up

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: ClinicoPathDescriptives
 Title: Descriptive Analysis Tools for Clinicopathological Research
-Version: 0.0.2.41
-Date: 2024-12-31
+Version: 0.0.2.45
+Date: 2025-01-10
 Authors@R: 
     person(given = "Serdar",
            family = "Balci",

R/agepyramid.h.R

@@ -125,9 +125,12 @@ agepyramidBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #'
 #' 
 #' @param data The data as a data frame.
-#' @param age .
-#' @param gender .
-#' @param female .
+#' @param age a string naming the variable from \code{data} that contains the
+#'   continuous values used for the report
+#' @param gender a string naming the variable from \code{data} that contains
+#'   the categorical values used for the report
+#' @param female a string naming the level from \code{gender} that contains
+#'   the level female
 #' @return A results object containing:
 #' \tabular{llllll}{
 #'   \code{results$pyramidTable} \tab \tab \tab \tab \tab a table \cr

R/alluvial.h.R

@@ -185,14 +185,14 @@ alluvialBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' @param vars a string naming the variables from \code{data} that contains
 #'   the values used for the Alluvial Diagram.
 #' @param condensationvar The primary variable to be used for condensation.
-#' @param excl .
-#' @param marg .
+#' @param excl Exclude missing values from the analysis.
+#' @param marg Include marginal plots.
 #' @param fill A list for the argument fill for selecting the variable to be
 #'   represented by color. Default is 'first_variable'.
 #' @param bin labels for the bins from low to high
-#' @param orient .
-#' @param usetitle .
-#' @param mytitle .
+#' @param orient Orientation of the plot. Default is 'vertical'.
+#' @param usetitle Use a custom title for the plot.
+#' @param mytitle Title for the plot.
 #' @return A results object containing:
 #' \tabular{llllll}{
 #'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr

R/benford.h.R

@@ -93,8 +93,9 @@ benfordBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' Benford Analysis
 #'
 #' 
-#' @param data .
-#' @param var .
+#' @param data The data as a data frame.
+#' @param var a string naming the variable from \code{data} that contains the
+#'   continuous values used for the report
 #' @return A results object containing:
 #' \tabular{llllll}{
 #'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr

R/tableone.h.R

@@ -145,8 +145,9 @@ tableoneBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' @param data The data as a data frame.
 #' @param vars a string naming the variables from \code{data} that contains
 #'   the values used for the Table One.
-#' @param sty .
-#' @param excl .
+#' @param sty a string naming the style of the table.
+#' @param excl a boolean argument whether to exclude missing values. Default
+#'   is false.
 #' @return A results object containing:
 #' \tabular{llllll}{
 #'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr

R/tumor_response_examples.R

@@ -0,0 +1,25 @@
+#' Example Tumor Response Datasets
+#'
+#' Example datasets demonstrating different scenarios for tumor response analysis
+#'
+#' @format A list containing 4 data frames:
+#' \describe{
+#'   \item{raw_with_time}{Raw tumor measurements with time points (20 obs. of 3 variables)}
+#'   \item{raw_no_time}{Raw tumor measurements without time (10 obs. of 2 variables)}
+#'   \item{percent_with_time}{Pre-calculated response percentages with time (20 obs. of 3 variables)}
+#'   \item{percent_no_time}{Pre-calculated response percentages without time (10 obs. of 2 variables)}
+#' }
+#' @details
+#' Each dataset represents a different scenario:
+#' \itemize{
+#'   \item raw_with_time: Longitudinal raw measurements
+#'   \item raw_no_time: Single timepoint raw measurements
+#'   \item percent_with_time: Longitudinal percentage changes
+#'   \item percent_no_time: Single timepoint percentage changes
+#' }
+#'
+#' @examples
+#' data(tumor_response_examples)
+#' head(tumor_response_examples$raw_with_time)
+#' head(tumor_response_examples$percent_no_time)
+"tumor_response_examples"

R/venn.h.R

@@ -174,14 +174,22 @@ vennBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #'
 #' 
 #' @param data The data as a data frame.
-#' @param var1 .
-#' @param var1true .
-#' @param var2 .
-#' @param var2true .
-#' @param var3 .
-#' @param var3true .
-#' @param var4 .
-#' @param var4true .
+#' @param var1 a string naming the variable from \code{data} that contains the
+#'   the first variable used for the report
+#' @param var1true a string naming the level from \code{var1} that contains
+#'   the the true level
+#' @param var2 a string naming the variable from \code{data} that contains the
+#'   the second variable used for the report
+#' @param var2true a string naming the level from \code{var2} that contains
+#'   the the true level
+#' @param var3 a string naming the variable from \code{data} that contains the
+#'   the third variable used for the report
+#' @param var3true a string naming the level from \code{var3} that contains
+#'   the the true level
+#' @param var4 a string naming the variable from \code{data} that contains the
+#'   the fourth variable used for the report
+#' @param var4true a string naming the level from \code{var4} that contains
+#'   the the true level
 #' @return A results object containing:
 #' \tabular{llllll}{
 #'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr