Merge branch 'rc0.5.0'

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: tableone
 Type: Package
 Title: Create "Table 1" to describe baseline characteristics
-Version: 0.4.0
-Date: 2014-03-30
+Version: 0.5.0
+Date: 2014-04-14
 Author: Kazuki Yoshida, Justin Bohn.
 Maintainer: Kazuki Yoshida <[email protected]>
 Description: This package creates "Table 1", i.e., description of baseline

NEWS

@@ -1,3 +1,13 @@
+tableone 0.5.0 (2014-04-14)
+----------------------------------------------------------------
+
+NEW FEATURES
+
+* The noSpaces argument was added to print.* functions. This allows
+  removal of spaces added for alignment using fixed-width fonts.
+  Use this option if you prefer to align your table in other software.
+
+
 tableone 0.4.0 (2014-03-30)
 ----------------------------------------------------------------
 

R/CreateCatTable.R

@@ -76,6 +76,9 @@
 ##' ## Excel does not mess up the cells.
 ##' print(catTableBySexTrt, exact = "ascites", quote = TRUE)
 ##'
+##' ## If you want to center-align values in Word, use noSpaces option.
+##' print(catTableBySexTrt, exact = "ascites", quote = TRUE, noSpaces = TRUE)
+##'
 ##' @export
 CreateCatTable <-
     function(vars,                                 # character vector of variable names

R/CreateContTable.R

@@ -75,6 +75,9 @@
 ##' ## Excel does not mess up the cells.
 ##' print(contTableBySexTrt, nonnormal = nonNormalVars, quote = TRUE)
 ##'
+##' ## If you want to center-align values in Word, use noSpaces option.
+##' print(contTableBySexTrt, nonnormal = nonNormalVars, quote = TRUE, noSpaces = TRUE)
+##'
 ##' @export
 CreateContTable <-
     function(vars,                                   # character vector of variable names

R/CreateTableOne.R

@@ -77,6 +77,10 @@
 ##' print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
 ##'       exact = c("status","stage"), quote = TRUE)
 ##'
+##' ## If you want to center-align values in Word, use noSpaces option.
+##' print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
+##'       exact = c("status","stage"), quote = TRUE, noSpaces = TRUE)
+##'
 ##' @export
 CreateTableOne <-
     function(vars,                                      # character vector of variable names

R/modules.R

@@ -366,6 +366,20 @@ ModuleReturnDimHeaders <- function(TableObject) {
 }
 
 
+## Module to remove spaces from the result matrix
+ModuleRemoveSpaces <- function(mat, noSpaces) {
+
+    ## Carry out these replacements to remove spaces if asked
+    if (noSpaces) {
+        mat <- gsub(pattern = "^ *| *$", replacement = "",  x = mat)
+        mat <- gsub(pattern = "\\( *",   replacement = "(", x = mat)
+    }
+
+    ## Return the matrix
+    mat
+}
+
+
 ### Modules by both print and summary methods
 ## ModuleQuoteAndPrintMat()
 ## Takes an matrix object format, print, and (invisibly) return it

R/print.CatTable.R

@@ -9,6 +9,7 @@
 ##' @param missing Whether to show missing data information (not implemented yet, placeholder)
 ##' @param explain Whether to add explanation to the variable names, i.e., (\%) is added to the variable names when percentage is shown.
 ##' @param printToggle Whether to print the output. If FLASE, no output is created, and a matrix is invisibly returned.
+##' @param noSpaces Whether to remove spaces added for alignment. Use this option if you prefer to align numbers yourself in other software.
 ##' @param format The default is "fp" frequency (percentage). You can also choose from "f" frequency only, "p" percentage only, and "pf" percentage (frequency).
 ##' @param showAllLevels Whether to show all levels. FALSE by default, i.e., for 2-level categorical variables, only the higher level is shown to avoid redundant information.
 ##' @param cramVars A character vector to specify the two-level categorical variables, for which both levels should be shown in one row.
@@ -78,6 +79,9 @@
 ##' ## Excel does not mess up the cells.
 ##' print(catTableBySexTrt, exact = "ascites", quote = TRUE)
 ##'
+##' ## If you want to center-align values in Word, use noSpaces option.
+##' print(catTableBySexTrt, exact = "ascites", quote = TRUE, noSpaces = TRUE)
+##'
 ##' @export
 print.CatTable <- function(x,                        # CatTable object
                            digits = 1, pDigits = 3,  # Number of digits to show
@@ -86,6 +90,7 @@ print.CatTable <- function(x,                        # CatTable object
                            missing       = FALSE,    # Show missing values (not implemented yet)
                            explain       = TRUE,     # Whether to show explanation in variable names
                            printToggle   = TRUE,     # Whether to print the result visibly
+                           noSpaces      = FALSE,    # Whether to remove spaces for alignments
 
