documentation of package and data now also generated via roxygen2

R/TopGear.R

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+# --------------------------------------
+# Author: Andreas Alfons
+#         Erasmus Universiteit Rotterdam
+# --------------------------------------
+
+#' Top Gear car data
+#'
+#' @description
+#' The data set contains information on cars featured on the website of the
+#' popular BBC television show \emph{Top Gear}.
+#'
+#' @usage
+#' data("TopGear")
+#'
+#' @format
+#' A data frame with 297 observations on the following 32 variables.
+#' \describe{
+#'   \item{\code{Maker}}{factor; the car maker.}
+#'   \item{\code{Model}}{factor; the car model.}
+#'   \item{\code{Type}}{factor; the exact model type.}
+#'   \item{\code{Fuel}}{factor; the type of fuel (\code{"Diesel"} or
+#'   \code{"Petrol"}).}
+#'   \item{\code{Price}}{numeric; the list price (in UK pounds)}
+#'   \item{\code{Cylinders}}{numeric; the number of cylinders in the engine.}
+#'   \item{\code{Displacement}}{numeric; the displacement of the engine (in
+#'   cc).}
+#'   \item{\code{DriveWheel}}{factor; the type of drive wheel (\code{"4WD"},
+#'   \code{"Front"} or \code{"Rear"}).}
+#'   \item{\code{BHP}}{numeric; the power of the engine (in bhp).}
+#'   \item{\code{Torque}}{numeric; the torque of the engine (in lb/ft).}
+#'   \item{\code{Acceleration}}{numeric; the time it takes the car to get from
+#'   0 to 62 mph (in seconds).}
+#'   \item{\code{TopSpeed}}{numeric; the car's top speed (in mph).}
+#'   \item{\code{MPG}}{numeric; the combined fuel consuption (urban + extra
+#'   urban; in miles per gallon).}
+#'   \item{\code{Weight}}{numeric; the car's curb weight (in kg).}
+#'   \item{\code{Length}}{numeric; the car's length (in mm).}
+#'   \item{\code{Width}}{numeric; the car's width (in mm).}
+#'   \item{\code{Height}}{numeric; the car's height (in mm).}
+#'   \item{\code{AdaptiveHeadlights}}{factor; whether the car has adaptive
+#'   headlights (\code{"no"}, \code{"optional"} or \code{"standard"}).}
+#'   \item{\code{AdjustableSteering}}{factor; whether the car has adjustable
+#'   steering (\code{"no"} or \code{"standard"}).}
+#'   \item{\code{AlarmSystem}}{factor; whether the car has an alarm system
+#'   (\code{"no/optional"} or \code{"standard"}).}
+#'   \item{\code{Automatic}}{factor; whether the car has an automatic
+#'   transmission (\code{"no"}, \code{"optional"} or \code{"standard"}).}
+#'   \item{\code{Bluetooth}}{factor; whether the car has bluetooth
+#'   (\code{"no"}, \code{"optional"} or \code{"standard"}).}
+#'   \item{\code{ClimateControl}}{factor; whether the car has climate control
+#'   (\code{"no"}, \code{"optional"} or \code{"standard"}).}
+#'   \item{\code{CruiseControl}}{factor; whether the car has cruise control
+#'   (\code{"no"}, \code{"optional"} or \code{"standard"}).}
+#'   \item{\code{ElectricSeats}}{factor; whether the car has electric seats
+#'   (\code{"no"}, \code{"optional"} or \code{"standard"}).}
+#'   \item{\code{Leather}}{factor; whether the car has a leather interior
+#'   (\code{"no"}, \code{"optional"} or \code{"standard"}).}
+#'   \item{\code{ParkingSensors}}{factor; whether the car has parking sensors
+#'   (\code{"no"}, \code{"optional"} or \code{"standard"}).}
+#'   \item{\code{PowerSteering}}{factor; whether the car has power steering
+#'   (\code{"no"} or \code{"standard"}).}
+#'   \item{\code{SatNav}}{factor; whether the car has a satellite navigation
+#'   system (\code{"no"}, \code{"optional"} or \code{"standard"}).}
+#'   \item{\code{ESP}}{factor; whether the car has ESP (\code{"no"},
+#'   \code{"optional"} or \code{"standard"}).}
+#'   \item{\code{Verdict}}{numeric; review score between 1 (lowest) and 10
+#'   (highest).}
+#'   \item{\code{Origin}}{factor; the origin of the car maker (\code{"Asia"},
+#'   \code{"Europe"} or \code{"USA"}).}
+#' }
+#'
+#' @source
+#' The data were scraped from \code{http://www.topgear.com/uk/} on 2014-02-24.
+#' Variable \code{Origin} was added based on the car maker information.
+#'
+#' @examples
+#' data("TopGear")
+#' summary(TopGear)
+
+"TopGear"

