381 pare down the number of exported functions

R/get_quantile.R

@@ -1,35 +1,33 @@
 #' @title Wrapper around quantile methods
 #'
-#' @description S3 method for extracting quantiles. 
+#' @description S3 method for extracting quantiles.
 #'   No default method is available at the moment.
-#' 
+#'
 #' @seealso \code{\link[survival]{quantile.survfit}}
-#' 
+#'
 #' @param x An object of class \code{survfit}
 #' @param probs  probabilities Default = c(0.25,0.50,0.75)
 #' @inheritParams survival::quantile.survfit
 #' @param ... other arguments passed on to the method
-#' 
+#'
 #' @examples
-#' 
+#'
 #' ## Kaplan-Meier estimates
 #' survfit_object <- visR::estimate_KM(data = adtte, strata = c("TRTP"))
-#' 
+#'
 #' ## visR quantiles
 #' visR::get_quantile(survfit_object)
-#' 
+#'
 #' ## survival quantiles
 #' quantile(survfit_object)
-#' 
+#'
 #' @return A data frame with quantiles of the object
-#'  
+#'
 #' @rdname get_quantile
-#' 
-#' @export
-
+#'
 get_quantile <- function(x, ...){
   UseMethod("get_quantile", x)
-} 
+}
 
 #' @rdname get_quantile
 #' @method get_quantile survfit
@@ -41,40 +39,40 @@ get_quantile.survfit <- function(x,
                                  conf.int = TRUE,
                                  tolerance = sqrt(.Machine$double.eps)
                                 ) {
-  
+
 
 # User input validation ---------------------------------------------------
 
   if (conf.int == TRUE & !base::all(c("lower", "upper") %in% names(x)))
     stop("Confidence limits were not part of original estimation.")
-  
+
   if (!base::all(is.numeric(probs) == TRUE) | (!base::all(probs < 1)))
     stop("probs should be a numeric vector.")
-  
+
   if (!is.numeric(tolerance))
     stop("tolerance should be numeric")
-    
+
 # Extract quantiles -------------------------------------------------------
-  
+
   q <- quantile( x
                 ,probs = probs
                 ,conf.int = conf.int
                 ,tolerance = tolerance
                 ,type = 3
                )
-  
+
   qdf <- do.call(rbind.data.frame, q)
-  
+
   strata <- as.character(unlist(lapply(q, rownames)))
   quantity <- unlist(lapply(strsplit(rownames(qdf), "\\.", fixed = FALSE), `[[`, 1))
-  
+
   final <- data.frame(
     cbind(strata, quantity, qdf)
    ,row.names = NULL
    ,check.names = FALSE
   )
-  
+
   final <- final[ order( final[, "strata"], final[, "quantity"] ),  ]
-  
+
   return(final)
 }

R/get_risktable.R

@@ -31,16 +31,13 @@
 #'   number of patients at risk per strata
 #' @rdname get_risktable
 #'
-#' @export
-
 get_risktable <- function(x, ...){
   UseMethod("get_risktable")
 }
 
 #' @rdname get_risktable
 #' @method get_risktable survfit
-#' @export
-
+#'
 get_risktable.survfit <- function(
   x
   ,times = NULL
@@ -225,7 +222,7 @@ get_risktable.survfit <- function(
 
 #' @rdname get_risktable
 #' @method get_risktable tidycuminc
-#' @export
+#'
 get_risktable.tidycuminc <- function(x
                                      ,times = pretty(x$tidy$time, 10)
                                      ,statlist = "n.risk"
@@ -340,5 +337,3 @@ get_risktable.tidycuminc <- function(x
 
   return(label[seq_along(statlist)])
 }
-
-

R/get_summary.R

@@ -11,13 +11,11 @@
 #'
 #' @rdname get_summary
 #'
-#' @export
-
 get_summary <- function(x, ...){
   UseMethod("get_summary", x)
 }
 
-#'  @examples
+#' @examples
 #'
 #' survfit_object <- survival::survfit(data = adtte, survival::Surv(AVAL, 1-CNSR) ~ TRTP)
 #' get_summary(survfit_object)
@@ -26,8 +24,7 @@ get_summary <- function(x, ...){
 #'
 #' @rdname get_summary
 #' @method get_summary survfit
-#' @export
-
+#'
 get_summary.survfit <- function(x,
                                 statlist = c("strata", "records", "events", "median", "LCL", "UCL", "CI"),
                                 ...) {