                            format        = c("fp","f","p","pf")[1], # Format f_requency and/or p_ercent
                            showAllLevels = FALSE,
@@ -421,6 +426,9 @@ print.CatTable <- function(x,                        # CatTable object
     ## Add stratification information to the column header depending on the dimension
     names(dimnames(out)) <- ModuleReturnDimHeaders(CatTable)
 
+    ## Remove spaces if asked.
+    out <- ModuleRemoveSpaces(mat = out, noSpaces = noSpaces)
+
     ## Modular version of quote/print toggle.
     out <- ModuleQuoteAndPrintMat(matObj = out,
                                   quote = quote, printToggle = printToggle)

R/print.ContTable.R

@@ -9,6 +9,7 @@
 ##' @param missing Whether to show missing data information (not implemented yet, placeholder)
 ##' @param explain Whether to add explanation to the variable names, i.e., (mean (sd) or median [IQR]) is added to the variable names.
 ##' @param printToggle Whether to print the output. If FLASE, no output is created, and a matrix is invisibly returned.
+##' @param noSpaces Whether to remove spaces added for alignment. Use this option if you prefer to align numbers yourself in other software.
 ##' @param nonnormal A character vector to specify the variables for which the p-values should be those of nonparametric tests. By default all p-values are from normal assumption-based tests (oneway.test).
 ##' @param minMax Whether to use [min,max] instead of [p25,p75] for nonnormal variables. The default is FALSE.
 ##' @param insertLevel Whether to add an empty level column to the left of strata.
@@ -77,6 +78,9 @@
 ##' ## Excel does not mess up the cells.
 ##' print(contTableBySexTrt, nonnormal = nonNormalVars, quote = TRUE)
 ##'
+##' ## If you want to center-align values in Word, use noSpaces option.
+##' print(contTableBySexTrt, nonnormal = nonNormalVars, quote = TRUE, noSpaces = TRUE)
+##' 
 ##' @export
 print.ContTable <- function(x,                       # ContTable object
                             digits = 2, pDigits = 3, # Number of digits to show
@@ -85,6 +89,7 @@ print.ContTable <- function(x,                       # ContTable object
                             missing      = FALSE,    # show missing values (not implemented yet)
                             explain      = TRUE,     # Whether to show explanation in variable names
                             printToggle  = TRUE,     # Whether to print the result visibly
+                            noSpaces     = FALSE,    # Whether to remove spaces for alignments
 
                             nonnormal    = NULL,     # Which variables should be treated as nonnormal
                             minMax       = FALSE,    # median [range] instead of median [IQR]
@@ -297,6 +302,9 @@ print.ContTable <- function(x,                       # ContTable object
     ## Add stratification information to the column header depending on the dimension
     names(dimnames(out)) <- ModuleReturnDimHeaders(ContTable)
 
+    ## Remove spaces if asked.
+    out <- ModuleRemoveSpaces(mat = out, noSpaces = noSpaces)
+
     ## (module) Takes an matrix object format, print if requested
     out <- ModuleQuoteAndPrintMat(matObj = out,
                                   quote = quote, printToggle = printToggle)

R/print.TableOne.R

@@ -11,6 +11,7 @@
 ##' @param explain Whether to add explanation to the variable names, i.e., (\%) is added to the variable names when percentage is shown.
 ##' @param printToggle Whether to print the output. If FLASE, no output is created, and a matrix is invisibly returned.
 ##' @param test Whether to show the p-values. TRUE by default. If FALSE, only the numerical summaries are shown.
+##' @param noSpaces Whether to remove spaces added for alignment. Use this option if you prefer to align numbers yourself in other software.
 ##' @param format The default is "fp" frequency (percentage). You can also choose from "f" frequency only, "p" percentage only, and "pf" percentage (frequency).
 ##' @param showAllLevels Whether to show all levels. FALSE by default, i.e., for 2-level categorical variables, only the higher level is shown to avoid redundant information.
 ##' @param cramVars A character vector to specify the two-level categorical variables, for which both levels should be shown in one row.
@@ -66,6 +67,16 @@
 ##' ## See the continuous part only using $ operator
 ##' tableOne$ContTable
 ##' summary(tableOne$ContTable)
+##' 
+##' ## If your work flow includes copying to Excel and Word when writing manuscripts,
+##' ## you may benefit from the quote argument. This will quote everything so that
+##' ## Excel does not mess up the cells.
+##' print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
+##'       exact = c("status","stage"), cramVars = "hepato", quote = TRUE)
+##'
+##' ## If you want to center-align values in Word, use noSpaces option.
+##' print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
+##'       exact = c("status","stage"), cramVars = "hepato", quote = TRUE, noSpaces = TRUE)
 ##'
 ##' @export
 print.TableOne <- function(x,                   # TableOne object
@@ -77,6 +88,7 @@ print.TableOne <- function(x,                   # TableOne object
                            explain       = TRUE,  # Whether to show explanation in variable names
                            printToggle   = TRUE,  # Whether to print the result visibly
                            test          = TRUE,  # Whether to add p-values
+                           noSpaces      = FALSE, # Whether to remove spaces for alignments
 
