Merge branch 'rc0.3.1' also changed README to version with cramVars

Conflicts: NEWS
kaz-yos · Feb 18, 2014 · ed56204 · ed56204
2 parents f935a2f + 2e1dc36
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,20 +1,21 @@
 Package: tableone
 Type: Package
 Title: Create "Table 1" to describe baseline characteristics
-Version: 0.3.0
-Date: 2014-02-17
+Version: 0.3.1
+Date: 2014-02-18
 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
     package provides functions to create such summaries for continuous and
     categorical variables, optionally with subgroups comparisons. The package
-    was insipired by and based on descriptive statistics functions in Deducer,
+    was inspired by and based on descriptive statistics functions in Deducer,
     a Java-based GUI package by Ian Fellows. This package does not require GUI
     or Java, and intended for CUI users.
 License: GPL-2
-Depends:
+Imports:
     e1071,
-    gmodels,
+    gmodels
+Suggests:
     survival
 URL: https://github.com/kaz-yos/tableone
diff --git a/NAMESPACE b/NAMESPACE
@@ -8,3 +8,5 @@ export(CreateCatTable)
 export(CreateContTable)
 export(CreateTableOne)
 export(ShowRegTable)
+import(e1071)
+import(gmodels)
diff --git a/NEWS b/NEWS
@@ -1,3 +1,14 @@
+tableone 0.3.1 (2014-02-18)
+----------------------------------------------------------------
+
+BUG FIXES
+
+* NAMESPACE now includes import(e1071) and import(gmodels).
+
+* DESCRIPTION now includes Imports e1071, gmodels and
+  Suggests survival, instead of Depends...
+
+
 tableone 0.3.0 (2014-02-17)
 ----------------------------------------------------------------
 NEW FEATURES

diff --git a/R/print.CatTable.R b/R/print.CatTable.R
@@ -428,7 +428,7 @@ print.CatTable <- function(x,                        # CatTable object
     ## Print CrossTable() if requested
     if (CrossTable) {
 
-        junk <- lapply(attributes(CatTable)$xtabs, CrossTable)
+        junk <- lapply(attributes(CatTable)$xtabs, gmodels::CrossTable)
     }
 
     ## Add attributes for column widths in characters

diff --git a/R/tableone-package.R b/R/tableone-package.R
@@ -5,6 +5,7 @@
 ##' @name tableone-package
 ##' @aliases tableone-package tableone
 ##' @docType package
+##' @import e1071 gmodels
 ##' @note Special Thanks:
 ##'
 ##' Ian Fellows for developing the Deducer package, which this package is based on.

diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@ tableone
 
 **An R package to create "Table 1", description of baseline characteristics**
 
-This package creates "Table 1", i.e., description of baseline patient characteristics, which 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 and based on descriptive statistics functions in Deducer, a Java-based GUI package by Ian Fellows. This package does not require GUI or Java, and intended for CUI users.
+This package creates "Table 1", i.e., description of baseline patient characteristics, which 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 inspired by and based on descriptive statistics functions in Deducer, a Java-based GUI package by Ian Fellows. This package does not require GUI or Java, and intended for CUI users.
 
 
 Examples
@@ -15,8 +15,10 @@ See also the demonstration here: http://rpubs.com/kaz_yos/tableone-demo-e
 
 ```
 > tableOne <- CreateTableOne(vars = vars, strata = "trt", data = pbc)
-> print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"), exact = c("status","stage"))
-                         Stratified by trt
+> print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
++       exact = c("status","stage"), cramVars = "sex")
+
+                          Stratified by trt
                           1                         2                         p      test   
   n                       158                       154                                     
   time (mean (sd))        2015.62 (1094.12)         1996.86 (1155.93)          0.883        
@@ -25,7 +27,7 @@ See also the demonstration here: http://rpubs.com/kaz_yos/tableone-demo-e
      1                         10 ( 6.3)                  9 ( 5.8)                          
      2                         65 (41.1)                 60 (39.0)                          
   age (mean (sd))           51.42 (11.01)             48.58 (9.96)             0.018        
-  sex = f (%)                 137 (86.7)                139 (90.3)             0.421        
+  sex = m/f (%)            21/137 (13.3/86.7)        15/139 (9.7/90.3)         0.421        
   ascites = 1 (%)              14 (8.9)                  10 (6.5)              0.567        
   hepato = 1 (%)               73 (46.2)                 87 (56.5)             0.088        
   spiders = 1 (%)              45 (28.5)                 45 (29.2)             0.985