fixed docs and args to be consistent with CRAN. no feature change

DESCRIPTION

@@ -3,14 +3,16 @@ Type: Package
 Title: Create the "Table 1" to describe baseline characteristics
 Version: 0.1.1
 Date: 2014-02-09
-Author: Kazuki Yoshida (based on Deducer by Ian Fellows)
+Author: Kazuki Yoshida
 Maintainer: Kazuki Yoshida <[email protected]>
-Description: For some reasons, there are no good functions to create the "Table
+Description: This package creates create the "Table
     1", i.e., description of baseline characteristics in R although it is
     essential in every medical research. The package was insipired by
     descriptive statistics functions in Deducer, Java-based GUI package. This
     package does not require GUI or Java, and intended for CUI users.
 License: GPL-2
 Depends:
     e1071,
-    gmodels
+    gmodels,
+    survival
+URL: https://github.com/kaz-yos/tableone

NAMESPACE

@@ -1 +1,7 @@
-exportPattern("^[[:alpha:]]+")
+export(CreateCatTable)
+export(CreateContTable)
+export(ShowRegTable)
+export(print.CatTable)
+export(print.ContTable)
+export(summary.CatTable)
+export(summary.ContTable)

R/CreateCatTable.R

@@ -6,8 +6,8 @@
 ##' also \code{\link{print.CatTable}} and \code{\link{summary.CatTable}}.
 ##' 
 ##' 
-##' @usage CreateCatTable(vars, strata, data, test = TRUE, testApprox =
-##' chisq.test, testExact = fisher.test)
+## @usage CreateCatTable(vars, strata, data, test = TRUE, testApprox =
+## chisq.test, testExact = fisher.test)
 ##' @param vars Variable(s) to be summarized given as a character vector.
 ##' @param strata Stratifying (grouping) variable name(s) given as a character
 ##' vector. If omitted, the overall results are returned.
@@ -24,8 +24,8 @@
 ##' fisher.test. If the cells have large numbers, it will fail because of
 ##' memory limitation. In this situation, the large sample approximation based
 ##' should suffice.
-##' @return An object of class ‘CatTable’, which really is a ‘by’ object with
-##' additional attributes. Each element of the ‘by’ part is a matrix with rows
+##' @return An object of class \code{CatTable}, which really is a \code{\link{by}} object with
+##' additional attributes. Each element of the \code{\link{by}} part is a matrix with rows
 ##' representing variables, and columns representing summary statistics.
 ##' @note Special Thanks:
 ##' 

R/CreateContTable.R

@@ -34,8 +34,8 @@
 ##' The default is kruskal.test (Kruskal-Wallis Rank Sum Test). This is
 ##' equivalent of the wilcox.test (Man-Whitney U test) when there are only two
 ##' groups.
-##' @return An object of class ‘ContTable’, which really is a ‘by’ object with
-##' additional attributes. Each element of the ‘by’ part is a matrix with rows
+##' @return An object of class \code{ContTable}, which really is a \code{\link{by}} object with
+##' additional attributes. Each element of the \code{\link{by}} part is a matrix with rows
 ##' representing variables, and columns representing summary statistics.
 ##' @note Special Thanks:
 ##' 
@@ -119,7 +119,7 @@ CreateContTable <- function(vars,                         # vector of characters
                             testNonNormal = kruskal.test  # test for nonnormally distributed variables
                             ) {
     ## Require dependencies (DELETE before CRAN release. Use Depends in DESCRIPTION)
-    require(e1071)      # for skewness and kurtosis
+    ## require(e1071)      # for skewness and kurtosis
 
