iRF: Iterative Random Forests

#' Random forest default function
#' @method randomForest default
#' @export
"randomForest.default" <-
  function(x, y=NULL,  xtest=NULL, ytest=NULL, ntree=500,
           mtry= if (!is.null(y) && !is.factor(y))
             max(floor(ncol(x)/3), 1) else floor(sqrt(ncol(x))),
           mtry.select.prob = rep(1/ncol(x), ncol(x)),
           keep.subset.var = NULL, 
           replace=TRUE, classwt=NULL, cutoff, strata,
           sampsize = if (replace) nrow(x) else ceiling(.632*nrow(x)),
           nodesize = if (!is.null(y) && !is.factor(y)) 5 else 1,
           maxnodes=NULL,
           importance=FALSE, localImp=FALSE, nPerm=1,
           proximity, oob.prox=proximity,
           norm.votes=TRUE, do.trace=FALSE,
           keep.forest=!is.null(y) && is.null(xtest), corr.bias=FALSE,
           keep.inbag=FALSE, ...) {
    
    if (length(mtry.select.prob)!=ncol(x))
      stop('length of mtry.select.prob != ncol(x)')
    
    #mtry <- mtry + length(keep.subset.var)
    #if (mtry > ncol(x))
    #  stop("mtry + length(keep.subset.var) exceeds total number of features")
    if (is.null(keep.subset.var)) {
      subsetVar <- as.integer(0)
      subsetVarCard <- rep(0L, ntree)
      maxCard <- 0L
    } else if (is.list(keep.subset.var)) {
      stopifnot (length(keep.subset.var) == ntree)
      subsetVarCard <- as.integer(sapply(keep.subset.var, length))
      maxCard <- as.integer(max(subsetVarCard))
      subsetVar <- sapply(keep.subset.var, function(vv) {
        keep.vars <- rep(0, maxCard)
        keep.vars[1:length(vv)] <- vv
        return(as.integer(keep.vars))
        })
      
    } else {
      subsetVar <- rep(as.integer(keep.subset.var), times=ntree)
      subsetVar <- matrix(subsetVar, ncol=ntree)
      maxCard <- as.integer(length(keep.subset.var))
      subsetVarCard <- rep(maxCard, ntree)
    }
    
    stopifnot(all(subsetVar) <= ncol(x))
    
    addclass <- is.null(y)
    classRF <- addclass || is.factor(y)
    if (!classRF && length(unique(y)) <= 5) {
      warning("The response has five or fewer unique values.  Are you sure you want to do regression?")
    }
    if (classRF && !addclass && length(unique(y)) < 2)
      stop("Need at least two classes to do classification.")
    n <- nrow(x)
    p <- ncol(x)
    if (n == 0) stop("data (x) has 0 rows")
    x.row.names <- rownames(x)
    x.col.names <- if (is.null(colnames(x))) 1:ncol(x) else colnames(x)
    
    ## overcome R's lazy evaluation:
    keep.forest <- keep.forest
    
    testdat <- !is.null(xtest)
    if (testdat) {
      if (ncol(x) != ncol(xtest))
        stop("x and xtest must have same number of columns")
      ntest <- nrow(xtest)
      xts.row.names <- rownames(xtest)
    }
    
    ## Make sure mtry is in reasonable range.
    if (mtry < 1 || mtry > p)
      warning("invalid mtry: reset to within valid range")
    mtry <- max(1, min(p, round(mtry)))
    if (!is.null(y)) {
      if (length(y) != n) stop("length of response must be the same as predictors")
      addclass <- FALSE
    } else {
      if (!addclass) addclass <- TRUE
      y <- factor(c(rep(1, n), rep(2, n)))
      x <- rbind(x, x)
    }
    
    ## Check for NAs.
    if (any(is.na(x))) stop("NA not permitted in predictors")
    if (testdat && any(is.na(xtest))) stop("NA not permitted in xtest")
    if (any(is.na(y))) stop("NA not permitted in response")
    if (!is.null(ytest) && any(is.na(ytest))) stop("NA not permitted in ytest")
    