                            ## Categorical options
                            format        = c("fp","f","p","pf")[1], # Format f_requency and/or p_ercent
@@ -199,6 +211,9 @@ print.TableOne <- function(x,                   # TableOne object
         names(dimnames(out)) <- c("", "")
     }
 
+    ## Remove spaces if asked.
+    out <- ModuleRemoveSpaces(mat = out, noSpaces = noSpaces)
+
     ## Modular version of quote/print toggle.
     out <- ModuleQuoteAndPrintMat(matObj = out,
                                   quote = quote, printToggle = printToggle)

R/tableone-package.R

@@ -84,4 +84,8 @@
 ##' print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
 ##'       exact = c("status","stage"), cramVars = "sex", quote = TRUE)
 ##'
+##' ## If you want to center-align values in Word, use noSpaces option.
+##' print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
+##'       exact = c("status","stage"), cramVars = "sex", quote = TRUE, noSpaces = TRUE)
+##'
 NULL

man/CreateCatTable.Rd

@@ -115,6 +115,9 @@ summary(catTableBySexTrt)
 ## you may benefit from the quote argument. This will quote everything so that
 ## Excel does not mess up the cells.
 print(catTableBySexTrt, exact = "ascites", quote = TRUE)
+
+## If you want to center-align values in Word, use noSpaces option.
+print(catTableBySexTrt, exact = "ascites", quote = TRUE, noSpaces = TRUE)
 }
 \author{
 Kazuki Yoshida (based on \code{Deducer::frequencies()})

man/CreateContTable.Rd

@@ -128,6 +128,9 @@ summary(contTableBySexTrt)
 ## you may benefit from the quote argument. This will quote everything so that
 ## Excel does not mess up the cells.
 print(contTableBySexTrt, nonnormal = nonNormalVars, quote = TRUE)
+
+## If you want to center-align values in Word, use noSpaces option.
+print(contTableBySexTrt, nonnormal = nonNormalVars, quote = TRUE, noSpaces = TRUE)
 }
 \author{
 Kazuki Yoshida (based on

man/CreateTableOne.Rd

@@ -152,6 +152,10 @@ summary(tableOne$ContTable)
 ## Excel does not mess up the cells.
 print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
       exact = c("status","stage"), quote = TRUE)
+
+## If you want to center-align values in Word, use noSpaces option.
+print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
+      exact = c("status","stage"), quote = TRUE, noSpaces = TRUE)
 }
 \author{
 Justin Bohn, Kazuki Yoshida

man/print.CatTable.Rd

@@ -3,9 +3,9 @@
 \title{Format and print the \code{CatTable} class objects}
 \usage{
 \method{print}{CatTable}(x, digits = 1, pDigits = 3, quote = FALSE,
-  missing = FALSE, explain = TRUE, printToggle = TRUE, format = c("fp",
-  "f", "p", "pf")[1], showAllLevels = FALSE, cramVars = NULL, test = TRUE,
-  exact = NULL, CrossTable = FALSE, ...)
+  missing = FALSE, explain = TRUE, printToggle = TRUE, noSpaces = FALSE,
+  format = c("fp", "f", "p", "pf")[1], showAllLevels = FALSE,
+  cramVars = NULL, test = TRUE, exact = NULL, CrossTable = FALSE, ...)
 }
 \arguments{
   \item{x}{The result of a call to the
@@ -31,6 +31,10 @@
   no output is created, and a matrix is invisibly
   returned.}
 