     ## Check if the data given is a dataframe
     if (is.data.frame(data) == FALSE) {

R/print.CatTable.R

@@ -1,4 +1,4 @@
-##' Format and print the ‘CatTable’ class objects
+##' Format and print the \code{CatTable} class objects
 ##' 
 ##' This is the print method for the CatTable class objects created by
 ##' CreateCatTable function.
@@ -8,7 +8,7 @@
 ## FALSE, format = c("fp", "f", "p", "pf")[1], digits = 1, exact = NULL, quote
 ## = FALSE, test = TRUE, pDigits = 3, showAllLevels = FALSE, explain = TRUE,
 ## CrossTable = FALSE)
-##' @param CatTable The result of a call to the ‘CreateCatTable’ function.
+##' @param x The result of a call to the \code{\link{CreateCatTable}} function.
 ##' @param missing Whether to show missing data information (not implemented
 ##' yet, placeholder)
 ##' @param format The default is "fp" frequency (percentage). You can also
@@ -31,6 +31,8 @@
 ##' @param CrossTable Whether to show the cross table objects held internally
 ##' using gmodels::CrossTable function. This will give an output similar to the
 ##' PROC FREQ in SAS.
+##' @param ... Additional arguments. Required for the generic print(x, ...).
+##' (not implemented yet, placeholder)
 ##' @return It is mainly for printing the result. But this function does return
 ##' a matrix containing what you see in the output invisibly. You can assign it
 ##' to an object to save it.
@@ -100,14 +102,17 @@
 ##' print(catTableBySexTrt, exact = "ascites", quote = TRUE)
 ##' 
 ##' @export print.CatTable
-print.CatTable <- function(CatTable, missing = FALSE,
+print.CatTable <- function(x, missing = FALSE,
                            format = c("fp","f","p","pf")[1], # Format f_requency and/or p_ercent
                            digits = 1, exact = NULL, quote = FALSE,
                            test = TRUE, pDigits = 3,
                            showAllLevels = FALSE,
                            explain = TRUE,
-                           CrossTable = FALSE) {
+                           CrossTable = FALSE, ...) {
 
+    ## x and ... required to be consistent with generic print(x, ...)
+    CatTable <- x
+
 ### Check the data structure first
 
     ## CatTable has a strata(list)-variable(list)-table(dataframe) structure
@@ -445,7 +450,7 @@ print.CatTable <- function(CatTable, missing = FALSE,
     if (CrossTable) {
 
         ## DELETE before CRAN release (Use Depends in DESCRIPTION instead)
-        require(gmodels)
+        ## require(gmodels)
 
         junk <- lapply(attributes(CatTable)$xtabs, CrossTable)
     }

R/print.ContTable.R

@@ -1,12 +1,12 @@
-##' Format and print the ‘ContTable’ class objects
+##' Format and print the \code{ContTable} class objects
 ##' 
 ##' This is the print method for the ContTable class objects created by
 ##' CreateContTable function.
 ##' 
 ##' 
 ## @usage print.ContTable(ContTable, missing = FALSE, digits = 2, nonnormal =
 ## NULL, quote = FALSE, test = TRUE, pDigits = 3, explain = TRUE)
-##' @param ContTable The result of a call to the ‘CreateContTable’ function.
+##' @param x The result of a call to the \code{\link{CreateContTable}} function.
 ##' @param missing Whether to show missing data information (not implemented
 ##' yet, placeholder)
 ##' @param digits Number of digits to print in the table.
@@ -21,6 +21,8 @@
 ##' @param pDigits Number of digits to print for p-values.
 ##' @param explain Whether to add explanation to the variable names, i.e.,
 ##' (mean (sd) or median [IQR]) is added to the variable names.
+##' @param ... Additional arguments. Required for the generic print(x, ...).
+##' (not implemented yet, placeholder)
 ##' @return It is mainly for printing the result. But this function does return
 ##' a matrix containing what you see in the output invisibly. You can assign it
 ##' to an object to save it.
@@ -88,12 +90,14 @@
 ##' print(contTableBySexTrt, nonnormal = nonNormalVars, quote = TRUE)
 ##' 
 ##' @export print.ContTable
-print.ContTable <- function(ContTable, missing = FALSE,
+print.ContTable <- function(x, missing = FALSE,
                             digits = 2, nonnormal = NULL, quote = FALSE,
                             test = TRUE, pDigits = 3,
-                            explain = TRUE
-                            ) {
+                            explain = TRUE, ...) {
 
+    ## x and ... required to be consistent with generic print(x, ...)
+    ContTable <- x
+
 ### Check data structure first
 
