randomForestSRC (version 2.8.0)

quantileReg: Quantile Regression Forests

Description

Grows a univariate or multivariate quantile regression forest and returns its conditional quantile and density values. Can be used for both training and testing purposes.

Usage

# S3 method for rfsrc
quantileReg(formula, data, object, newdata,
  method = "forest", prob = NULL, prob.epsilon = NULL,
  oob = TRUE, fast = FALSE, maxn = 1e3, ...)

Arguments

formula

A symbolic description of the model to be fit. Must be specified unless object is given.

data

Data frame containing the y-outcome and x-variables in the model. Must be specified unless object is given.

object

(Optional) A previously grown quantile regression forest.

method

Method used to calculate quantiles. Forest weighted averaging is used by default. While this works well for standard data, consider using the Greenwald-Khanna algorithm for big data. The latter is specified by any one of the following: "gk", "GK", "G-K", "g-k".

prob

Target quantile probabilities when training. If left unspecified, uses percentiles (1 through 99) for method = "forest", and for Greenwald-Khanna selects equally spaced percentiles optimized for accuracy (see below).

prob.epsilon

Greenwald-Khanna allowable error for quantile probabilities when training.

newdata

Test data (optional) over which conditional quantiles are evaluated over.

oob

Return OOB (out-of-bag) quantiles? If false, in-bag values are returned.

fast

Use fast random forests, rfsrcFast, in place of rfsrc? Improves speed but may be less accurate.

maxn

Maximum number of unique y training values used when calculating the conditional density.

...

Further arguments to be passed to the rfsrc function used for fitting the quantile regression forest.

Value

Returns quantiles for each of the requested probabilities. Also returns the conditional density (and conditional cdf) for unique y-values in the training data (or test data if provided). The conditional density can be used to calculate conditional moments, such as the mean and standard deviation. For convenience, the mean is returned as the object yhat.

For multivariate forests, the returned object will be a list of length equal to the number of target outcomes.

Details

Grows a univariate or multivariate quantile regression forest using quantile regression splitting using the new splitrule quantile.regr based on the quantile loss function (often called the "check function").

The default method for calculating quantiles is method="forest" which uses forest weights as in Meinshausen (2006). However, because quantile regression splitting is used, and not mean-squared error splitting (as used by Meinshuasen), results may differ substantially from Meinshausen. We believe quantile regression splitting will provide superior performance.

While calculating quantiles using forest weights works well for standard data, a second approach, the Greenwald-Khanna (2001) algorithm, will be more appropriate for big data due to its high memory efficiency.

The Greenwald-Khanna algorithm is implemented roughly as follows. To form a distribution of values for each case, from which we sample to determine quantiles, we create a chain of values for the case as we grow the forest. Every time a case lands in a terminal node, we insert all of its co-inhabitants to its chain of values.

The best case scenario is when tree node size is 1 because each case gets only one insert into its chain for that tree. The worst case scenario is when node size is so large that trees stump. This is because each case receives insertions for the entire in-bag population.

What the user needs to know is that Greenwald-Khanna can become slow in counter-intutive settings such as when node size is large. The easy fix is to change the epsilon quantile approximation that is requested. You will see a significant speed-up just by doubling prob.epsilon. This is because the chains stay a lot smaller as epsilon increases, which is exactly what you want when node sizes are large. Both time and space requirements for the algorithm are affected by epsilon.

The best results for Greenwald-Khanna come from setting the number of quantiles equal to 2 times the sample size and epsilon to 1 over 2 times the sample size which is the default values used if left unspecified. This will be slow, especially for big data, and less stringent choices should be used if computational speed is of concern.

References

Greenwald M. and Khanna S. (2001). Space-efficient online computation of quantile summaries. Proceedings of ACM SIGMOD, 30(2):58--66.

Meinshausen N. (2006) Quantile regression forests, Journal of Machine Learning Research, 7:983--999.

