initial commit

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^\.travis\.yml$
+^\.git$
+^test$
+^Makefile$
+^COPYRIGHT$
+^LICENSE$
+^TODO.org$

.gitignore

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+*.tar.gz
+*.Rcheck/
+*.*~
+*~
+
+# History files
+.Rhistory
+.Rapp.history
+
+# Example code in package build process
+*-Ex.R
+
+# RStudio files
+*.Rproj
+.Rproj.user
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+

Makefile

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+dir = $(shell pwd)
+pkg = survem
+cprt = COPYRIGHT
+
+Rpkg: build
+	make check
+
+Rd: R/
+	Rscript -e "library(methods); roxygen2::roxygenise();"
+
+build: Rd
+	R CMD build --compact-vignettes $(dir)
+
+check: $(pkg)_*.tar.gz
+	R CMD check --as-cran $(pkg)_*.tar.gz
+
+INSTALL: build
+	R CMD INSTALL --build $(pkg)_*.tar.gz
+
+preview:
+	Rscript -e "rmarkdown::render('vignettes/$(pkg)-intro.Rmd')"
+
+## update copyright year in HEADER, R script and date in DESCRIPTION
+updateHeader:
+	yr=$$(date +"%Y");\
+	sed -i "s/Copyright (C) 2016-[0-9]\{4\}/Copyright (C) 2016-$$yr/" $(cprt);\
+# add HEADER file if there is no header
+	for Rfile in R/*.R; do \
+	if ! grep -e 'Copyright (C)' $$Rfile ;\
+	then cat $(cprt) $$Rfile > tmp ;\
+	mv tmp $$Rfile;\
+	fi;\
+	yr=$$(date +"%Y");\
+	sed -i "s/Copyright (C) 2016-[0-9]*/Copyright (C) 2016-$$yr/" $$Rfile;\
+	done;\
+	dt=$$(date +"%Y-%m-%d");\
+	sed -i "s/Date: [0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}/Date: $$dt/" DESCRIPTION;
+
+clean:
+	rm -rf *~ */*~ *.Rhistroy *.tar.gz *.Rcheck/ .\#*

R/class.R

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+#' Formula Response for survival data with uncertain records
+#'
+#' \code{Surve} is an S3 class that represents
+#' formula response for survival data with
+#' uncertain records.
+#' The last letter 'e' in 'Surve' represents 'EM'.
+#'
+#' @param ID Identificator of each subject.
+#' @param time Time of reccurence event or censoring.
+#' @param event The status indicator, 0 = censored, 1 = event.
+#' @aliases Surve
+#' @export
+Surve <- function (ID, time, event) {
+    ## inpDat <- data.frame(ID, time, event)
+    ## FIXME: function to check the date structure of
+    ## uncertained records
+    ## dat <- checkSurve(inpDat)
+    ## outDat <- with(dat, as.matrix(cbind(ID, time, event)))
+    outDat <- as.matrix(cbind(ID, time, event))
+    ## attr(outDat, "ID") <- attr(dat, "ID")
+    oldClass(outDat) <- "Surve"
+    invisible(outDat)
+}
+
+
+#' An S4 Class to Represent a Fitted Model
+#'
+#' \code{survEm-class} is an S4 class that represents a fitted model.
+#' Function \code{\link{survEm}} produces objects of this class.
+#' See ``Slots'' for details.
+#'
+#' @slot call Function call.
+#' @slot formula Formula.
+#' @slot data A data frame.
+#' @slot nObs A positive integer.
+#' @slot estimates A list.
+#' @slot control A list.
+#' @slot start A list.
+#' @slot na.action A length-one character vector.
+#' @slot xlevels A list.
+#' @slot contrasts A list.
+#' @slot convergCode A nonnegative integer.
+#' @slot partLogL A numeric value.
+#' @slot logL A numeric value.
+#' @slot fisher A numeric matrix.
+#' @aliases survEm-class
+#' @seealso \code{\link{survEm}} for details of slots.
+#' @export
+setClass(Class = "coxEm",
+         slots = c(call = "call",
+                   formula = "formula",
+                   data = "data.frame",
+                   nObs = "integer",
+                   estimates = "list",
+                   control = "list",
+                   start = "list",
+                   na.action = "character",
+                   xlevels = "list",
+                   contrasts = "list",
+                   convergCode = "integer",
+                   partLogL = "numeric",
+                   logL = "numeric",
+                   fisher = "matrix"))

R/coef.R

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+## collation after class.R
+#' @include class.R
+NULL
+
+
+#' Estimated Coefficients of Covariates
+#'
+#' \code{coef,coxEm-method} is a S4 class method that extracts
+#' estimated coefficients of covariates from
+#' \code{\link{coxEm-class}} object produced by
+#' function \code{\link{coxEm}}.
+#'
+#' @param object \code{\link{coxEm-class}} object.
+#' @param ... Other arguments for future usage.
+#' @return A named numeric vector.
+#' @aliases coef,coxEm-method
+#' @seealso
+#' \code{\link{coxEm}} for model fitting;
+#' \code{\link{confint,coxEm-method}} for confidence intervals
+#' for covariate coefficients;
+#' \code{\link{summary,coxEm-method}} for summary of a fitted model.
+#' @examples
+#' ## See examples given in function coxEm.
+#' @importFrom stats coef
+#' @export
+setMethod(f = "coef", signature = "coxEm",
+          definition = function(object, ...) {
+              object@estimates$beta[, 1]
+          })
+
+