R/riskRegressionLight-package.R

In bozenne/riskRegressionLight: Light version of the package riskRegression

### riskRegressionLight-package.R --- 
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## Author: Brice Ozenne
## Created: maj  6 2019 (14:57) 
## Version: 
## Last-Updated: maj  6 2019 (15:02) 
##           By: Brice Ozenne
##     Update #: 4
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### Commentary: 
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### Change Log:
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### Code:

#' Malignant melanoma data
#' 
#' In the period 1962-77, 205 patients with malignant melanoma (cancer of the
#' skin) had a radical operation performed at Odense University Hospital,
#' Denmark. All patients were followed until the end of 1977 by which time 134
#' were still alive while 71 had died (of out whom 57 had died from cancer and
#' 14 from other causes).
#' 
#' The object of the study was to assess the effect of risk factors on
#' survival. Among such risk factors were the sex and age of the patients and
#' the histological variables tumor thickness and ulceration (absent vs.
#' present).
#' 
#
#' 
#' @name Melanoma
#' @docType data
#' @format A data frame with 205 observations on the following 12 variables.
#' \describe{
#' \item{time}{ time in days from operation}
#' \item{status}{a numeric with values \code{0=censored} \code{1=death.malignant.melanoma} \code{2=death.other.causes}}
#' \item{event}{a factor with levels \code{censored} \code{death.malignant.melanoma} \code{death.other.causes}}
#' \item{invasion}{a factor with levels \code{level.0}, \code{level.1}, \code{level.2}}
#' \item{ici}{inflammatory cell infiltration (IFI): 0, 1, 2 or 3}
#' \item{epicel}{a factor with levels \code{not present} \code{present}}
#' \item{ulcer}{a factor with levels \code{not present} \code{present}}
#' \item{thick}{tumour thickness (in 1/100 mm)}
#' \item{sex}{a factor with levels \code{Female} \code{Male}}
#' \item{age}{age at operation (years)} 
#' \item{logthick}{tumour thickness on log-scale}
#' }
#' @references Regression with linear predictors (2010)
#' 
#' Andersen, P.K. and Skovgaard, L.T.
#' 
#' Springer Verlag
#'
#' @keywords datasets
##' @examples
##' 
##' data(Melanoma)

#' @docType package
#' @name riskRegressionLight
#' @useDynLib riskRegressionLight, .registration=TRUE
#' @importFrom Rcpp sourceCpp evalCpp
#' @importFrom rms strat cph
#' @importFrom ggplot2 autoplot aes aes_string element_blank element_line element_rect geom_errorbar geom_line geom_point geom_ribbon ggplot labs guide_legend guides scale_colour_manual scale_color_continuous scale_fill_manual scale_linetype_manual scale_y_continuous theme theme_bw "%+replace%"  unit xlab  ylab
#' @importFrom survival Surv strata coxph
#' @importFrom lava transform<-
#' @importFrom data.table as.data.table copy data.table is.data.table melt rbindlist setnames setorder setcolorder setkey ":=" ".N" ".SD"
#' @importFrom prodlim Hist dimColor prodlim
#' @importFrom foreach "%dopar%" foreach
#' @importFrom prodlim Hist jackknife prodlim sindex
#' @importFrom graphics bxp  abline axis box legend lines mtext par plot points segments text title polygon par boxplot
#' @importFrom utils capture.output find head select.list setTxtProgressBar tail txtProgressBar
#' @importFrom stats confint cov as.formula coef delete.response drop.terms family formula get_all_vars glm median model.frame model.matrix model.response na.fail na.omit optim pnorm predict qnorm quantile rbinom reformulate rexp runif sd setNames smooth terms terms.formula time uniroot update update.formula var wilcox.test
NULL



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### riskRegressionLight-package.R ends here