export as S3 method, @Usage removal

kaz-yos · Feb 9, 2014 · 79fe0af · 79fe0af
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: tableone
 Type: Package
 Title: Create the "Table 1" to describe baseline characteristics
-Version: 0.1.1
+Version: 0.1.2
 Date: 2014-02-09
 Author: Kazuki Yoshida
 Maintainer: Kazuki Yoshida <[email protected]>

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,3 +1,7 @@
+S3method(print,CatTable)
+S3method(print,ContTable)
+S3method(summary,CatTable)
+S3method(summary,ContTable)
 export(CreateCatTable)
 export(CreateContTable)
 export(ShowRegTable)

diff --git a/R/CreateCatTable.R b/R/CreateCatTable.R
@@ -6,8 +6,6 @@
 ##' also \code{\link{print.CatTable}} and \code{\link{summary.CatTable}}.
 ##' 
 ##' 
-## @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.
@@ -38,8 +36,6 @@
 ##' @author Kazuki YOSHIDA
 ##' @seealso print.CatTable, summary.CatTable, CreateContTable,
 ##' print.ContTable, summary.ContTable
-## @references
-## @keywords ~kwd1 ~kwd2
 ##' @examples
 ##' 
 ##' ## Load

diff --git a/R/CreateContTable.R b/R/CreateContTable.R
@@ -5,10 +5,6 @@
 ##' object gives a table that is easy to use in medical research papers.
 ##' 
 ##' 
-## @usage CreateContTable(vars, strata, data, func.names = c("n", "miss",
-## "mean", "sd", "median", "p25", "p75", "min", "max", "skew", "kurt"),
-## func.additional, test = TRUE, testNormal = oneway.test, testNonNormal =
-## kruskal.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.
@@ -48,8 +44,6 @@
 ##' @author Kazuki YOSHIDA
 ##' @seealso print.ContTable, summary.ContTable, CreateCatTable,
 ##' print.CatTable, summary.CatTable
-## @references
-## @keywords ~kwd1 ~kwd2
 ##' @examples
 ##' 
 ##' ## Load

diff --git a/R/ShowRegTable.R b/R/ShowRegTable.R
@@ -4,8 +4,6 @@
 ##' usually the form used in medical research papers.
 ##' 
 ##' 
-## @usage ShowRegTable(model, exp = TRUE, digits = 2, pDigits = 3, quote =
-## FALSE)
 ##' @param model Regression model result objects that have the summary and
 ##' confint methods.
 ##' @param exp TRUE by default. You need to specify exp = FALSE if your model
@@ -24,8 +22,6 @@
 ##' @author Kazuki Yoshida
 ##' @seealso CreateContTable, print.ContTable, summary.ContTable,
 ##' CreateCatTable, print.CatTable, summary.CatTable
-## @references
-## @keywords ~kwd1 ~kwd2
 ##' @examples
 ##' 
 ##' ## Load

diff --git a/R/print.CatTable.R b/R/print.CatTable.R
@@ -4,10 +4,6 @@
 ##' CreateCatTable function.
 ##' 
 ##' 
-## @usage ## S3 method for class 'CatTable' print.CatTable(CatTable, missing =
-## 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 x The result of a call to the \code{\link{CreateCatTable}} function.
 ##' @param missing Whether to show missing data information (not implemented
 ##' yet, placeholder)
@@ -46,8 +42,6 @@
 ##' @author Kazuki YOSHIDA
 ##' @seealso CreateCatTable, summary.CatTable, CreateContTable,
 ##' print.ContTable, summary.ContTable
-## @references
-## @keywords ~kwd1 ~kwd2
 ##' @examples
 ##' 
 ##' ## Load
@@ -100,6 +94,7 @@
 ##' ## Excel does not mess up the cells.
 ##' print(catTableBySexTrt, exact = "ascites", quote = TRUE)
 ##' 
+##' @S3method print CatTable
 ##' @export print.CatTable
 print.CatTable <- function(x, missing = FALSE,
                            format = c("fp","f","p","pf")[1], # Format f_requency and/or p_ercent

diff --git a/R/print.ContTable.R b/R/print.ContTable.R
@@ -4,8 +4,6 @@
 ##' CreateContTable function.
 ##' 
 ##' 
-## @usage print.ContTable(ContTable, missing = FALSE, digits = 2, nonnormal =
-## NULL, quote = FALSE, test = TRUE, pDigits = 3, explain = TRUE)
 ##' @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)
@@ -35,8 +33,6 @@
 ##' @author Kazuki YOSHIDA
 ##' @seealso CreateContTable, summary.ContTable, CreateCatTable,
 ##' print.CatTable, summary.CatTable
-## @references
-## @keywords ~kwd1 ~kwd2
 ##' @examples
 ##' 
 ##' ## Load
@@ -88,6 +84,7 @@
 ##' ## Excel does not mess up the cells.
 ##' print(contTableBySexTrt, nonnormal = nonNormalVars, quote = TRUE)
 ##' 
+##' @S3method print ContTable
 ##' @export print.ContTable
 print.ContTable <- function(x, missing = FALSE,
                             digits = 2, nonnormal = NULL, quote = FALSE,