R/get_tableone.R

@@ -18,7 +18,7 @@
 #'
 #' @note All columns in the table will be summarized. If only some columns shall be used, please select only those
 #' variables prior to creating the summary table by using dplyr::select()
-
+#'
 #' @examples
 #'
 #' # Example using the ovarian data set
@@ -68,8 +68,6 @@
 #'
 #' @rdname get_tableone
 #'
-#' @export
-
 get_tableone <- function(data, strata = NULL, overall=TRUE, summary_function = summarize_short){
   UseMethod("get_tableone")
 }
@@ -78,7 +76,7 @@ get_tableone <- function(data, strata = NULL, overall=TRUE, summary_function = s
 #' @method get_tableone default
 #' @return object of class tableone. That is a list of data specified summaries
 #'   for all input variables.
-#' @export
+#'
 get_tableone.default <- function(data, strata = NULL, overall=TRUE, summary_function = summarize_short){
 
   summary_FUN <- match.fun(summary_function)

R/utils_pipe.R

@@ -1,14 +1,9 @@
 
 #' @title Find the "lhs" in the pipeline
-#'
 #' @description This function finds the left-hand sided symbol in a magrittr pipe and returns it as a character.
-#'
 #' @return Left-hand sided symbol as string in the magrittr pipe.
-#'
 #' @references \url{https://github.com/tidyverse/magrittr/issues/115#issuecomment-173894787}
 #'
-#' @export
-#'
 #' @examples
 #' blah <- function(x) the_lhs()
 #' adtte %>%

R/utils_table.R

@@ -4,15 +4,13 @@
 #'
 #' @param x an object
 #' @return A summarized version of the input.
-#' @export
 summarize_long <- function(x) UseMethod("summarize_long")
 
 
 #' Create variable summary for factors
 #'
 #' @param x an object of class "factor"
 #' @return Long list of summary statistics for the input factors.
-#' @export
 summarize_long.factor <- function(x){
   x1 <- forcats::fct_explicit_na(x, na_level = "Missing")
 
@@ -29,7 +27,6 @@ summarize_long.factor <- function(x){
 #'
 #' @param x an object of class "integer"
 #' @return Long list of summary statistics for the input.
-#' @export
 summarize_long.integer <- function(x){
   summarize_long.numeric(x)
 }
@@ -38,7 +35,6 @@ summarize_long.integer <- function(x){
 #'
 #' @param x an object of class "numeric"
 #' @return Long list of summary statistics for the input.
-#' @export
 summarize_long.numeric <- function(x){
   dat <- list(
     mean = mean(x, na.rm = TRUE),
@@ -56,7 +52,6 @@ summarize_long.numeric <- function(x){
 #'
 #' @param x an object of any other class
 #' @return List of counts for unique and missing values in `x`.
-#' @export
 summarize_long.default <- function(x){
   dat <- list(
     unique_values = length(unique(x)),
@@ -71,7 +66,6 @@ summarize_long.default <- function(x){
 #'
 #' @param x a vector to be summarized
 #' @return A summarized less detailed version of the input.
-#' @export
 summarize_short <- function(x) UseMethod("summarize_short")
 
 #' Create variable summary for factors
@@ -80,7 +74,6 @@ summarize_short <- function(x) UseMethod("summarize_short")
 #'
 #' @param x an object of class "factor"
 #' @return Short list of summary statistics for the input factors.
-#' @export
 summarize_short.factor <- function(x){
   x1 <- forcats::fct_explicit_na(x, na_level = "Missing")
 
@@ -101,7 +94,6 @@ summarize_short.factor <- function(x){
 #'
 #' @param x an object of class "numeric"
 #' @return Short list of summary statistics for the input.
-#' @export
 summarize_short.numeric <- function(x){
   dat <- list(
     `Mean (SD)` = paste0(format(mean(x, na.rm = TRUE), digits = 3), " (", format(sd(x, na.rm = TRUE), digits = 3), ")"),
@@ -121,7 +113,6 @@ summarize_short.numeric <- function(x){
 #'
 #' @param x an object of class "integer"
 #' @return Short list of summary statistics for the input.
-#' @export
 summarize_short.integer <- function(x){
   summarize_short.numeric(x)
 }
@@ -130,11 +121,10 @@ summarize_short.integer <- function(x){
 #'
 #' @param x an object of any other class
 #' @return List of counts for unique and missing values in `x`.
-#' @export
 summarize_short.default <- function(x){
   dat <- list(
     `Unique values` = format(length(unique(x))),
     `Missing (%)` = paste0(format(sum(is.na(x))), " (", format(100 * sum(is.na(x))/length(x), trim=TRUE), "%)")
   )
   list(dat)
-}
+}

R/utils_visr.R

@@ -28,9 +28,6 @@
 #'                    align = "none",
 #'                    nrow=2)
 #' }
-#' @export
-
-
 align_plots <- function(pltlist) {
 
   if (missing(pltlist) | is.null(pltlist)) {