R/utilities.R

In gcdnet: The (Adaptive) LASSO and Elastic Net Penalized Least Squares, Logistic Regression, Hybrid Huberized Support Vector Machines, Squared Hinge Loss Support Vector Machines and Expectile Regression using a Fast Generalized Coordinate Descent Algorithm

##' @importFrom stats approx
##' @importFrom methods new
##' @import Matrix
##' @importFrom graphics segments
#####################################################################
## These functions are minor modifications or direct copies
## from the `glmnet` package:
##
## Jerome Friedman, Trevor Hastie, Robert Tibshirani (2010).
## Regularization Paths for Generalized Linear Models via Coordinate Descent.
##   Journal of Statistical Software, 33(1), 1-22.
##   URL: https://www.jstatsoft.org/v33/i01/.
##
## The reason they are copied here is because they are internal functions
## and hence are not exported into the global environment.
## The original comments and header are preserved.


err <- function(n, maxit, pmax) {
  if (n == 0)
    msg <- ""
  if (n > 0) {
    if (n < 7777)
      msg <- "Memory allocation error"
    if (n == 7777)
      msg <- "All used predictors have zero variance"
    if (n == 10000)
      msg <- "All penalty factors are <= 0"
    n <- 1
    msg <- paste("in gcdnet fortran code -", msg)
  }
  if (n < 0) {
    if (n > -10000)
      msg <- paste("Convergence for ", -n,
                   "th lambda value not reached after maxit=", maxit,
                   " iterations; solutions for larger lambdas returned",
                   sep = "")
    if (n < -10000)
      msg <- paste("Number of nonzero coefficients along the path exceeds pmax=",
                   pmax, " at ", -n - 10000,
                   "th lambda value; solutions for larger lambdas returned",
                   sep = "")
    n <- -1
    msg <- paste("from gcdnet fortran code -", msg)
  }
  list(n = n, msg = msg)
}



error.bars <- function(x, upper, lower, width = 0.02,
                       ...) {
  xlim <- range(x)
  barw <- diff(xlim) * width
  segments(x, upper, x, lower, ...)
  segments(x - barw, upper, x + barw, upper, ...)
  segments(x - barw, lower, x + barw, lower, ...)
  range(upper, lower)
}


getmin <- function(lambda, cvm, cvsd) {
  cvmin <- min(cvm)
  idmin <- cvm <= cvmin
  lambda.min <- max(lambda[idmin])
  idmin <- match(lambda.min, lambda)
  semin <- (cvm + cvsd)[idmin]
  idmin <- cvm <= semin
  ## cat('\n\nidmin\n\n',idmin)
  ## cat('\n\nlambda[idmin]\n\n',lambda[idmin])
  ## cat('\n\nmax\n\n',max(lambda[idmin]))
  lambda.1se <- max(lambda[idmin])
  list(lambda.min = lambda.min, lambda.1se = lambda.1se)
}


getoutput <- function(fit, maxit, pmax, nvars, vnames) {
  nalam <- fit$nalam
  nbeta <- fit$nbeta[seq(nalam)]
  nbetamax <- max(nbeta)
  lam <- fit$alam[seq(nalam)]
  stepnames <- paste("s", seq(nalam) - 1, sep = "")
  errmsg <- err(fit$jerr, maxit, pmax)
  switch(paste(errmsg$n), `1` = stop(errmsg$msg, call. = FALSE),
         `-1` = print(errmsg$msg, call. = FALSE))
  dd <- c(nvars, nalam)
  if (nbetamax > 0) {
    beta <- matrix(fit$beta[seq(pmax * nalam)],
                   pmax, nalam)[seq(nbetamax), , drop = FALSE]
    df <- apply(abs(beta) > 0, 2, sum)
    ja <- fit$ibeta[seq(nbetamax)]
    oja <- order(ja)
    ja <- rep(ja[oja], nalam)
    ibeta <- cumsum(c(1, rep(nbetamax, nalam)))
    beta <- new("dgCMatrix", Dim = dd,
                Dimnames = list(vnames, stepnames),
                x = as.vector(beta[oja, ]),
                p = as.integer(ibeta - 1),
                i = as.integer(ja - 1))
  } else {
    beta <- zeromat(nvars, nalam, vnames, stepnames)
    df <- rep(0, nalam)
  }
  b0 <- fit$b0
  if (!is.null(b0)) {
    b0 <- b0[seq(nalam)]
    names(b0) <- stepnames
  }
  list(b0 = b0, beta = beta, df = df, dim = dd, lambda = lam)
}



lambda.interp <- function(lambda, s) {
  ## lambda is the index sequence that is produced by the model
  ## s is the new vector at which evaluations are required.
  ## the value is a vector of left and right indices, and a vector of fractions.
  ## the new values are interpolated bewteen the two using the fraction
  ## Note: lambda decreases. you take: sfrac*left+(1-sfrac*right)
  if (length(lambda) == 1) {
    nums <- length(s)
    left <- rep(1, nums)
    right <- left
    sfrac <- rep(1, nums)
  } else {
    s[s > max(lambda)] <- max(lambda)
    s[s < min(lambda)] <- min(lambda)
    k <- length(lambda)
    sfrac <- (lambda[1] - s)/(lambda[1] - lambda[k])
    lambda <- (lambda[1] - lambda)/(lambda[1] - lambda[k])
    coord <- approx(lambda, seq(lambda), sfrac)$y
    left <- floor(coord)
    right <- ceiling(coord)
    sfrac <- (sfrac - lambda[right])/(lambda[left] - lambda[right])
    sfrac[left == right] <- 1
  }
  list(left = left, right = right, frac = sfrac)
}


lamfix <- function(lam) {
  llam <- log(lam)
  lam[1] <- exp(2 * llam[2] - llam[3])
  lam
}


nonzero <- function(beta, bystep = FALSE) {
  ns <- ncol(beta)
  ##beta should be in 'dgCMatrix' format
  if (nrow(beta) == 1) {
    if (bystep)
      apply(beta, 2,
            function(x) if (abs(x) > 0) 1 else NULL) else {
                                                       if (any(abs(beta) > 0))
                                                         1 else NULL
                                                     }
  } else {
    beta <- t(beta)
    which <- diff(beta@p)
    which <- seq(which)[which > 0]
    if (bystep) {
      nzel <- function(x, which) if (any(x))
                                   which[x] else NULL
      beta <- abs(as.matrix(beta[, which])) > 0
      if (ns == 1)
        apply(beta, 2, nzel, which) else apply(beta, 1, nzel, which)
    } else which
  }
}



zeromat <- function(nvars, nalam, vnames, stepnames) {
  ca <- rep(0, nalam)
  ia <- seq(nalam + 1)
  ja <- rep(1, nalam)
  dd <- c(nvars, nalam)
  new("dgCMatrix", Dim = dd, Dimnames = list(vnames, stepnames),
      x = as.vector(ca), p = as.integer(ia - 1), i = as.integer(ja - 1))
}