     ## ContTable is by() object

R/summary.CatTable.R

@@ -1,4 +1,4 @@
-##' Shows all results in a ‘CatTable’ class object
+##' Shows all results in a \code{CatTable} class object
 ##'
 ##' This method shows all the data a CatTable class object has. This includes
 ##' the (optionally stratified) part with summary statistics and p-values from
@@ -7,8 +7,10 @@
 ##'
 ##'
 ## @usage summary.CatTable(CatTable, digits = 1)
-##' @param CatTable An object that has the ‘CatTable’ class to be shown.
+##' @param object An object that has the \code{CatTable} class to be shown.
 ##' @param digits Number of digits to print.
+##' @param ... Additional arguments. Required for the generic summary(object, ...).
+##' (not implemented yet, placeholder)
 ##' @return It will print the results.
 ##' @note Special Thanks:
 ##'
@@ -48,8 +50,11 @@
 ##' summary(catTableOverall)
 ##'
 ##' @export summary.CatTable
-summary.CatTable <- function(CatTable, digits = 1) {
+summary.CatTable <- function(object, digits = 1, ...) {
 
+    ## object and ... required to be consistent with generic summary(object, ...)
+    CatTable <- object
+
     ## Create format
     fmt <- paste0("%.", digits, "f")
 

R/summary.ContTable.R

@@ -1,14 +1,16 @@
-##' Shows all results in a ‘ContTable’ class object
+##' Shows all results in a \code{ContTable} class object
 ##'
-##' This method shows all the data a ‘ContTable’ class object has. This includes
+##' This method shows all the data a \code{ContTable} class object has. This includes
 ##' the (optionally stratified) part with summary statistics and p-values from
 ##' the normal assupmtion-based test (oneway.test by default) and nonparametric
 ##' test (kruskal.test by default).
 ##'
 ##'
 ## @usage summary.ContTable(ContTable, digits = 2)
-##' @param ContTable An object that has the ‘ContTable’ class to be shown.
+##' @param object An object that has the \code{ContTable} class to be shown.
 ##' @param digits Number of digits to print.
+##' @param ... Additional arguments. Required for the generic summary(object, ...).
+##' (not implemented yet, placeholder)
 ##' @return It will print the results.
 ##' @note Special Thanks:
 ##'
@@ -48,14 +50,14 @@
 ##' summary(contTableOverall)
 ##'
 ##' @export summary.ContTable
-summary.ContTable <- function(ContTable, digits = 2) {
+summary.ContTable <- function(object, digits = 2, ...) {
 
     ## Just call print.by
-    print.by(ContTable, digits = digits)
+    print.by(object, digits = digits)
 
     ## Print p-values if it exist
-    if (!is.null(attributes(ContTable)$pValues)) {
+    if (!is.null(attributes(object)$pValues)) {
         cat("\np-values\n")
-        print(attributes(ContTable)$pValues)
+        print(attributes(object)$pValues)
     }
 }

R/tableone-package.R

@@ -1,13 +1,14 @@
-##' Create the Table 1 to describe baseline characteristics
+##' Create "Table 1" to describe baseline characteristics
 ##' 
-##' For some reasons, there are no good functions to create the Table 1, i.e.,
-##' description of baseline characteristics in R although it is essential in
-##' every medical research. The package was insipired by descriptive statistics
+##' Table 1, i.e., description of baseline patient characteristics is essential
+##' every medical research. This package provides functions to create such
+##' summaries for continuous and categorical variables, optionally with subgroups
+##' and groupwise comparison. The package was insipired by descriptive statistics
 ##' functions in Deducer, Java-based GUI package. This package does not require
 ##' GUI or Java, and intended for CUI users.
 ##' 
 ##' \tabular{ll}{ Package: \tab tableone\cr Type: \tab Package\cr Version: \tab
-##' 0.1.0\cr Date: \tab 2014-02-08\cr License: \tab GPL-2\cr } Create an object
+##' 0.1.1\cr Date: \tab 2014-02-08\cr License: \tab GPL-2\cr } Create an object
 ##' summarizing continous and categorical variables optionally stratifying by
 ##' one or more startifying variables and performing statistical tests. The
 ##' object gives a table that is easy to use in medical research papers.