    if (is.data.frame(x)) {
      xlevels <- lapply(x, mylevels)
      ncat <- sapply(xlevels, length)
      ## Treat ordered factors as numerics.
      ncat <- ifelse(sapply(x, is.ordered), 1, ncat)
      x <- data.matrix(x)
      if(testdat) {
        if(!is.data.frame(xtest))
          stop("xtest must be data frame if x is")
        xfactor <- which(sapply(xtest, is.factor))
        if (length(xfactor) > 0) {
          for (i in xfactor) {
            if (any(! levels(xtest[[i]]) %in% xlevels[[i]]))
              stop("New factor levels in xtest not present in x")
            xtest[[i]] <-
              factor(xlevels[[i]][match(xtest[[i]], xlevels[[i]])],
                     levels=xlevels[[i]])
          }
        }
        xtest <- data.matrix(xtest)
      }
    } else {
      ncat <- rep(1, p)
      xlevels <- as.list(rep(0, p))
    }
    maxcat <- max(ncat)
    if (maxcat > 53)
      stop("Can not handle categorical predictors with more than 53 categories.")
    
    if (classRF) {
      nclass <- length(levels(y))
      ## Check for empty classes:
      if (any(table(y) == 0)) stop("Can't have empty classes in y.")
      if (!is.null(ytest)) {
        if (!is.factor(ytest)) stop("ytest must be a factor")
        if (!all(levels(y) == levels(ytest)))
          stop("y and ytest must have the same levels")
      }
      if (missing(cutoff)) {
        cutoff <- rep(1 / nclass, nclass)
      } else {
        if (sum(cutoff) > 1 || sum(cutoff) < 0 || !all(cutoff > 0) ||
            length(cutoff) != nclass) {
          stop("Incorrect cutoff specified.")
        }
        if (!is.null(names(cutoff))) {
          if (!all(names(cutoff) %in% levels(y))) {
            stop("Wrong name(s) for cutoff")
          }
          cutoff <- cutoff[levels(y)]
        }
      }
      if (!is.null(classwt)) {
        if (length(classwt) != nclass)
          stop("length of classwt not equal to number of classes")
        ## If classwt has names, match to class labels.
        if (!is.null(names(classwt))) {
          if (!all(names(classwt) %in% levels(y))) {
            stop("Wrong name(s) for classwt")
          }
          classwt <- classwt[levels(y)]
        }
        if (any(classwt <= 0)) stop("classwt must be positive")
        ipi <- 1
      } else {
        classwt <- rep(1, nclass)
        ipi <- 0
      }
    } else addclass <- FALSE
    
    if (missing(proximity)) proximity <- addclass
    if (proximity) {
      prox <- matrix(0.0, n, n)
      proxts <- if (testdat) matrix(0, ntest, ntest + n) else double(1)
    } else {
      prox <- proxts <- double(1)
    }
    
    if (localImp) {
      importance <- TRUE
      impmat <- matrix(0, p, n)
    } else impmat <- double(1)
    
    if (importance) {
      if (nPerm < 1) nPerm <- as.integer(1) else nPerm <- as.integer(nPerm)
      if (classRF) {
        impout <- matrix(0.0, p, nclass + 2)
        impSD <- matrix(0.0, p, nclass + 1)
      } else {
        impout <- matrix(0.0, p, 2)
        impSD <- double(p)
        names(impSD) <- x.col.names
      }
    } else {
      impout <- double(p)
      impSD <- double(1)
    }
    
    nsample <- if (addclass) 2 * n else n
    Stratify <- length(sampsize) > 1
    if ((!Stratify) && sampsize > nrow(x)) stop("sampsize too large")
    if (Stratify && (!classRF)) stop("sampsize should be of length one")
    if (classRF) {
      if (Stratify) {
        if (missing(strata)) strata <- y
        if (!is.factor(strata)) strata <- as.factor(strata)
        nsum <- sum(sampsize)
        if (length(sampsize) > nlevels(strata))
          stop("sampsize has too many elements.")
        if (any(sampsize <= 0) || nsum == 0)
          stop("Bad sampsize specification")
        ## If sampsize has names, match to class labels.
        if (!is.null(names(sampsize))) {
          sampsize <- sampsize[levels(strata)]
        }
        if (any(sampsize > table(strata)))
          stop("sampsize can not be larger than class frequency")
      } else {
        nsum <- sampsize
      }
      nrnodes <- 2 * trunc(nsum / nodesize) + 1
    } else {
      ## For regression trees, need to do this to get maximal trees.
      nrnodes <- 2 * trunc(sampsize/max(1, nodesize - 4)) + 1
    }
    if (!is.null(maxnodes)) {
      ## convert # of terminal nodes to total # of nodes
      maxnodes <- 2 * maxnodes - 1
      if (maxnodes > nrnodes) warning("maxnodes exceeds its max value.")
      nrnodes <- min(c(nrnodes, max(c(maxnodes, 1))))
    }
    ## Compiled code expects variables in rows and observations in columns.
    x <- t(x)
    storage.mode(x) <- "double"
    if (testdat) {
      xtest <- t(xtest)
      storage.mode(xtest) <- "double"
      if (is.null(ytest)) {
        ytest <- labelts <- 0
      } else {
        labelts <- TRUE
      }
    } else {
      xtest <- double(1)
      ytest <- double(1)
      ntest <- 1
      labelts <- FALSE
    }
    nt <- if (keep.forest) ntree else 1
    
