Merge branch 'hotfix/align-missing' (fix Missing alignment)

The demonstrating case in the README.md was a corner case that breaks alignments between categorical and continuous variables. The following was used to reproduce the issue. library(tableone) library(survival); data(pbc) vars <- names(pbc)[-1] tableOne <- CreateTableOne(vars = vars, strata = c("trt"), data = pbc, factorVars = c("status","edema","stage")) print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"), exact = c("status","stage"), test = FALSE, smd = TRUE, missing = TRUE)
kaz-yos · Jun 16, 2017 · 1de0d1d · 1de0d1d
2 parents a91c08c + 79648ea
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: tableone
 Type: Package
 Title: Create "Table 1" to Describe Baseline Characteristics
-Version: 0.8.0
-Date: 2017-06-15
+Version: 0.8.1
+Date: 2017-06-16
 Author: Kazuki Yoshida, Justin Bohn.
 Maintainer: Kazuki Yoshida <[email protected]>
 Description: Creates "Table 1", i.e., description of baseline patient

diff --git a/NEWS b/NEWS
@@ -1,3 +1,12 @@
+tableone 0.8.1 (2017-06-16)
+----------------------------------------------------------------
+
+BUG FIX
+
+* Fix alignment issue with the Missing column. Note currently the
+  percentage is shown with 1 decimal and this is hard-coded.
+
+
 tableone 0.8.0 (2017-06-15)
 ----------------------------------------------------------------
 

diff --git a/R/print.TableOne.R b/R/print.TableOne.R
@@ -133,6 +133,11 @@ function(x,                   # TableOne object
         names(dimnames(out)) <- c("", "")
     }
 
+    ## Right-justify Missing column if showing and not removing spaces.
+    if (missing & !noSpaces) {
+        out[,"Missing"] <- format(out[,"Missing"], justify = "right")
+    }
+
     ## Center-justify column names if asked and not removing spaces.
     if (padColnames & !noSpaces) {
         out <- ModuleMidJustifyColnames(mat = out)

diff --git a/cran-check.txt b/cran-check.txt
@@ -3,15 +3,15 @@
 * checking DESCRIPTION meta-information ... OK
 * checking for LF line-endings in source and make files
 * checking for empty or unneeded directories
-* building ‘tableone_0.8.0.tar.gz’
+* building ‘tableone_0.8.1.tar.gz’
 * using log directory ‘/Users/kazuki/Documents/programming/r/tableone/tableone.Rcheck’
 * using R version 3.4.0 (2017-04-21)
 * using platform: x86_64-apple-darwin15.6.0 (64-bit)
 * using session charset: UTF-8
 * using option ‘--as-cran’
 * checking for file ‘tableone/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘tableone’ version ‘0.8.0’
+* this is package ‘tableone’ version ‘0.8.1’
 * checking package namespace information ... OK
 * checking package dependencies ... OK
 * checking if this is a source package ... OK

diff --git a/cran-comment.md b/cran-comment.md
@@ -1,46 +1,11 @@
 ## What's new
 The following changes are included.
 
-tableone 0.8.0 (2017-06-15)
+tableone 0.8.1 (2017-06-16)
 ----------------------------------------------------------------
-NEW FEATURES
-* The "missing" option for the print methods was implemented. If
-  TRUE, a column called "Missing" is added as the rightmost column
-  of the formatted table. This represents percentage of missing
-  observation in each variable. Please note this is the percentage
-  with respect to the unweighted raw observations even in weighted
-  tables.
-* The "padColnames" option was added the print.TableOne method. If
-  TRUE, the column names of the formatted table become space-padded
-  to center them.
-
-tableone 0.7.6 (2016-07-12)
-----------------------------------------------------------------
-BUG FIXES
-* The explanation for the "factorVars" argument for the functions
-  CreateTableOne and svyCreateTableOne were changed for clarity.
-  When factor variables are included in the argument, they are
-  releveled to exlude empty levels. This was not clearly documented
-  in the previous documentation. Thanks @eribul.
-* svyrep.design objects (survey design objects with replicate weights)
-  are allowed for the data argument in svyTableOne. This is considered
-  experimental. Thanks @przemo.
-
-tableone 0.7.5 (2016-04-10)
-----------------------------------------------------------------
-BUG FIXES
-* ShowRegTable() now correctly supports models fit with geepack,
-  nlme, and lme4.
-
-tableone 0.7.4 (2016-03-31)
-----------------------------------------------------------------
-NEW FEATURE
-* Define SMD := 0 when the numerator is 0 even if the denominator
-  is also 0. This is more intuitive because a constant compared
-  across two groups will give an SMD of 0 rather than NaN (0/0).
-  For example, if two groups being compared both only have one
-  gender (all female or all male), then SMD for the gender
-  variable is defined as 0.
+BUG FIX
+* Fix alignment issue with the Missing column. Note currently the
+  percentage is shown with 1 decimal and this is hard-coded.
 