diff --git a/R/summary.CatTable.R b/R/summary.CatTable.R
@@ -6,7 +6,6 @@
 ##' (fisher.test by default).
 ##'
 ##'
-## @usage summary.CatTable(CatTable, digits = 1)
 ##' @param object An object that has the \code{CatTable} class to be shown.
 ##' @param digits Number of digits to print.
 ##' @param ... For compatibility with generic. Ignored.
@@ -22,8 +21,6 @@
 ##' @author Kazuki YOSHIDA
 ##' @seealso CreateCatTable, print.CatTable, CreateContTable, print.ContTable,
 ##' summary.ContTable
-## @references
-## @keywords ~kwd1 ~kwd2
 ##' @examples
 ##'
 ##' ## Load
@@ -48,12 +45,13 @@
 ##' ## which will show more details.
 ##' summary(catTableOverall)
 ##'
+##' @S3method summary CatTable
 ##' @export summary.CatTable
 summary.CatTable <- function(object, digits = 1, ...) {
 
     ## object and ... required to be consistent with generic summary(object, ...)
     CatTable <- object
-    
+
     ## Create format
     fmt <- paste0("%.", digits, "f")
 

diff --git a/R/summary.ContTable.R b/R/summary.ContTable.R
@@ -6,7 +6,6 @@
 ##' test (kruskal.test by default).
 ##'
 ##'
-## @usage summary.ContTable(ContTable, digits = 2)
 ##' @param object An object that has the \code{ContTable} class to be shown.
 ##' @param digits Number of digits to print.
 ##' @param ... For compatibility with generic. Ignored.
@@ -22,8 +21,6 @@
 ##' @author Kazuki YOSHIDA
 ##' @seealso CreateContTable, print.ContTable, CreateCatTable, print.CatTable,
 ##' summary.CatTable
-## @references
-## @keywords ~kwd1 ~kwd2
 ##' @examples
 ##'
 ##' ## Load
@@ -48,6 +45,7 @@
 ##' ## which will show more details.
 ##' summary(contTableOverall)
 ##'
+##' @S3method summary ContTable
 ##' @export summary.ContTable
 summary.ContTable <- function(object, digits = 2, ...) {
 

diff --git a/R/tableone-package.R b/R/tableone-package.R
@@ -8,7 +8,7 @@
 ##' GUI or Java, and intended for CUI users.
 ##' 
 ##' \tabular{ll}{ Package: \tab tableone\cr Type: \tab Package\cr Version: \tab
-##' 0.1.1\cr Date: \tab 2014-02-08\cr License: \tab GPL-2\cr } Create an object
+##' 0.1.2\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.

diff --git a/man/print.CatTable.Rd b/man/print.CatTable.Rd
@@ -48,8 +48,7 @@
   held internally using gmodels::CrossTable function. This
   will give an output similar to the PROC FREQ in SAS.}
 
-  \item{...}{Additional arguments. Required for the generic
-  print(x, ...). (not implemented yet, placeholder)}
+  \item{...}{For compatibility with generic. Ignored.}
 }
 \value{
 It is mainly for printing the result. But this function

diff --git a/man/print.ContTable.Rd b/man/print.ContTable.Rd
@@ -35,8 +35,7 @@
   names, i.e., (mean (sd) or median [IQR]) is added to the
   variable names.}
 
-  \item{...}{Additional arguments. Required for the generic
-  print(x, ...). (not implemented yet, placeholder)}
+  \item{...}{For compatibility with generic. Ignored.}
 }
 \value{
 It is mainly for printing the result. But this function

diff --git a/man/summary.CatTable.Rd b/man/summary.CatTable.Rd
@@ -10,8 +10,7 @@
 
   \item{digits}{Number of digits to print.}
 
-  \item{...}{Additional arguments. Required for the generic
-  summary(object, ...). (not implemented yet, placeholder)}
+  \item{...}{For compatibility with generic. Ignored.}
 }
 \value{
 It will print the results.

diff --git a/man/summary.ContTable.Rd b/man/summary.ContTable.Rd
@@ -10,8 +10,7 @@
 
   \item{digits}{Number of digits to print.}
 
-  \item{...}{Additional arguments. Required for the generic
-  summary(object, ...). (not implemented yet, placeholder)}
+  \item{...}{For compatibility with generic. Ignored.}
 }
 \value{
 It will print the results.

diff --git a/man/tableone-package.Rd b/man/tableone-package.Rd
@@ -15,7 +15,7 @@ or Java, and intended for CUI users.
 }
 \details{
 \tabular{ll}{ Package: \tab tableone\cr Type: \tab
-Package\cr Version: \tab 0.1.1\cr Date: \tab 2014-02-08\cr
+Package\cr Version: \tab 0.1.2\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