    # pre allocate matrices for tracking feature and observation data at each
    # node
   
    if (classRF) {
      cwt <- classwt
      threshold <- cutoff
      error.test <- if (labelts) double((nclass+1) * ntree) else double(1)
      rfout <- .C("classRF",
                  x = x,
                  xdim = as.integer(c(p, n)),
                  y = as.integer(y),
                  nclass = as.integer(nclass),
                  ncat = as.integer(ncat),
                  maxcat = as.integer(maxcat),
                  sampsize = as.integer(sampsize),
                  strata = if (Stratify) as.integer(strata) else integer(1),
                  Options = as.integer(c(addclass,
                                         importance,
                                         localImp,
                                         proximity,
                                         oob.prox,
                                         do.trace,
                                         keep.forest,
                                         replace,
                                         Stratify,
                                         keep.inbag)),
                  ntree = as.integer(ntree),
                  mtry = as.integer(mtry),
                  selprob = as.double(mtry.select.prob),
                  subsetVar = subsetVar, 
                  subsetVarCard = subsetVarCard, 
                  maxCard = maxCard,
                  ipi = as.integer(ipi),
                  classwt = as.double(cwt),
                  cutoff = as.double(threshold),
                  nodesize = as.integer(nodesize),
                  outcl = integer(nsample),
                  counttr = integer(nclass * nsample),
                  prox = prox,#
                  impout = impout,
                  impSD = impSD,
                  impmat = impmat,
                  nrnodes = as.integer(nrnodes),#
                  ndbigtree = integer(ntree),
                  nodestatus = integer(nt * nrnodes),
                  bestvar = integer(nt * nrnodes),#
                  treemap = integer(nt * 2 * nrnodes),
                  nodepred = integer(nt * nrnodes),
                  xbestsplit = double(nt * nrnodes),
                  errtr = double((nclass+1) * ntree),
                  testdat = as.integer(testdat),
                  xts = as.double(xtest),
                  clts = as.integer(ytest),
                  nts = as.integer(ntest),
                  countts = double(nclass * ntest),
                  outclts = as.integer(numeric(ntest)),
                  labelts = as.integer(labelts),
                  proxts = proxts,
                  errts = error.test,
                  inbag = if (keep.inbag)
                    matrix(integer(n * ntree), n) else integer(n),
                  DUP=FALSE,
                  PACKAGE="iRF"
      )[-1]  
      if (keep.forest) {
        ## deal with the random forest outputs
        max.nodes <- max(rfout$ndbigtree)
        treemap <- aperm(array(rfout$treemap, dim = c(2, nrnodes, ntree)),
                         c(2, 1, 3))[1:max.nodes, , , drop=FALSE]
      }
      if (!addclass) {
        ## Turn the predicted class into a factor like y.
        out.class <- factor(rfout$outcl, levels=1:nclass,
                            labels=levels(y))
        names(out.class) <- x.row.names
        con <- table(observed = y,
                     predicted = out.class)[levels(y), levels(y)]
        con <- cbind(con, class.error = 1 - diag(con)/rowSums(con))
      }
      out.votes <- t(matrix(rfout$counttr, nclass, nsample))[1:n, ]
      oob.times <- rowSums(out.votes)
      if (norm.votes)
        out.votes <- t(apply(out.votes, 1, function(x) x/sum(x)))
      dimnames(out.votes) <- list(x.row.names, levels(y))
      class(out.votes) <- c(class(out.votes), "votes")
      if (testdat) {
        out.class.ts <- factor(rfout$outclts, levels=1:nclass,
                               labels=levels(y))
        names(out.class.ts) <- xts.row.names
        out.votes.ts <- t(matrix(rfout$countts, nclass, ntest))
        dimnames(out.votes.ts) <- list(xts.row.names, levels(y))
        if (norm.votes)
          out.votes.ts <- t(apply(out.votes.ts, 1,
                                  function(x) x/sum(x)))
        class(out.votes.ts) <- c(class(out.votes.ts), "votes")
        if (labelts) {
          testcon <- table(observed = ytest,
                           predicted = out.class.ts)[levels(y), levels(y)]
          testcon <- cbind(testcon,
                           class.error = 1 - diag(testcon)/rowSums(testcon))
        }
      }
      cl <- match.call()
      cl[[1]] <- as.name("randomForest")
      out <- list(call = cl,
                  type = if (addclass) "unsupervised" else "classification",
                  predicted = if (addclass) NULL else out.class,
                  err.rate = if (addclass) NULL else t(matrix(rfout$errtr,
                                                              nclass+1, ntree,
                                                              dimnames=list(c("OOB", levels(y)), NULL))),
                  confusion = if (addclass) NULL else con,
                  votes = out.votes,
                  oob.times = oob.times,
                  classes = levels(y),
                  importance = if (importance)
                    matrix(rfout$impout, p, nclass+2,
                           dimnames = list(x.col.names,
                                           c(levels(y), "MeanDecreaseAccuracy",
                                             "MeanDecreaseGini")))
                  else matrix(rfout$impout, ncol=1,
                              dimnames=list(x.col.names, "MeanDecreaseGini")),
                  importanceSD = if (importance)
                    matrix(rfout$impSD, p, nclass + 1,
                           dimnames = list(x.col.names,
                                           c(levels(y), "MeanDecreaseAccuracy")))
                  else NULL,
                  localImportance = if (localImp)
                    matrix(rfout$impmat, p, n,
                           dimnames = list(x.col.names,x.row.names)) else NULL,
                  proximity = if (proximity) matrix(rfout$prox, n, n,
                                                    dimnames = list(x.row.names, x.row.names)) else NULL,
                  ntree = ntree,
                  mtry = mtry,
                  forest = if (!keep.forest) NULL else {
                    list(ndbigtree = rfout$ndbigtree,
                         nodestatus = matrix(rfout$nodestatus,
                                             ncol = ntree)[1:max.nodes,, drop=FALSE],
                         bestvar = matrix(rfout$bestvar, ncol = ntree)[1:max.nodes,, drop=FALSE],
                         treemap = treemap,
                         nodepred = matrix(rfout$nodepred,
                                           ncol = ntree)[1:max.nodes,, drop=FALSE],
                         xbestsplit = matrix(rfout$xbestsplit,
                                             ncol = ntree)[1:max.nodes,, drop=FALSE],
                         pid = rfout$classwt, cutoff=cutoff, ncat=ncat,
                         maxcat = maxcat,
                         nrnodes = max.nodes, ntree = ntree,
                         nclass = nclass, xlevels=xlevels)
                  },
                  test = if(!testdat) NULL else list(
                    predicted = out.class.ts,
                    err.rate = if (labelts) t(matrix(rfout$errts, nclass+1,
                                                     ntree,
                                                     dimnames=list(c("Test", levels(y)), NULL))) else NULL,
                    confusion = if (labelts) testcon else NULL,
                    votes = out.votes.ts,
                    proximity = if(proximity) matrix(rfout$proxts, nrow=ntest,
                                                     dimnames = list(xts.row.names, c(xts.row.names,
                                                                                      x.row.names))) else NULL),
                  inbag = if (keep.inbag) rfout$inbag else NULL)
    }
    