 ## Test environments
 * Local OS X 10.12.5, R 3.4.0

diff --git a/tableone.Rcheck/tableone-Ex.Rout b/tableone.Rcheck/tableone-Ex.Rout
@@ -3316,7 +3316,7 @@ detaching ‘package:survey’, ‘package:survival’, ‘package:Matrix’,
 > ###
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  9.621 0.285 9.982 0.006 0.006 
+Time elapsed:  7.4 0.285 8.882 0.005 0.005 
 > grDevices::dev.off()
 null device 
           1 

diff --git a/test-all.txt b/test-all.txt
@@ -132,6 +132,38 @@ Unit tests for the CreateTableOne function: .......................
      2                       4 (19.0)          2 (13.3)         31 ( 22.6)        30 ( 21.6)                      
      3                       7 (33.3)          5 (33.3)         49 ( 35.8)        59 ( 42.4)                      
      4                       8 (38.1)          7 (46.7)         47 ( 34.3)        47 ( 33.8)                      
+.                         Stratified by trt
+                          1                         2                         SMD    Missing
+  n                           158                       154                                 
+  time (mean (sd))        2015.62 (1094.12)         1996.86 (1155.93)          0.017  0.0   
+  status (%)                                                                   0.054  0.0   
+     0                         83 (52.5)                 85 ( 55.2)                         
+     1                         10 ( 6.3)                  9 (  5.8)                         
+     2                         65 (41.1)                 60 ( 39.0)                         
+  trt = 2 (%)                   0 ( 0.0)                154 (100.0)            NaN   25.4   
+  age (mean (sd))           51.42 (11.01)             48.58 (9.96)             0.270  0.0   
+  sex = f (%)                 137 (86.7)                139 ( 90.3)            0.111  0.0   
+  ascites = 1 (%)              14 ( 8.9)                 10 (  6.5)            0.089 25.4   
+  hepato = 1 (%)               73 (46.2)                 87 ( 56.5)            0.207 25.4   
+  spiders = 1 (%)              45 (28.5)                 45 ( 29.2)            0.016 25.4   
+  edema (%)                                                                    0.058  0.0   
+     0                        132 (83.5)                131 ( 85.1)                         
+     0.5                       16 (10.1)                 13 (  8.4)                         
+     1                         10 ( 6.3)                 10 (  6.5)                         
+  bili (median [IQR])        1.40 [0.80, 3.20]         1.30 [0.72, 3.60]       0.171  0.0   
+  chol (median [IQR])      315.50 [247.75, 417.00]   303.50 [254.25, 377.00]   0.038 32.1   
+  albumin (mean (sd))        3.52 (0.44)               3.52 (0.40)             0.018  0.0   
+  copper (median [IQR])     73.00 [40.00, 121.00]     73.00 [43.00, 139.00]   <0.001 25.8   
+  alk.phos (median [IQR]) 1214.50 [840.75, 2028.00] 1283.00 [922.50, 1949.75]  0.037 25.4   
+  ast (mean (sd))          120.21 (54.52)            124.97 (58.93)            0.084 25.4   
+  trig (median [IQR])      106.00 [84.50, 146.00]    113.00 [84.50, 155.00]    0.017 32.5   
+  platelet (mean (sd))     258.75 (100.32)           265.20 (90.73)            0.067  2.6   
+  protime (mean (sd))       10.65 (0.85)              10.80 (1.14)             0.146  0.5   
+  stage (%)                                                                    0.246  1.4   
+     1                         12 ( 7.6)                  4 (  2.6)                         
+     2                         35 (22.2)                 32 ( 20.8)                         
+     3                         56 (35.4)                 64 ( 41.6)                         
+     4                         55 (34.8)                 54 ( 35.1)                         
 .                      Stratified by trt
                        1                 2                 p      test
   n                        158               154                      
@@ -2838,6 +2870,6 @@ C1      NaN      NaN      0      0      0
 ..
 
