Merge branch 'rc-0.7.1'

* Fix unit tests to work on SPARC
* Correct vignette entry name

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: tableone
 Type: Package
 Title: Create "Table 1" to Describe Baseline Characteristics
-Version: 0.7.0
-Date: 2015-08-10
+Version: 0.7.1
+Date: 2015-08-11
 Author: Kazuki Yoshida, Justin Bohn.
 Maintainer: Kazuki Yoshida <[email protected]>
 Description: Creates "Table 1", i.e., description of baseline patient

NEWS

@@ -1,3 +1,14 @@
+tableone 0.7.1 (2015-08-11)
+----------------------------------------------------------------
+
+BUG FIXES
+
+* Solve problems with unit testing on the sparc architecture
+  without extended-precision arithmetic support.
+
+* Fix title for second vignette.
+
+
 tableone 0.7.0 (2015-08-10)
 ----------------------------------------------------------------
 

R/modules-smd.R

@@ -191,6 +191,8 @@ StdDiff <- function(variable, group, binary = FALSE, na.rm = TRUE) {
 
     out <- meanDiffs / sqrt(varMeans)
 
+    ## This lower.tri() approach is actually giving 2vs1, 3vs1, etc
+    ## opposite of stated 1vs2, 1vs3. Only correct if abs() is used.
     abs(out[lower.tri(out)])
 }
 
@@ -277,6 +279,8 @@ svyStdDiff <- function(varName, groupName, design, binary = FALSE, na.rm = TRUE)
 
     out <- meanDiffs / sqrt(varMeans)
 
+    ## This lower.tri() approach is actually giving 2vs1, 3vs1, etc
+    ## opposite of stated 1vs2, 1vs3. Only correct if abs() is used.
     abs(out[lower.tri(out)])
 }
 

cran-check.txt

@@ -5,9 +5,11 @@
 * using option ‘--as-cran’
 * checking for file ‘tableone/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘tableone’ version ‘0.7.0’
-* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
+* this is package ‘tableone’ version ‘0.7.1’
+* checking CRAN incoming feasibility ... NOTE
 Maintainer: ‘Kazuki Yoshida <[email protected]>’
+
+Days since last update: 1
 * checking package namespace information ... OK
 * checking package dependencies ... OK
 * checking if this is a source package ... OK
@@ -62,4 +64,4 @@ Maintainer: ‘Kazuki Yoshida <[email protected]>’
 * checking re-building of vignette outputs ... OK
 * checking PDF version of manual ... OK
 * DONE
-Status: OK
+Status: 1 NOTE

cran-comment.md

@@ -1,18 +1,18 @@
 ## What's new
-* Weighted data support
-* Standardized mean difference support
+* Solve problems with unit testing on the sparc architecture without extended-precision arithmetic support at request of a CRAN maintainer.
+* Fix title for second vignette.
 
 ## Test environments
-* Local OS X 10.10.4, R 3.2.1; R-devel (2015-08-06 r68871)
+* Local OS X 10.10.4, R 3.2.1 (--disable-long-double) and R develop
 * Ubuntu Linux (on Travis-CI), R 3.2.1
-* winb-builder (devel and release)
+* win-builder (devel and release)
 
 ## R CMD check results
 * ERRORs: None
 * WARNINGs: None
 * NOTEs:
- - Package author e-mail confirmation.
- - "No repository set, so cyclic dependency check skipped" on R 3.2.1 on win-builder (not a package problem)
+ - Author e-mail check
+ - Short interval from last submission (0.7.0 on 2015-08-10)
 
 ## Downstream dependencies
-RcmdrPlugin.EZR GUI frontend: Manually examined "Summary table of sample characteristics" for compatibility; EZR author also examined compatibility.
+RcmdrPlugin.EZR GUI frontend: No change was made to APIs.

tableone.Rcheck/tableone-Ex.Rout

@@ -3273,7 +3273,7 @@ detaching ‘package:survey’, ‘package:grid’
 > ###
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  4.533 0.144 4.746 0.005 0.007 
+Time elapsed:  3.646 0.098 3.78 0.005 0.006 
 > grDevices::dev.off()
 null device 
           1 

tests/testthat/test-modules-smd.R

@@ -433,19 +433,21 @@ test_that("decent results are returned for anomalous/difficult data", {
     ## NaN due to division by zero variance
     by(nhanes$onlyOne, nhanes$RIAGENDR, summary)
     expect_equal(StdDiff(nhanes$onlyOne, group = nhanes$RIAGENDR), NaN)
-    ## 0 because [0]^-  = 0, and [1]^T [0]^-1 [1] = 0
+    ## 0 because [0]^-  = 0, and [1]^T [0]^-1 [1] = 0; defined NaN in (svy)StdDiffMulti
     table(nhanes$onlyOne, nhanes$RIAGENDR)
     expect_equal(StdDiffMulti(nhanes$onlyOne, group = nhanes$RIAGENDR), NaN)
     ## When weighted problematic
     means1 <- svyby(~ onlyOne, by = ~ RIAGENDR, nhanesSvy, FUN = svymean)[,2]
     vars1  <- svyby(~ onlyOne, by = ~ RIAGENDR, nhanesSvy, FUN = svyvar)[,2]
     ## Very small difference is inflated by even smaller variance
+    ## on sparc-sun-solaris sign was opposite; abs() solves this issue
+    ## as svyStdDiff() uses abs() internally
     expect_equal(svyStdDiff("onlyOne", "RIAGENDR", nhanesSvy),
-    (means1[1] - means1[2]) / sqrt(sum(vars1)  / 2))
+                 abs((means1[1] - means1[2]) / sqrt(sum(vars1)  / 2)))
     ## NaN should be the case, but it's not, but it's consistent with survey
     ## expect_equal(svyStdDiff("onlyOne", "RIAGENDR", nhanesSvy), NaN)
 