See Also

rfsrc

Examples

# NOT RUN {
## ------------------------------------------------------------
## regression example
## ------------------------------------------------------------

## standard call
o <- quantileReg(mpg ~ ., mtcars)
qo <- o$quantileReg

## calculate the conditional mean, compare to OOB predicted value
## note that the conditional mean is returned as "yhat"
c.mean <- qo$density %*% qo$yunq
print(data.frame(c.mean = c.mean, yhat = qo$yhat, pred.oob = o$predicted.oob))

## calculate conditional standard deviation
c.std <- sqrt(qo$density %*% qo$yunq^2 - c.mean ^ 2)
quant <- qo$quantile
colnames(quant) <- paste("q", 100 * qo$prob, sep = "")
print(data.frame(quant, c.std))


## ------------------------------------------------------------
## train/test regression example
## ------------------------------------------------------------

## train (grow) call followed by test call
trn <- quantileReg(mpg ~ ., mtcars[1:20,])
test <- quantileReg(object = trn, newdata = mtcars[-(1:20),-1])

## calculate test set conditional mean and standard deviation
qo <- test$quantileReg
c.mean <- qo$density %*% qo$yunq
c.std <- sqrt(qo$density %*% qo$yunq^2 - c.mean ^ 2)
quant <- qo$quant
colnames(quant) <- paste("q", 100 * qo$prob, sep = "")
print(data.frame(quant, c.mean, c.std))


## ------------------------------------------------------------
## multivariate mixed outcomes example
## ------------------------------------------------------------

dta <- mtcars
dta$cyl <- factor(dta$cyl)
dta$carb <- factor(dta$carb, ordered = TRUE)
o <- quantileReg(cbind(carb, mpg, cyl, disp) ~., data = dta)

print(head(o$quantileReg$mpg$quant))
print(head(o$quantileReg$disp$quant))


## ------------------------------------------------------------
## quantile regression plot for Boston Housing data
## ------------------------------------------------------------

if (library("mlbench", logical.return = TRUE)) {

  ## apply quantile regression to Boston Housing data
  data(BostonHousing)
  o <- quantileReg(medv ~ ., BostonHousing, nodesize = 1)
  y <- o$yvar
  qo <- o$quantileReg

  ## pull desired quantiles - nice little wrapper for doing this
  get.quantile <- function(q, target.prob) {
    target.prob <- sort(unique(target.prob))
    q.dta <- do.call(cbind, lapply(target.prob, function(pr) {
      q$quant[, which.min(abs(pr - q$prob))]
    }))
    colnames(q.dta) <-  paste("q.", 100 * target.prob, sep = "")
    q.dta
   }

  ## extract 25,50,75 quantiles
  quant.dat <- get.quantile(qo, c(.25, .50, .75))
  
  ## quantile regression plot
  plot(range(y), range(quant.dat), xlab = "y",
       ylab = ".25-.75 Quantiles", type = "n")
  jitter.y <- jitter(y, 10)
  points(jitter.y, quant.dat[, 2], pch = 15, col = 4, cex = 0.75)
  segments(jitter.y, quant.dat[, 2], jitter.y, quant.dat[, 1], col = "grey")
  segments(jitter.y, quant.dat[, 2], jitter.y, quant.dat[, 3], col = "grey")
  points(jitter.y, quant.dat[, 1], pch = "-", cex = 1)
  points(jitter.y, quant.dat[, 3], pch = "-", cex = 1)
  abline(0, 1, lty = 2, col = 2)

  ## compare 25-75 percentiles to values expected under normality
  c.mean <- qo$density %*% qo$yunq
  c.std <- sqrt(qo$density %*% qo$yunq^2 - c.mean ^ 2)
  q.25.est <- c.mean + qnorm(.25) * c.std
  q.75.est <- c.mean + qnorm(.75) * c.std
  print(head(data.frame(quant.dat[, -2],  q.25.est, q.75.est)))

  ## compare performance of quantile regression estimator to
  ## standard random forest estimator of averaged tree mean
  cat("quantile regression yhat error:", mean((o$yvar-qo$yhat)^2), "\n")
  cat("RF averaged tree mean error:", mean((o$yvar-o$predicted.oob)^2), "\n")


}

## ------------------------------------------------------------
## example of quantile regression for ordinal data
## ------------------------------------------------------------

 ## use the wine data for illustration
 data(wine, package = "randomForestSRC")

 ## run quantile regression
 o <- quantileReg(quality ~ ., wine, ntree = 100)

 ## extract "probabilities" = density values
 qo <- o$quantileReg
 yunq <- qo$yunq
 yvar <- factor(cut(o$yvar, c(-1, yunq), labels = yunq)) 
 qo.dens <- qo$density
 colnames(qo.dens) <- yunq 
 qo.class <- randomForestSRC:::bayes.rule(qo.dens)
 qo.confusion <- table(yvar, qo.class)
 qo.err <- 1 - diag(qo.confusion) / rowSums(qo.confusion)
 qo.confusion <- cbind(qo.confusion, qo.err)
 print(qo.confusion)
 cat("Normalized Brier:", 100 * randomForestSRC:::brier(yvar, qo.dens), "\n")

# }