Merge branch 'rc0.4.0'

Conflicts: NEWS
kaz-yos · Mar 30, 2014 · a255085 · a255085
2 parents ee3a953 + 7aec132
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,9 +1,9 @@
 Package: tableone
 Type: Package
 Title: Create "Table 1" to describe baseline characteristics
-Version: 0.3.5
-Date: 2014-03-07
-Author: Kazuki Yoshida, Justin Bohn
+Version: 0.4.0
+Date: 2014-03-30
+Author: Kazuki Yoshida, Justin Bohn.
 Maintainer: Kazuki Yoshida <[email protected]>
 Description: This package creates "Table 1", i.e., description of baseline
     patient characteristics, which is essential in every medical research. This

diff --git a/NEWS b/NEWS
@@ -1,3 +1,15 @@
+tableone 0.4.0 (2014-03-30)
+----------------------------------------------------------------
+
+NEW FEATURES
+
+* The showAllLevels argument to show all levels of categorical
+  variables regardless of numbers of levels was added to
+  print.TableOne. Previously, it was only available in
+  print.CatTable. To accommodate this feature, insertLevel argument
+  to insert an empty level column was added to print.ContTable.
+
+
 tableone 0.3.5 (2014-03-07)
 ----------------------------------------------------------------
 

diff --git a/R/print.CatTable.R b/R/print.CatTable.R
@@ -10,7 +10,7 @@
 ##' @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 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
+##' @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.
 ##' @param test Whether to show the p-values. TRUE by default. If FALSE, only the numerical summaries are shown.
 ##' @param exact A character vector to specify the variables for which the p-values should be those of exact tests. By default all p-values are from large sample approximation tests (chisq.test).

diff --git a/R/print.ContTable.R b/R/print.ContTable.R
@@ -11,6 +11,7 @@
 ##' @param printToggle Whether to print the output. If FLASE, no output is created, and a matrix is invisibly returned.
 ##' @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.
 ##' @param test Whether to show the p-values. TRUE by default. If FALSE, only the numerical summaries are shown.
 ##' @param ... For compatibility with generic. Ignored.
 ##' @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.
@@ -77,18 +78,19 @@
 ##' print(contTableBySexTrt, nonnormal = nonNormalVars, quote = TRUE)
 ##'
 ##' @export
-print.ContTable <- function(x,                        # ContTable object
-                            digits = 2, pDigits = 3,  # Number of digits to show
-                            quote       = FALSE,      # Whether to show quotes
+print.ContTable <- function(x,                       # ContTable object
+                            digits = 2, pDigits = 3, # Number of digits to show
+                            quote        = FALSE,    # Whether to show quotes
 
-                            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
+                            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
 
-                            nonnormal   = NULL,       # Which variables should be treated as nonnormal
-                            minMax      = FALSE,      # median [range] instead of median [IQR]
+                            nonnormal    = NULL,     # Which variables should be treated as nonnormal
+                            minMax       = FALSE,    # median [range] instead of median [IQR]
+                            insertLevel  = FALSE,    # insert the level column to match showAllLevels in print.CatTable
 
-                            test        = TRUE,       # Whether to add p-values
+                            test         = TRUE,     # Whether to add p-values
 
                             ...) {
 
@@ -286,6 +288,12 @@ print.ContTable <- function(x,                        # ContTable object
     ## Put back the column names (overkill for non-multivariable cases)
     colnames(out) <- outColNames
 
+    ## Add the level column if requested
+    if (insertLevel) {
+        out <- cbind(level = rep("", nrow(out)),
+                     out)
+    }
+
     ## Add stratification information to the column header depending on the dimension
     names(dimnames(out)) <- ModuleReturnDimHeaders(ContTable)
 

diff --git a/R/print.TableOne.R b/R/print.TableOne.R
@@ -12,6 +12,7 @@
 ##' @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 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.
 ##' @param exact A character vector to specify the variables for which the p-values should be those of exact tests. By default all p-values are from large sample approximation tests (chisq.test).
 ##' @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).
@@ -69,23 +70,24 @@
 ##' @export
 print.TableOne <- function(x,                   # TableOne object
                            catDigits = 1, contDigits = 2, pDigits = 3, # Number of digits to show
-                           quote = FALSE,       # Whether to show quotes
+                           quote         = FALSE,       # Whether to show quotes
 
                            ## Common options
-                           missing     = FALSE, # Not implemented yet
-                           explain     = TRUE,  # Whether to show explanation in variable names
-                           printToggle = TRUE,  # Whether to print the result visibly
-                           test        = TRUE,  # Whether to add p-values
+                           missing       = FALSE, # Not implemented yet
+                           explain       = TRUE,  # Whether to show explanation in variable names
+                           printToggle   = TRUE,  # Whether to print the result visibly
+                           test          = TRUE,  # Whether to add p-values
 
