R/riskRegression-package.R

#' Paquid sample
#'
#' PAQUID is a prospective cohort study initiated in 1988 in South Western
#' France to explore functional and cerebral ageing. This sample includes
#' n=2561 subjects. Data contains a time-to-event, a type of event and 
#' two cognitive scores measured at baseline.
#' 
#' 
#' @name Paquid
#' @docType data
#' @format A data frame with 2561 observations on the following 4 variables.
#' \describe{
#' \item{\code{time}}{the time-to-event (in years).}
#' \item{\code{status}}{the type of event \code{0} = censored, \code{1} = dementia onset and \code{2} = death without dementia.}
#' \item{\code{DSST}}{score at the Digit Symbol Substitution Score Test. This test explores attention and psychomotor speed.}
#' \item{\code{MMSE}}{score at the Mini Mental State Examination. This test is often used as an index of global cognitive performance.}
#' }
#' @references
#'
#' Dartigues, J., Gagnon, M., Barberger-Gateau, P., Letenneur, L., Commenges, D.,
#' Sauvel, C., Michel, P., and Salamon, R. (1992). The paquid epidemiological program
#' on brain ageing. Neuroepidemiology, 11(1):14--18.
#'
#' 
#' Blanche, P., Dartigues, J. F., & Jacqmin-Gadda, H. (2013). Estimating and
#' comparing time-dependent areas under receiver operating characteristic curves
#' for censored event times with competing risks. Statistics in Medicine, 32(30),
#' 5381-5397.
#'
#' @source
#' The data have been first made publicly available via the package timeROC.
#' @keywords datasets
#' @examples
#' data(Paquid)
NULL

#' 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)
NULL

#' @docType package
#' @name riskRegression
#' @useDynLib riskRegression, .registration=TRUE
#' @importFrom Rcpp sourceCpp evalCpp
#' @importFrom grDevices rainbow
#' @importFrom rms strat cph
#' @importFrom mets phreg
#' @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 iid information score transform<- 
#' @importFrom data.table data.table set dcast setkeyv setDT 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 cmprsk predict.crr
#' @importFrom timereg comp.risk Event 
#' @importFrom prodlim Hist jackknife prodlim sindex
#' @importFrom grDevices col2rgb gray
#' @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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riskRegression documentation built on Jan. 13, 2021, 11:12 a.m.