R/samEL.R

In SAM: Sparse Additive Modelling

#-----------------------------------------------------------------------#
# Package: SAM                                                          #
# Method: Sparse Additive Modelling using Exponential Loss              #
#-----------------------------------------------------------------------#

#' Training function of Sparse Additive Poisson Regression
#'
#' Fit a sparse additive Poisson regression model on training data.
#'
#' The solver combines block coordinate descent, fast iterative soft-thresholding,
#' and Newton updates. Computation is accelerated by warm starts and active-set
#' screening.
#'
#' @param X Numeric training matrix with \code{n} rows (samples) and \code{d}
#'   columns (features).
#' @param y Response vector of length \code{n}; values must be non-negative integers.
#' @param p The number of basis spline functions. The default value is 3.
#' @param lambda Optional user-supplied regularization sequence. If provided,
#'   use a decreasing sequence; warm starts are used along the path and are
#'   usually much faster than fitting a single value.
#' @param nlambda The number of lambda values. The default value is 20.
#' @param lambda.min.ratio Smallest lambda as a fraction of \code{lambda.max}
#'   (the smallest value that keeps all component functions at zero). The
#'   default is \code{0.25}.
#' @param thol Stopping tolerance. The default value is \code{1e-5}.
#' @param max.ite Maximum number of iterations. The default value is \code{1e5}.
#' @param regfunc A string indicating the regularizer. The default value is "L1". You can also assign "MCP" or "SCAD" to it.
#' @param dfmax Maximum number of non-zero groups allowed. When the number of
#'   non-zero groups reaches \code{dfmax}, the regularization path is
#'   terminated early. \code{NULL} (default) means no limit.
#' @param verbose Logical; if \code{TRUE}, print iteration info for each lambda.
#' @param dev.ratio.thr Deviance ratio threshold for early stopping.
#'   When the deviance ratio \eqn{1 - D(\lambda)/D_0} exceeds this value the
#'   regularization path is terminated early. \code{NULL} (default) disables
#'   this criterion.
#' @param dev.change.thr Relative deviance change threshold for early stopping.
#'   When the relative change in deviance over the last few lambda steps falls
#'   below this value, the path is terminated. \code{NULL} (default) disables
#'   this criterion.
#' @return
#' \item{p}{
#'   The number of basis spline functions used in training.
#' }
#' \item{X.min}{
#'   Per-feature minimums from training data (used to rescale test data).
#' }
#' \item{X.ran}{
#'   Per-feature ranges from training data (used to rescale test data).
#' }
#' \item{lambda}{
#'   Sequence of regularization parameters used in training.
#' }
#' \item{w}{
#'   Solution path matrix with size \code{d*p+1} by \code{length(lambda)}; each column corresponds to one regularization parameter.
#' }
#' \item{df}{
#'   Degrees of freedom along the solution path (number of non-zero component
#'   functions).
#' }
#' \item{knots}{
#'   The \code{p-1} by \code{d} matrix. Each column contains the knots applied to the corresponding variable.
#' }
#' \item{Boundary.knots}{
#'   The \code{2} by \code{d} matrix. Each column contains the boundary points applied to the corresponding variable.
#' }
#' \item{func_norm}{
#'   Functional norm matrix (\code{d} by \code{length(lambda)}); each column
#'   corresponds to one regularization parameter.
#' }
#' @seealso \code{\link{SAM}},\code{\link{plot.samEL},\link{print.samEL},\link{predict.samEL}}
#' @examples
#'
#' ## generating training data
#' n = 200
#' d = 100
#' X = 0.5*matrix(runif(n*d),n,d) + matrix(rep(0.5*runif(n),d),n,d)
#' u = exp(-2*sin(X[,1]) + X[,2]^2-1/3 + X[,3]-1/2 + exp(-X[,4])+exp(-1)-1+1)
#' y = rep(0,n)
#' for(i in 1:n) y[i] = rpois(1,u[i])
#'
#' ## Training
#' out.trn = samEL(X,y)
#' out.trn
#'
#' ## plotting solution path
#' plot(out.trn)
#'
#' ## generating testing data
#' nt = 1000
#' Xt = 0.5*matrix(runif(nt*d),nt,d) + matrix(rep(0.5*runif(nt),d),nt,d)
#' ut = exp(-2*sin(Xt[,1]) + Xt[,2]^2-1/3 + Xt[,3]-1/2 + exp(-Xt[,4])+exp(-1)-1+1)
#' yt = rep(0,nt)
#' for(i in 1:nt) yt[i] = rpois(1,ut[i])
#'
#' ## predicting response
#' out.tst = predict(out.trn,Xt)
#' @export
samEL = function(X, y, p=3, lambda = NULL, nlambda = NULL, lambda.min.ratio = 0.25, thol=1e-5, max.ite = 1e5, regfunc="L1", dfmax = NULL, verbose = FALSE, dev.ratio.thr = NULL, dev.change.thr = NULL){

  p = .sam_validate_p(p)
  checked = .sam_validate_xy(X, y, "samEL")
  X = checked$X
  y = checked$y
  n = checked$n
  d = checked$d
  m = d * p