    else {
      ymean <- mean(y)
      y <- y - ymean
      ytest <- ytest - ymean
      
      rfout <- .C("regRF",
           x,
           as.double(y),
           as.integer(c(n, p)),
           as.integer(sampsize),
           as.integer(nodesize),
           as.integer(nrnodes),
           as.integer(ntree),
           as.integer(mtry),
           selprob = as.double(mtry.select.prob),
           subsetVar = subsetVar,
           subsetVarCard = subsetVarCard,
           as.integer(c(importance, localImp, nPerm)),
           as.integer(ncat),
           as.integer(maxcat),
           as.integer(do.trace),
           as.integer(proximity),
           as.integer(oob.prox),
           as.integer(corr.bias),
           ypred = double(n),
           impout = impout,
           impmat = impmat,
           impSD = impSD,
           prox = prox,
           ndbigtree = integer(ntree),
           nodestatus = matrix(integer(nrnodes * nt), ncol=nt),
           leftDaughter = matrix(integer(nrnodes * nt), ncol=nt),
           rightDaughter = matrix(integer(nrnodes * nt), ncol=nt),
           nodepred = matrix(double(nrnodes * nt), ncol=nt),
           bestvar = matrix(integer(nrnodes * nt), ncol=nt),
           xbestsplit = matrix(double(nrnodes * nt), ncol=nt),
           mse = double(ntree),
           keep = as.integer(c(keep.forest, keep.inbag)),
           replace = as.integer(replace),
           testdat = as.integer(testdat),
           xts = xtest,
           ntest = as.integer(ntest),
           yts = as.double(ytest),
           labelts = as.integer(labelts),
           ytestpred = double(ntest),
           proxts = proxts,
           msets = double(if (labelts) ntree else 1),
           coef = double(2),
           oob.times = integer(n),
           inbag = if (keep.inbag)
             matrix(integer(n * ntree), n) else integer(1),
           DUP=FALSE,
           PACKAGE="iRF")[-1]
    
