R/crossval.R

Defines functions default.args simple.cv crossval

Documented in crossval

##' Cross-validation function for quadrupen fitting methods.
##'
##' Function that computes K-fold (double) cross-validated error of a
##' \code{quadrupen} fit. If no \code{lambda2} is provided, simple
##' cross validation on the \code{lambda1} parameter is performed. If
##' a vector \code{lambda2} is passed as an argument, double
##' cross-validation is performed.
##'
##' @param penalty a string for the fitting procedure used for
##' cross-validation. Either \code{"elastic.net"} or
##' \code{"bounded.reg"}, at the moment. Default is \code{elastic.net}.
##'
##' @param x matrix of features, possibly sparsely encoded
##' (experimental). Do NOT include intercept.
##'
##' @param y response vector.
##'
##' @param K integer indicating the number of folds. Default is 10.
##'
##' @param folds list of \code{K} vectors that describes the folds to
##' use for the cross-validation. By default, the folds are randomly
##' sampled with the specified K. The same folds are used for each
##' values of \code{lambda2}.
##'
##' @param lambda2 tunes the \eqn{\ell_2}{l2}-penalty (ridge-like) of
##' the fit. If none is provided, the default scalar value of the
##' corresponding fitting method is used and a simple CV is
##' performed. If a vector of values is given, double cross-validation
##' is performed (both on \code{lambda1} and \code{lambda2}, using the
##' same folds for each \code{lambda2}).
##'
##' @param verbose logical; indicates if the progression (the current
##' lambda2) should be displayed. Default is \code{TRUE}.
##'
##' @param mc.cores the number of cores to use. The default uses all
##' the cores available.
##'
##' @param ... additional parameters to overwrite the defaults of the
##' fitting procedure identified by the \code{'penalty'} argument. See
##' the corresponding documentation (\code{\link{elastic.net}} or
##' \code{\link{bounded.reg}}).
##'
##' @note If the user runs the fitting method with option
##' \code{'bulletproof'} set to \code{FALSE}, the algorithm may stop
##' at an early stage of the path. Early stops are handled internally,
##' in order to provide results on the same grid of penalty tuned by
##' \eqn{\lambda_1}{lambda1}.  This is done by means of \code{NA}
##' values, so as mean and standard error are consistently
##' evaluated. If, while cross-validating, the procedure experiences
##' too many early stoppings, a warning is sent to the user, in which
##' case you should reconsider the grid of \code{lambda1} used for the
##' cross-validation.  If \code{bulletproof} is \code{TRUE} (the
##' default), there is nothing to worry about, except a possible slow
##' down when any switching to the proximal algorithm is required.
##'
##' @return An object of class "cvpen" for which a \code{plot} method
##' is available.
##'
##' @seealso \code{\linkS4class{quadrupen}}, \code{\link{plot,cvpen-method}}
##' and \code{\linkS4class{cvpen}}.
##'
##' @examples \dontrun{
##' ## Simulating multivariate Gaussian with blockwise correlation
##' ## and piecewise constant vector of parameters
##' beta <- rep(c(0,1,0,-1,0), c(25,10,25,10,25))
##' cor  <- 0.75
##' Soo  <- toeplitz(cor^(0:(25-1))) ## Toeplitz correlation for irrelevant variable
##' Sww  <- matrix(cor,10,10) ## bloc correlation between active variables
##' Sigma <- bdiag(Soo,Sww,Soo,Sww,Soo) + 0.1
##' diag(Sigma) <- 1
##' n <- 100
##' x <- as.matrix(matrix(rnorm(95*n),n,95) %*% chol(Sigma))
##' y <- 10 + x %*% beta + rnorm(n,0,10)
##'
##' ## Use fewer lambda1 values by overwritting the default parameters
##' ## and cross-validate over the sequences lambda1 and lambda2
##' cv.double <- crossval(x,y, lambda2=10^seq(2,-2,len=50), nlambda1=50)
##' ## Rerun simple cross-validation with the appropriate lambda2
##' cv.10K <- crossval(x,y, lambda2=slot(cv.double, "lambda2.min"))
##' ## Try leave one out also
##' cv.loo <- crossval(x,y, K=n, lambda2=slot(cv.double, "lambda2.min"))
##'
##' plot(cv.double)
##' plot(cv.10K)
##' plot(cv.loo)
##'
##' ## Performance for selection purpose
##' beta.min.10K <- slot(cv.10K, "beta.min")
##' beta.min.loo <- slot(cv.loo, "beta.min")
##'
##' cat("\nFalse positives with the minimal 10-CV choice: ", sum(sign(beta) != sign(beta.min.10K)))
##' cat("\nFalse positives with the minimal LOO-CV choice: ", sum(sign(beta) != sign(beta.min.loo)))
##' }
##'
##' @importFrom utils modifyList
##' @keywords models, regression
##' @name crossval
##' @aliases crossval
##' @rdname crossval
##'
##' @export
crossval <- function(x,
                     y,
                     penalty  = c("elastic.net", "bounded.reg"),
                     K        = 10,
                     folds    = split(sample(1:nrow(x)), rep(1:K, length=nrow(x))),
                     lambda2  = 0.01,
                     verbose  = TRUE,
                     mc.cores = detectCores(),
                     ...) {

