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#' Tools for Models Available in \code{train}
#'
#' These function show information about models and packages that are
#' accessible via \code{\link{train}}
#'
#' \code{modelLookup} is good for getting information related to the tuning
#' parameters for a model. \code{getModelInfo} will return all the functions
#' and metadata associated with a model. Both of these functions will only
#' search within the models bundled in this package.
#'
#' \code{checkInstall} will check to see if packages are installed. If they are
#' not and the session is interactive, an option is given to install the
#' packages using \code{\link[utils]{install.packages}} using that functions
#' default arguments (the missing packages are listed if you would like to
#' install them with other options). If the session is not interactive, an
#' error is thrown.
#'
#' @aliases modelLookup getModelInfo checkInstall
#' @param model a character string associated with the \code{method} argument
#' of \code{\link{train}}. If no value is passed, all models are returned. For
#' \code{getModelInfo}, regular expressions can be used.
#' @param regex a logical: should a regular expressions be used? If
#' \code{FALSE}, a simple match is conducted against the whole name of the
#' model.
#' @param pkg a character string of package names.
#' @param ... options to pass to \code{\link[base]{grepl}}
#' @return \code{modelLookup} produces a data frame with columns \item{model
#' }{a character string for the model code} \item{parameter }{the tuning
#' parameter name} \item{label }{a tuning parameter label (used in plots)}
#' \item{forReg }{a logical; can the model be used for regression?}
#' \item{forClass }{a logical; can the model be used for classification?}
#' \item{probModel }{a logical; does the model produce class probabilities?}
#'
#' \code{getModelInfo} returns a list containing one or more lists of the
#' standard model information.
#'
#' \code{checkInstall} returns not value.
#' @note The column \code{seq} is no longer included in the output of
#' \code{modelLookup}.
#' @author Max Kuhn
#' @seealso \code{\link{train}}, \code{\link[utils]{install.packages}},
#' \code{\link[base]{grepl}}
#' @keywords utilities
#' @examples
#'
#' \dontrun{
#' modelLookup()
#' modelLookup("gbm")
#'
#' getModelInfo("pls")
#' getModelInfo("^pls")
#' getModelInfo("pls", regex = FALSE)
#'
#' checkInstall(getModelInfo("pls")$library)
#' }
#'
#' @export modelLookup
modelLookup <- function(model = NULL){
load(system.file("models", "models.RData", package = "caret"))
if(!is.null(model)){
if(!(model %in% names(models))) stop(paste("Model '", method, "' is not in the ",
"set of existing models", sep = ""))
models <- models[model == names(models)]
}
out <- lapply(models,
function(x) {
out <- x$parameters[, c("parameter", "label")]
out$forReg <- "Regression" %in% x$type
out$forClass <- "Classification" %in% x$type
out$probModel <- !is.null(x$prob)
out
})
for(i in seq(along.with = out)) out[[i]]$model <- names(models)[i]
out <- do.call("rbind", out)
rownames(out) <- NULL
out <- out[, c('model', 'parameter', 'label', 'forReg', 'forClass', 'probModel')]
out[order(out$model),]
}
#' @importFrom utils installed.packages
missing_packages <- function(mods = getModelInfo()) {
libs <- unique(unlist(lapply(mods, function(x) x$library)))
here <- rownames(installed.packages())
libs[!(libs %in% here)]
}
#' @rdname modelLookup
#' @importFrom utils install.packages menu
#' @export
checkInstall <- function(pkg){
good <- rep(TRUE, length(pkg))
for(i in seq(along.with = pkg)){
tested <- try(find.package(pkg[i]), silent = TRUE)
if (inherits(tested, "try-error")) good[i] <- FALSE
}
if(any(!good)){
pkList <- paste(pkg[!good], collapse = ", ")
msg <- paste(sum(!good),
ifelse(sum(!good) > 1, " packages are", " package is"),
" needed and",
ifelse(sum(!good) > 1, " are", " is"),
" not installed. (",
pkList,
"). Would you like to try to install",
ifelse(sum(!good) > 1, " them", " it"),
" now?",
sep = "")
if(interactive()) {
cat(msg)
bioc <- c("affy", "logicFS", "gpls", "vbmp")
installChoice <- menu(c("yes", "no"))
if(installChoice == 1){
hasBioc <- any(pkg[!good] %in% bioc)
if(!hasBioc) {
install.packages(pkg[!good])
} else {
inst <- pkg[!good]
instC <- inst[!(inst %in% bioc)]
instB <- inst[inst %in% bioc]
if(length(instC) > 0) install.packages(instC)
biocLite <- NULL
source("http://bioconductor.org/biocLite.R")
biocLite(instB)
}
} else {
stop("Required packages are missing: ", pkList, call. = FALSE)
}
} else {
stop("Required packages are missing: ", pkList, call. = FALSE)
}
}
}
#' @rdname modelLookup
#' @export
getModelInfo <- function(model = NULL, regex = TRUE, ...) {
load(system.file("models", "models.RData", package = "caret"))
if(!is.null(model)){
keepers <- if(regex) grepl(model, names(models), ...) else which(model == names(models))[1]
models <- models[keepers]
}
if(length(models) == 0) stop("That model is not in caret's built-in library")
models
}
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