  if(sum(y<0)>0){
    stop("Please check the responses. (Must be non-negative)", call. = FALSE)
  }
  if (mean(y) <= 0) {
    stop("At least one positive response is required.", call. = FALSE)
  }

  lambda.info = .sam_validate_lambda(lambda, nlambda, lambda.min.ratio, default_nlambda = 20)
  if (lambda.info$supplied) {
    lambda = lambda.info$lambda
    nlambda = lambda.info$nlambda
  } else {
    nlambda = lambda.info$nlambda
  }

  scaled = .sam_scale_training(X)
  X = scaled$X

  fit = list(p = p, X.min = scaled$X.min, X.ran = scaled$X.ran)

  basis = .sam_build_basis(X, p)
  Z = basis$Z
  fit$knots = basis$knots
  fit$Boundary.knots = basis$Boundary.knots

  L0 = norm(Z,"f")^2

  #if(n>d) L0 = max(eigen(Z%*%t(Z), symmetric=T, only.values = T)$values) else L0 = max(eigen(t(Z)%*%Z, symmetric=T, only.values = T)$values)


  Z = cbind(Z,rep(1,n))

  a0 = log(mean(y))

  z = colSums(matrix(rep(y,m+1),n,m+1)*Z)

  if(!lambda.info$supplied){
    g = -z + colSums(matrix(rep(exp(a0),m+1),n,m+1)*Z)

    lambda_max=max(sqrt(colSums(matrix(g[1:(p*d)],p,d)^2)))
    lambda = exp(seq(log(1),log(lambda.min.ratio),length=nlambda))*lambda_max
  }

  dfmax_c = if (is.null(dfmax)) -1L else as.integer(dfmax)
  verbose_c = as.integer(verbose)

  runtime = proc.time()
  dev_ratio_c = if (is.null(dev.ratio.thr)) -1.0 else as.double(dev.ratio.thr)
  dev_change_c = if (is.null(dev.change.thr)) -1.0 else as.double(dev.change.thr)

  out = .C("grpPR", A = as.double(Z), y = as.double(y), lambda = as.double(lambda), nlambda = as.integer(nlambda),
           LL0 = as.double(L0), nn = as.integer(n), dd = as.integer(d), pp = as.integer(p),
           xx = as.double(matrix(0,m+1,nlambda)), aa0 = as.double(a0), mmax_ite = as.integer(max.ite),
           tthol = as.double(thol), regfunc = as.character(regfunc), aalpha = as.double(0.5),
           z = as.double(z),df = as.integer(rep(0,nlambda)),func_norm = as.double(matrix(0,d,nlambda)), ddfmax = dfmax_c, vverbose = verbose_c, ddev_ratio_thr = dev_ratio_c, ddev_change_thr = dev_change_c, PACKAGE="SAM")
  runtime = proc.time() - runtime

  fit$lambda = out$lambda
  fit$w = matrix(out$xx,ncol=nlambda)
  fit$df = out$df
  fit$func_norm = matrix(out$func_norm,ncol=nlambda)
  fit$runtime = runtime

  class(fit) = "samEL"
  return(fit)
}

#' Printing function for S3 class \code{"samEL"}
#'
#' Print a summary of an object of class \code{"samEL"}.
#'
#' The output includes the regularization path length and its degrees of
#' freedom.
#'
#' @param x An object with S3 class \code{"samEL"}
#' @param \dots Additional arguments passed to methods; currently unused.
#' @seealso \code{\link{samEL}}
#' @export
print.samEL = function(x,...){
  .sam_print_path(x, ...)
}

#' Plot function for S3 class \code{"samEL"}
#'
#' Plot the regularization path (regularization parameter versus functional
#' norm).
#'
#' The x-axis shows regularization parameters on a log scale. The y-axis shows
#' the functional norm of each component function.
#'
#' @param x An object with S3 class \code{"samEL"}
#' @param \dots Additional arguments passed to methods; currently unused.
#' @seealso \code{\link{samEL}}
#' @export
plot.samEL = function(x,...){
  .sam_plot_path(x, ...)
}

#' Prediction function for S3 class \code{"samEL"}
#'
#' Predict expected counts for test data.
#'
#' The test matrix is rescaled using the training \code{X.min}/\code{X.ran},
#' truncated to \code{[0, 1]}, and expanded with the same spline basis used
#' during training.
#'
#' @param object An object with S3 class \code{"samEL"}.
#' @param newdata Numeric test matrix with \code{n} rows and \code{d} columns.
#' @param \dots Additional arguments passed to methods; currently unused.
#' @return
#' \item{expectations}{
#'   Estimated expected counts as an \code{n} by \code{length(lambda)} matrix.
#' }
#' \item{expectation}{
#'   Alias of \code{expectations} kept for backward compatibility.
#' }
#' @seealso \code{\link{samEL}}
#' @export
predict.samEL = function(object, newdata,...){
  newdata = .sam_scale_newdata(object, newdata)
  nt = nrow(newdata)
  Zt = .sam_build_basis_newdata(object, newdata)

  out = list()
  out$expectation = exp(cbind(Zt, rep(1, nt)) %*% object$w)
  out$expectations = out$expectation

  return(out)
}