  ## =============================================================
  ## INITIALIZATION & PARAMETERS RECOVERY
  if (Sys.info()[['sysname']] == "Windows") {
    warning("\nWindows does not support fork, enforcing mc.cores to '1'.")
    mc.cores <- 1
  }
  penalty <- match.arg(penalty)
  get.lambda1 <- switch(penalty,
                        "elastic.net" = get.lambda1.l1,
                        "bounded.reg" = get.lambda1.li)
  user <- list(...)
  defs <- default.args(penalty,nrow(x)-max(sapply(folds,length)),ncol(x),user)
  args <- modifyList(defs, user)
  
  ## Compute a grid of lambda1 (the same for each fold)
  if (is.null(args$lambda1)) {
    input <- standardize(x,y,args$intercept,args$normalize,args$penscale)
    args$lambda1 <- get.lambda1(input$xty,args$nlambda1,args$min.ratio)
    rm(input)
  }
  ## =============================================================
  if (length(lambda2) > 1) {
    ## DOUBLE CROSS-VALIDATION WORK
    if (verbose){
      cat("\nDOUBLE CROSS-VALIDATION FOR ",penalty," REGULARIZER \n\n")
      cat(length(folds),"-fold CV on the lambda1 grid for each lambda2\n", sep="")
    }
    cv <- sapply(1:length(lambda2), function(i) {
      if(verbose){
        cat(round(lambda2[i],3),"\t")
        if (i %% 5 == 0) {cat("\n")}
      }
      simple.cv(folds, x, y, args, lambda2[i], mc.cores)
    }, simplify=FALSE)
    if(verbose){cat("\n")}

    ## Recovering the best lambda1 and lambda2
    lambda1.cv <- sapply(1:length(lambda2), function(j) {
      cv.min <- min(cv[[j]]$mean)
      lambda1.min   <- max(args$lambda1[cv[[j]]$mean <= cv.min], na.rm=TRUE)
      lambda1.1se   <- max(args$lambda1[cv[[j]]$mean <(cv[[j]]$mean+cv[[j]]$serr+1e-5)[match(lambda1.min,cv[[j]]$lambda1)]], na.rm=TRUE)
      return(c(cv.min, lambda1.min, lambda1.1se))
    })
    ind.lb2.min <- which.min(lambda1.cv[1,])
    lambda2.min <- lambda2[ind.lb2.min]
    lambda1.min <- lambda1.cv[2, ind.lb2.min]
    lambda1.1se <- lambda1.cv[3, ind.lb2.min]

    ## formatting cv.error for ggplot
    cv <- data.frame(do.call(rbind,cv),lambda2=rep(lambda2,sapply(cv, function(x) length(x$lambda1))))
  } else {
    ## SIMPLE CROSS-VALIDATION WORK
    if (verbose) {
      cat("\nSIMPLE CROSS-VALIDATION FOR ",penalty," REGULARIZER \n\n")
      cat(length(folds),"-fold CV on the lambda1 grid, lambda2 is fixed.\n", sep="")
    }
    cv <- simple.cv(folds, x, y, args, lambda2, mc.cores)

