split"){
    cat("alpha = 0.01:")
    cat(" Selected predictors:", which(x$pval.corr <= 0.01), "\n")
    cat("alpha = 0.05:")
    cat(" Selected predictors:", which(x$pval.corr <= 0.05), "\n")
    cat("------\n")
    cat("Familywise error rate controlled at level alpha.\n")
  }

  ###############
  ## Stability ##
  ###############

  else if(method == "stability"){
    cat("Selected predictors:\n")
    cat("--------------------\n")
    if(is.null(x$select)){
      cat("none\n")
    }else{
      print(x$select)
    }

    ##for(i in 1:length(x$select)){
    ##  cat("EV = ", x$EV[[i]], ":", sep = "")
    ##  cat(" Selected predictors:", x$select[[i]], "\n")
    #}
    cat("--------------------\n")
    cat("Expected number of false positives controlled at level", x$EV, "\n")
  }

  #########################
  ## Cluster Lower-Bound ##
  #########################

  else if(method == "clusterGroupBound"){
    cat("lower l1-norm group bounds in a hierarchical clustering:")
    cat("\n- lower bound on l1-norm of *all* regression coefficients:",
        signif(max(x$lowerBound),4))

    leaf.p.bnd <- x$isLeaf & x$lowerBound > 0
    if(sum(leaf.p.bnd) == 1){
      tmp <- sum(x$noMembers[which(leaf.p.bnd)])
      cat("\n- only 1 significant non-overlapping cluster with", tmp ,
          if(tmp == 1) "member" else "members")
    }else{
      cat("\n- number of non-overlapping significant clusters:",
          sum(leaf.p.bnd))
      tmp <- range(x$noMembers[which(leaf.p.bnd)])
      if(diff(tmp) == 0){
        cat("\n  (with", tmp[1],
          if(tmp[1] == 1) "member in each non-overlapping cluster)" else
            "members in each non-overlapping cluster)")
      }else{
        cat("\n  (with", paste(tmp, collapse = " "), "members each)")
      }
    }
    cat("\n ")
  }

  ######################
  ## Other situations ##
  ######################

  else{
    print.default(x, ...)
  }
  
  invisible(x) # as *every* print() method
}

## ---> help page is ../man/plotClusterGroupBound.rd
##                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
plot.clusterGroupBound <- function(x, cexfactor = 1, yaxis = "members",
                                   xlab = "", col = NULL, pch = 20, ...)
{
  if(yaxis == "members") {
    hh <- x$noMembers
    hh2 <- sqrt(x$lowerBound)
  } else { # not "members" : "reverse" behavior:
    hh  <- x$lowerBound
    hh2 <- sqrt(x$noMembers)
  }
  hh2 <- hh2 / max(hh2)
  xvec <- x$position

  col <- if(yaxis == "members") rgb(0.8,0.2,0.2,0.6) else rgb(0.2,0.2,0.8,0.6)

  plot(xvec, hh, cex = 1, axes = FALSE, xlab = xlab,
       ylab = if(yaxis == "members") "cluster size" else "lower l1-norm bound",
       pch=pch, col = "white", log = if(yaxis == "members") "y" else "",
       ...)

  axis(2)
  coll <- rgb(0.1, 0.1, 0.1, 0.7)

  for(k in length(x$position):1){
    if((nm <- x$leftChild[k]) > 0){
      lines(c(xvec[k],  xvec[nm]), c(hh[k], hh[k]),  col=coll)
      lines(c(xvec[nm], xvec[nm]), c(hh[k], hh[nm]), col=coll)
    }
    if((nm <- x$rightChild[k]) > 0){
      lines(c(xvec[k],  xvec[nm]), c(hh[k],hh[k]),  col= coll)
      lines(c(xvec[nm], xvec[nm]), c(hh[k],hh[nm]), col= coll)
    }
  }
  points(xvec, hh, cex = sqrt(hh2) * 4 * cexfactor, col = "white", pch=pch)
  points(xvec, hh, cex = sqrt(hh2) * 4 * cexfactor, col = col,     pch=pch)
}

## FIXME: provide help page
plot.clusterGroupTest <- function(x, ...)
{
  ## Purpose:
  ## facilitate the creation of clusterGrouptest based on the
  ## group.testing.function
  ## Author: Ruben Dezeure, original version 26th of May 2014

  p <- length(x$hh$order)