      ## Format the forest component, if present.
      if (keep.forest) {
        max.nodes <- max(rfout$ndbigtree)
        rfout$nodestatus <-
          rfout$nodestatus[1:max.nodes, , drop=FALSE]
        rfout$bestvar <-
          rfout$bestvar[1:max.nodes, , drop=FALSE]
        rfout$nodepred <-
          rfout$nodepred[1:max.nodes, , drop=FALSE] + ymean
        rfout$xbestsplit <-
          rfout$xbestsplit[1:max.nodes, , drop=FALSE]
        rfout$leftDaughter <-
          rfout$leftDaughter[1:max.nodes, , drop=FALSE]
        rfout$rightDaughter <-
          rfout$rightDaughter[1:max.nodes, , drop=FALSE]
      }
      cl <- match.call()
      cl[[1]] <- as.name("randomForest")
      ## Make sure those obs. that have not been OOB get NA as prediction.
      ypred <- rfout$ypred
      if (any(rfout$oob.times < 1)) {
        ypred[rfout$oob.times == 0] <- NA
      }
      out <- list(call = cl,
                  type = "regression",
                  predicted = structure(ypred + ymean, names=x.row.names),
                  mse = rfout$mse,
                  rsq = 1 - rfout$mse / (var(y) * (n-1) / n),
                  oob.times = rfout$oob.times,
                  importance = if (importance) matrix(rfout$impout, p, 2,
                                                      dimnames=list(x.col.names,
                                                                    c("%IncMSE","IncNodePurity"))) else
                                                                      matrix(rfout$impout, ncol=1,
                                                                             dimnames=list(x.col.names, "IncNodePurity")),
                  importanceSD=if (importance) rfout$impSD else NULL,
                  localImportance = if (localImp)
                    matrix(rfout$impmat, p, n, dimnames=list(x.col.names,
                                                             x.row.names)) else NULL,
                  proximity = if (proximity) matrix(rfout$prox, n, n,
                                                    dimnames = list(x.row.names, x.row.names)) else NULL,
                  ntree = ntree,
                  mtry = mtry,
                  forest = if (keep.forest)
                    c(rfout[c("ndbigtree", "nodestatus", "leftDaughter",
                              "rightDaughter", "nodepred", "bestvar",
                              "xbestsplit")],
                      list(ncat = ncat), list(nrnodes=max.nodes),
                      list(ntree=ntree), list(xlevels=xlevels)) else NULL,
                  coefs = if (corr.bias) rfout$coef else NULL,
                  y = y + ymean,
                  feature.nodes = rfout$featurenodes,
                  test = if(testdat) {
                    list(predicted = structure(rfout$ytestpred + ymean,
                                               names=xts.row.names),
                         mse = if(labelts) rfout$msets else NULL,
                         rsq = if(labelts) 1 - rfout$msets /
                           (var(ytest) * (n-1) / n) else NULL,
                         proximity = if (proximity)
                           matrix(rfout$proxts / ntree, nrow = ntest,
                                  dimnames = list(xts.row.names,
                                                  c(xts.row.names,
                                                    x.row.names))) else NULL)
                  } else NULL,
                  inbag = if (keep.inbag)
                    matrix(rfout$inbag, nrow(rfout$inbag),
                           dimnames=list(x.row.names, NULL)) else NULL)
    }
    # HACK!
    out$y <- y
    class(out) <- "randomForest"
    return(out)
}

## mylevels() returns levels if given a factor, otherwise 0.
mylevels <- function(x) if (is.factor(x)) levels(x) else 0