                            ## Categorical options
-                           format      = c("fp","f","p","pf")[1], # Format f_requency and/or p_ercent
-                           cramVars    = NULL,  # Which 2-level variables to show both levels in one row
-                           exact       = NULL,  # Which variables should be tested with exact tests
+                           format        = c("fp","f","p","pf")[1], # Format f_requency and/or p_ercent
+                           showAllLevels = FALSE, # Show all levels of a categorical variable
+                           cramVars      = NULL,  # Which 2-level variables to show both levels in one row
+                           exact         = NULL,  # Which variables should be tested with exact tests
 
                            ## Continuous options
-                           nonnormal   = NULL,  # Which variables should be treated as nonnormal
-                           minMax      = FALSE, # Whether to show median
-                           
+                           nonnormal     = NULL,  # Which variables should be treated as nonnormal
+                           minMax        = FALSE, # Whether to show median
+
                            ...) {
 
     ## Get the mixed element only
@@ -100,14 +102,17 @@ print.TableOne <- function(x,                   # TableOne object
     formattedTables <- sapply(seq_along(TableOne),
                               FUN = function(i) {
 
+                                  ## print.CatTable or print.ContTable called depending on the class
                                   print(TableOne[[i]], printToggle = FALSE, test = test, explain = explain,
                                         digits = digits[i],
+
                                         ## print.CatTable arguments
                                         format = format, exact = exact,
-                                        showAllLevels = FALSE,  # must be FALSE to get same column counts
+                                        showAllLevels = showAllLevels,  # Returns one more column if TRUE
                                         cramVars = cramVars,
+
                                         ## print.ContTable argument
-                                        nonnormal = nonnormal, minMax = minMax
+                                        nonnormal = nonnormal, minMax = minMax, insertLevel = showAllLevels
                                         )  # Method dispatch at work
                               },
                               simplify = FALSE)
@@ -142,11 +147,22 @@ print.TableOne <- function(x,                   # TableOne object
                                        matObj <- formattedTables[[i]]
                                        nSpaces <- nSpacesToAdd[, i]
 
-                                       ## For j-th stratum (column). Be aware of the p-value column
+                                       ## For j-th stratum (column), add spaces.
+                                       ## Be aware of the p-value column (last. not included in first palce)
+                                       ## and level column (1st. explicitly ignore).
                                        for (j in seq_along(nSpaces)) {
 
-                                           matObj[, j] <- paste0(paste0(rep(" ", nSpaces[j]), collapse = ""),
-                                                                 matObj[, j])
+                                           ## If showAllLevels is requested, ignore the first column (level column).
+                                           if (showAllLevels) {
+                                               matObj[, (j + 1)] <- paste0(paste0(rep(" ", nSpaces[j]), collapse = ""),
+                                                                           matObj[, (j + 1)])
+
+                                           } else {
+                                               ## if not, no need to ignore the first column
+                                               matObj[, j] <- paste0(paste0(rep(" ", nSpaces[j]), collapse = ""),
+                                                                     matObj[, j])
+                                           }
+
                                        }
 
                                        ## Return the adjusted table

diff --git a/man/print.CatTable.Rd b/man/print.CatTable.Rd
@@ -37,7 +37,8 @@
 
   \item{showAllLevels}{Whether to show all levels. FALSE by
   default, i.e., for 2-level categorical variables, only
-  the higher level is shown to avoid}
+  the higher level is shown to avoid redundant
+  information.}
 
   \item{cramVars}{A character vector to specify the
   two-level categorical variables, for which both levels

diff --git a/man/print.ContTable.Rd b/man/print.ContTable.Rd
@@ -4,7 +4,7 @@
 \usage{
 \method{print}{ContTable}(x, digits = 2, pDigits = 3, quote = FALSE,
   missing = FALSE, explain = TRUE, printToggle = TRUE, nonnormal = NULL,
-  minMax = FALSE, test = TRUE, ...)
+  minMax = FALSE, insertLevel = FALSE, test = TRUE, ...)
 }
 \arguments{
   \item{x}{The result of a call to the
@@ -38,6 +38,9 @@
   \item{minMax}{Whether to use [min,max] instead of
   [p25,p75] for nonnormal variables. The default is FALSE.}
 
+  \item{insertLevel}{Whether to add an empty level column
+  to the left of strata.}
+
   \item{test}{Whether to show the p-values. TRUE by
   default. If FALSE, only the numerical summaries are
   shown.}

diff --git a/man/print.TableOne.Rd b/man/print.TableOne.Rd
@@ -4,8 +4,8 @@
 \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], cramVars = NULL,
-  exact = NULL, nonnormal = NULL, minMax = FALSE, ...)
+  test = TRUE, 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
@@ -44,6 +44,11 @@
   You can also choose from "f" frequency only, "p"
   percentage only, and "pf" percentage (frequency).}
 
+  \item{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.}
+
   \item{cramVars}{A character vector to specify the
   two-level categorical variables, for which both levels
   should be shown in one row.}