    ## Recovering the best lambda1 and lambda2
    lambda1.min <- max(cv$lambda1[cv$mean <= min(cv$mean)], na.rm=TRUE)
    lambda1.1se <- max(cv$lambda1[cv$mean <(cv$mean+cv$serr+1e-5)[match(lambda1.min,cv$lambda1)]], na.rm=TRUE)
    lambda2.min <- lambda2
  }

  ## Apply the fitting procedure with these best lambda2 parameter
  args$lambda2 <- lambda2.min
  best.fit <- do.call(quadrupen, c(list(x=x,y=y),args))

  ## Finally recover the CV choice (minimum and 1-se rule)
  ind.max <- nrow(best.fit@coefficients)
  ind.min <- min(match(lambda1.min, args$lambda1),ind.max)
  ind.1se <- min(match(lambda1.1se, args$lambda1),ind.max)

  beta.min <- best.fit@coefficients[ind.min,]
  beta.1se <- best.fit@coefficients[ind.1se,]

  return(new("cvpen",
             lambda1     = args$lambda1,
             lambda1.min = lambda1.min,
             lambda1.1se = lambda1.1se,
             lambda2     = lambda2,
             lambda2.min = lambda2.min,
             cv.error    = cv,
             folds       = folds,
             beta.min    = beta.min,
             beta.1se    = beta.1se))
}

simple.cv <- function(folds, x, y, args, lambda2, mc.cores) {

  K <- length(folds)
  n <- length(y)

  ## overwrite irrelevant arguments
  args$control$verbose <- 0
  args$lambda2  <- lambda2
  args$max.feat <- ncol(x)

  ## Multicore approach
  one.fold <- function(k) {
    omit <- folds[[k]]
    fit <- do.call(quadrupen, c(list(x=x[-omit, ], y=y[-omit]), args))
    fold.err <- sweep(matrix(predict(fit,matrix(x[omit,], nrow=length(omit))), nrow=length(omit)), 1L, y[omit], check.margin = FALSE)^2
    if (ncol(fold.err) < length(args$lambda1)) {
      NAs <- length(args$lambda1)-ncol(fold.err)
      fold.err <- cbind(fold.err, matrix(NA,nrow(fold.err),NAs))
    }
    return(fold.err)
  }
  ## turn a list to matrix
  err  <- do.call(rbind,mclapply(1:K, one.fold, mc.cores=mc.cores,
                                 mc.preschedule=ifelse(K > 10,TRUE,FALSE)))
  ## efficient computation of means and the standard error
  mean <- colMeans(err, na.rm=TRUE)
  if (any(is.nan(mean))) {
    warning("\nThere have been a lot of early stops along the path: I keep on running, but you really should reconsider 'min.ratio' regarding the n<<p setting.")
  }
  mean[is.nan(mean)] <- NA
  serr <- sqrt((colSums(sweep(err, 2L, mean, check.margin = FALSE)^2,na.rm=TRUE)/(n-1)) /K)

  return(data.frame(mean=mean, serr=serr, lambda1=args$lambda1))
}

default.args <- function(penalty,n,p,user) {
  lambda2 <- ifelse(is.null(user$lambda2),0.01,user$lambda2)
  return(list(
    beta0     = NULL,
    lambda1   = NULL,
    lambda2   = 0.01,
    penalty   = penalty,
    penscale  = rep(1,p),
    struct    = NULL,
    intercept = TRUE,
    normalize = TRUE,
    naive     = FALSE,
    nlambda1  = ifelse(is.null(user$lambda1),100,length(user$lambda1)),
    min.ratio = ifelse(n<p,0.01,5e-3),
    max.feat  = ifelse(lambda2<1e-2,min(n,p),min(4*n,p)),
    control   = list()))
}

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quadrupen documentation built on April 30, 2018, 5:04 p.m.