R/nci60.R

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+# --------------------------------------
+# Author: Andreas Alfons
+#         Erasmus Universiteit Rotterdam
+# --------------------------------------
+
+#' @name nci60
+#' @aliases protein
+#' @aliases gene
+#'
+#' @docType data
+#'
+#' @title NCI-60 cancer cell panel
+#'
+#' @description
+#' The data set is a pre-processed version of the NCI-60 cancer cell panel as
+#' used in Alfons, Croux & Gelper (2013).  One observation was removed since
+#' all values in the gene expression data were missing.
+#'
+#' @usage
+#' data("nci60")
+#'
+#' @format
+#' Protein and gene expression data on 59 observations are stored in two
+#' separate matrices:
+#' \describe{
+#'   \item{\code{protein}}{a matrix containing protein expressions based on
+#'   antibodies (162 variables), acquired via reverse-phase protein lysate
+#'   arrays and log2 transformed.}
+#'   \item{\code{gene}}{a matrix containing gene expression data (22283
+#'   variables), obtained with an Affymetrix HG-U133A chip and normalized
+#'   with the GCRMA method.}
+#' }
+#'
+#' @source
+#' The original data were downloaded from
+#' \url{https://discover.nci.nih.gov/cellminer/} on 2012-01-27.  They can be
+#' obtained from \url{https://github.com/aalfons/nci60}, together with our
+#' script for pre-processing.
+#'
+#' @references
+#' Reinhold, W.C., Sunshine, M., Liu, H., Varma, S., Kohn, K.W., Morris, J.,
+#' Doroshow, J. and Pommier, Y. (2012) CellMiner: A Web-Based Suite of Genomic
+#' and Pharmacologic Tools to Explore Transcript and Drug Patterns in the
+#' NCI-60 Cell Line Set. \emph{Cancer Research}, \bold{72}(14), 3499--3511.
+#'
+#' Alfons, A., Croux, C. and Gelper, S. (2013) Sparse least trimmed squares
+#' regression for analyzing high-dimensional large data sets. \emph{The Annals
+#' of Applied Statistics}, \bold{7}(1), 226--248.
+#'
+#' @examples
+#' \dontrun{
+#'
+#' # load data
+#' data("nci60")
+#' # define response variable
+#' y <- protein[, 92]
+#' # screen most correlated predictor variables
+#' correlations <- apply(gene, 2, corHuber, y)
+#' keep <- partialOrder(abs(correlations), 100, decreasing = TRUE)
+#' X <- gene[, keep]
+#' }
+
+NULL

R/robustHD-package.R

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+# --------------------------------------
+# Author: Andreas Alfons
+#         Erasmus Universiteit Rotterdam
+# --------------------------------------
+
+#' @name robustHD-package
+#'
+#' @docType package
+#'
+#' @title \packageTitle{robustHD}
+#'
+#' @description \packageDescription{robustHD}
+#'
+#' @details
+#' The DESCRIPTION file:
+#' \packageDESCRIPTION{robustHD}
+#' \packageIndices{robustHD}
+#'
+#' @references
+#' Alfons (2021) \pkg{robustHD}: An \R package for robust regression with
+#' high-dimensional data. \emph{Journal of Open Source Software}, \bold{6}(67),
+#' 3786. \doi{10.21105/joss.03786}.
+#'
+#' @author
+#' \packageAuthor{robustHD}
+#'
+#' Maintainer: \packageMaintainer{robustHD}
+#'
+#' @keywords package
+
+NULL