 Warnings ---------------------------------------------------------------------------------------------------------------
-1. svyrep.design is allowed (@test-svyCreateTableOne.R#504) - No sampling weights provided: equal probability assumed
+1. svyrep.design is allowed (@test-svyCreateTableOne.R#507) - No sampling weights provided: equal probability assumed
 
 DONE ===================================================================================================================
diff --git a/tests/testthat/ref-TableOne_print_missing b/tests/testthat/ref-TableOne_print_missing
diff --git a/tests/testthat/test-CreateTableOne.R b/tests/testthat/test-CreateTableOne.R
@@ -182,10 +182,13 @@ test_that("Missing percentages are correctly stored and printed", {
     ## Check printing
     ## Gold standard
     percentMissingString <- format(sprintf("%.1f", percentMissing), justify = "right")
-    ## Function to drop empty "" elements.
+    ## Function to drop empty elements like "" or "   ".
     DropEmptyString <- function(x) {
         ## as.character() drops names.
-        as.character(Filter(f = function(elt) {!(elt == "")}, x = x))
+        as.character(Filter(f = function(elt) {
+            !grepl("^ *$", elt)
+        },
+        x = x))
     }
     ## Check against gold standard
     expect_equal(DropEmptyString(print(pbcOverall, missing = TRUE)[,"Missing"]),
@@ -197,6 +200,21 @@ test_that("Missing percentages are correctly stored and printed", {
     expect_equal(DropEmptyString(print(pbcByTrtSex, missing = TRUE)[,"Missing"]),
                  percentMissingString)
 
+    ## Regression test for missing column
+    ## This corner case breaks alignment.
+    data(pbc)
+    vars <- names(pbc)[-1]
+    ## Create Table 1 stratified by trt (can add more stratifying variables)
+    tableOne <- CreateTableOne(vars = vars, strata = c("trt"), data = pbc,
+                               factorVars = c("status","edema","stage"))
+    ## Specifying nonnormal variables will show the variables appropriately,
+    ## and show nonparametric test p-values. Specify variables in the exact
+    ## argument to obtain the exact test p-values.
+    expect_equal_to_reference(print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
+                                    exact = c("status","stage"), test = FALSE, smd = TRUE, missing = TRUE,
+                                    printToggle = TRUE),
+                              "ref-TableOne_print_missing")
+
 })
 
 

diff --git a/tests/testthat/test-svyCreateTableOne.R b/tests/testthat/test-svyCreateTableOne.R
@@ -140,10 +140,13 @@ test_that("Missing percentages are correctly stored and printed", {
     ## Check printing
     ## Gold standard
     percentMissingString <- format(sprintf("%.1f", percentMissing), justify = "right")
-    ## Function to drop empty "" elements.
+    ## Function to drop empty elements like "" or "   ".
     DropEmptyString <- function(x) {
         ## as.character() drops names.
-        as.character(Filter(f = function(elt) {!(elt == "")}, x = x))
+        as.character(Filter(f = function(elt) {
+            !grepl("^ *$", elt)
+        },
+        x = x))
     }
     ## Check against gold standard
     expect_equal(DropEmptyString(print(mwOverall, missing = TRUE)[,"Missing"]),