+  \item{noSpaces}{Whether to remove spaces added for
+  alignment. Use this option if you prefer to align numbers
+  yourself in other software.}
+
   \item{format}{The default is "fp" frequency (percentage).
   You can also choose from "f" frequency only, "p"
   percentage only, and "pf" percentage (frequency).}
@@ -123,6 +127,9 @@ summary(catTableBySexTrt)
 ## you may benefit from the quote argument. This will quote everything so that
 ## Excel does not mess up the cells.
 print(catTableBySexTrt, exact = "ascites", quote = TRUE)
+
+## If you want to center-align values in Word, use noSpaces option.
+print(catTableBySexTrt, exact = "ascites", quote = TRUE, noSpaces = TRUE)
 }
 \author{
 Kazuki Yoshida

man/print.ContTable.Rd

@@ -3,8 +3,9 @@
 \title{Format and print the \code{ContTable} class objects}
 \usage{
 \method{print}{ContTable}(x, digits = 2, pDigits = 3, quote = FALSE,
-  missing = FALSE, explain = TRUE, printToggle = TRUE, nonnormal = NULL,
-  minMax = FALSE, insertLevel = FALSE, test = TRUE, ...)
+  missing = FALSE, explain = TRUE, printToggle = TRUE, noSpaces = FALSE,
+  nonnormal = NULL, minMax = FALSE, insertLevel = FALSE, test = TRUE,
+  ...)
 }
 \arguments{
   \item{x}{The result of a call to the
@@ -30,6 +31,10 @@
   no output is created, and a matrix is invisibly
   returned.}
 
+  \item{noSpaces}{Whether to remove spaces added for
+  alignment. Use this option if you prefer to align numbers
+  yourself in other software.}
+
   \item{nonnormal}{A character vector to specify the
   variables for which the p-values should be those of
   nonparametric tests. By default all p-values are from
@@ -112,6 +117,9 @@ summary(contTableBySexTrt)
 ## you may benefit from the quote argument. This will quote everything so that
 ## Excel does not mess up the cells.
 print(contTableBySexTrt, nonnormal = nonNormalVars, quote = TRUE)
+
+## If you want to center-align values in Word, use noSpaces option.
+print(contTableBySexTrt, nonnormal = nonNormalVars, quote = TRUE, noSpaces = TRUE)
 }
 \author{
 Kazuki Yoshida

man/print.TableOne.Rd

@@ -4,8 +4,9 @@
 \usage{
 \method{print}{TableOne}(x, catDigits = 1, contDigits = 2, pDigits = 3,
   quote = FALSE, missing = FALSE, explain = TRUE, printToggle = TRUE,
-  test = TRUE, format = c("fp", "f", "p", "pf")[1], showAllLevels = FALSE,
-  cramVars = NULL, exact = NULL, nonnormal = NULL, minMax = FALSE, ...)
+  test = TRUE, noSpaces = FALSE, format = c("fp", "f", "p", "pf")[1],
+  showAllLevels = FALSE, cramVars = NULL, exact = NULL,
+  nonnormal = NULL, minMax = FALSE, ...)
 }
 \arguments{
   \item{x}{The result of a call to the
@@ -40,6 +41,10 @@
   default. If FALSE, only the numerical summaries are
   shown.}
 
+  \item{noSpaces}{Whether to remove spaces added for
+  alignment. Use this option if you prefer to align numbers
+  yourself in other software.}
+
   \item{format}{The default is "fp" frequency (percentage).
   You can also choose from "f" frequency only, "p"
   percentage only, and "pf" percentage (frequency).}
@@ -119,6 +124,16 @@ summary(tableOne$CatTable)
 ## See the continuous part only using $ operator
 tableOne$ContTable
 summary(tableOne$ContTable)
+
+## If your work flow includes copying to Excel and Word when writing manuscripts,
+## you may benefit from the quote argument. This will quote everything so that
+## Excel does not mess up the cells.
+print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
+      exact = c("status","stage"), cramVars = "hepato", quote = TRUE)
+
+## If you want to center-align values in Word, use noSpaces option.
+print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
+      exact = c("status","stage"), cramVars = "hepato", quote = TRUE, noSpaces = TRUE)
 }
 \author{
 Kazuki Yoshida, Justin Bohn

man/tableone-package.Rd

@@ -87,6 +87,10 @@ summary(tableOne$ContTable)
 ## Excel does not mess up the cells.
 print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
       exact = c("status","stage"), cramVars = "sex", quote = TRUE)
+
+## If you want to center-align values in Word, use noSpaces option.
+print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
+      exact = c("status","stage"), cramVars = "sex", quote = TRUE, noSpaces = TRUE)
 }
 \author{
 Kazuki Yoshida, Justin Bohn