  ## need to change the ordering for the plot function plot.clusterGroupBound
  clusters   <- x$clusters
  lowerbound <- ifelse(x$pval <= x$alpha, 1, 0)
  leftChild  <- x$leftChild
  rightChild <- x$rightChild
  hh         <- x$hh

  ## order clustering according to increasing sizes
  ## orig.indexing <- 1:length(clusters)
  sizes         <- vapply(clusters, length, 1L)
  new.indexing  <- sort.list(sizes)
  clusters      <- clusters[new.indexing]
  lowerbound    <- lowerbound[new.indexing]

  ## need to reorganise this reordering of leftchild rightchild better!
  w.child               <- leftChild[new.indexing] > 0
  n.leftChild           <- rep(-1, length(leftChild))
  n.leftChild[w.child]  <- match(leftChild[new.indexing][w.child], new.indexing)
  w.child               <- rightChild[new.indexing] > 0
  n.rightChild          <- rep(-1, length(rightChild))
  n.rightChild[w.child] <- match(rightChild[new.indexing][w.child], new.indexing)

  ## get the positioning
  ord      <- hh$order##ordering from the cluster
  position <- numeric(length(clusters))
  for(i in 1:length(clusters)){
    position[i] <- mean(((1:length(ord)))[ord %in% clusters[[i]]] / p)
  }
  ## Get left child and right child of each signif node from the clustering

  input <- list("noMembers"  = unlist(lapply(clusters,FUN=length)),
                ## A vector containing the number of members in each group
                "lowerBound" = lowerbound,
                ## The lower bound on the l1-norm in each group
                "position"   = position,
                ## The position on the x-axis of each group (used for plotting)
                "leftChild"  = n.leftChild,
                ## Gives the index of the group that corresponds to the left
                ## child node in the tested tree (negative values correspond
                ## to leaf nodes)
                "rightChild" = n.rightChild)
                ## Same as leftChild for the right child of each node

  plot.clusterGroupBound(input,...)
}

## not on any help page yet:
confint.hdi <- function(object, parm, level = 0.95, ...)
{
  ## Author: Lukas Meier, Date: 27 Jun 2014, 11:30
  
  meth <- object$method
  obj <- switch(meth,
                "lasso.proj"  = object$bhat,
                "boot.lasso.proj"  = object$bhat,
                "ridge.proj"  = object$bhat,
                "multi.split" = object$pval.corr,
                ## otherwise :
                stop("Not supported object type ", meth))
  
  pnames <- if(is.null(names(obj))) seq_along(obj) else names(obj)
  if(missing(parm))
    parm <- pnames
  else if (is.numeric(parm))
    parm <- pnames[parm]

  if(meth %in% c("lasso.proj", "ridge.proj")){
    quant <- qnorm(1 - (1 - level) / 2)
    delta <- if(meth == "ridge.proj") object$delta[parm] else 0
    add   <- object$se[parm] * (quant + delta)
    m     <- cbind(obj[parm] - add,
                   obj[parm] + add)
  }
  else if(meth == "multi.split") {
    if(is.na(object$ci.level))
      stop("No confidence interval information available in fitted object")
    if(!missing(level) && level != object$ci.level)
      warning("Ignoring argument 'level', using 'ci.level' of fitted object")
    m <- cbind(object$lci[parm],
               object$uci[parm])
  } else if(meth == "boot.lasso.proj"){
    if(is.null(object$cboot.dist))
    {
      stop("Bootstrap output is missing the bootstrap distribution necessary to compute confidence intervals. Rerun the bootstrap with the correct options to pass on the bootstrap distribution.")
    }

    alpha <- 1 - level
    
    if((alpha/2 * object$B)%%1 == 0)
    {
      quantile.type <- 1
    }else{
      quantile.type <- 7##this is the default
    }
    
    qstar <- apply(object$cboot.dist,1,quantile,probs=c(alpha/2,1-alpha/2),
                   type=quantile.type)
    m <- cbind(obj[parm] - qstar[2,parm],
                obj[parm] - qstar[1,parm])
  }

  dimnames(m) <- list(parm, c("lower", "upper"))
  m
}

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hdi documentation built on May 31, 2017, 2:57 a.m.