-    ## 0 because [0]^-  = 0, and [1]^T [0]^-1 [1] = 0
+    ## 0 because [0]^-  = 0, and [1]^T [0]^-1 [1] = 0; defined NaN in (svy)StdDiffMulti
     ## No error even with a single level variable (constant) as redundant
     ## level drop from table occurs only when 2+ levels are present.
     ## If any group has more than 2 levels, then strata-by-level table
@@ -456,7 +458,7 @@ test_that("decent results are returned for anomalous/difficult data", {
     ## NaN due to division by zero variance
     by(nhanes$onlyOne, nhanes$race, summary)
     expect_equal(StdDiff(nhanes$onlyOne, group = nhanes$race), rep(NaN, 6))
-    ## 0 because [0]^-  = 0, and [1]^T [0]^-1 [1] = 0
+    ## 0 because [0]^-  = 0, and [1]^T [0]^-1 [1] = 0; defined NaN in (svy)StdDiffMulti
     expect_equal(StdDiffMulti(nhanes$onlyOne, group = nhanes$race), rep(NaN, 6))
     ## When weighted problematic; not in this case??
     means2 <- svyby(~ onlyOne, by = ~ race, nhanesSvy, FUN = svymean)[,2]
@@ -467,9 +469,19 @@ test_that("decent results are returned for anomalous/difficult data", {
                     (means2[2] - means2[3]) / sqrt((vars2[2] + vars2[3]) / 2),
                     (means2[2] - means2[4]) / sqrt((vars2[2] + vars2[4]) / 2),
                     (means2[3] - means2[4]) / sqrt((vars2[3] + vars2[4]) / 2))
-    expect_equal(svyStdDiff("onlyOne", "race", nhanesSvy),  meanDiffs2)
-    expect_equal(svyStdDiff("onlyOne", "race", nhanesSvy), rep(NaN, 6))
-    ## 0 because [0]^-  = 0, and [1]^T [0]^-1 [1] = 0
+    ## on sparc-sun-solaris sign was opposite; abs() solves this issue
+    ## as svyStdDiff() uses abs() internally
+    expect_equal(svyStdDiff("onlyOne", "race", nhanesSvy), abs(meanDiffs2))
+    ## This one is rep(NaN,6) for most platforms except for sparc-sun-solaris
+    ## where ./configure --disable-long-double is used.
+    ## capabilities()["long.double"] was added in R 3.1.3.
+    ## As of 2015-08-11, only r-oldrel-windows-ix86+x86_64 is R 3.1.3.
+    ## https://cran.r-project.org/web/checks/check_results_tableone.html
+    if (capabilities()["long.double"]) {
+        ## Cannot run on sparc-sun-solaris due to lack of extended precision arithmetic
+        expect_equal(svyStdDiff("onlyOne", "race", nhanesSvy), rep(NaN, 6))
+    }
+    ## 0 because [0]^-  = 0, and [1]^T [0]^-1 [1] = 0; defined NaN in (svy)StdDiffMulti
     expect_equal(svyStdDiffMulti("onlyOne", "race", nhanesSvy), rep(NaN, 6))
 
 
@@ -490,15 +502,15 @@ test_that("decent results are returned for anomalous/difficult data", {
     expect_warning(expect_equal(svyStdDiff("onlyNa", "RIAGENDR", nhanesSvy),
                                 as.numeric(NA)),
                    "onlyNa has only NA's in at least one stratum. na.rm turned off.")
-    ## 0 because [0]^-  = 0, and [1]^T [0]^-1 [1] = 0
+    ## 0 because [0]^-  = 0, and [1]^T [0]^-1 [1] = 0; defined NaN in (svy)StdDiffMulti
     expect_warning(expect_equal(svyStdDiffMulti("onlyNa", "RIAGENDR", nhanesSvy), NaN),
                    "onlyNa has only NA's in all strata. Regarding NA as a level.")
 
     ## Four groups (six contrasts)
     ## NaN due to division by zero variance
     expect_warning(expect_equal(StdDiff(nhanes$onlyNa, group = nhanes$race), rep(NaN, 6)),
                    "Variable has only NA's in at least one stratum. na.rm turned off.")
-    ## 0 because [0]^-  = 0, and [1]^T [0]^-1 [1] = 0
+    ## 0 because [0]^-  = 0, and [1]^T [0]^-1 [1] = 0; defined NaN in (svy)StdDiffMulti
     expect_warning(expect_equal(StdDiffMulti(nhanes$onlyNa, group = nhanes$race), rep(NaN, 6)),
                    "Variable has only NA's in all strata. Regarding NA as a level.")
     ## When weighted problematic; not in this case??
@@ -514,7 +526,7 @@ test_that("decent results are returned for anomalous/difficult data", {
                    "onlyNa has only NA's in at least one stratum. na.rm turned off.")
     expect_warning(expect_equal(svyStdDiff("onlyNa", "race", nhanesSvy), rep(NaN, 6)),
                    "onlyNa has only NA's in at least one stratum. na.rm turned off.")
-    ## 0 because [0]^-  = 0, and [1]^T [0]^-1 [1] = 0
+    ## 0 because [0]^-  = 0, and [1]^T [0]^-1 [1] = 0; defined NaN in (svy)StdDiffMulti
     expect_warning(expect_equal(svyStdDiffMulti("onlyNa", "race", nhanesSvy), rep(NaN, 6)),
                    "onlyNa has only NA's in all strata. Regarding NA as a level.")
 

vignettes/smd.Rmd

@@ -4,7 +4,7 @@ author: "Kazuki Yoshida"
 date: "2015-08-07"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Introduction to tableone}
+  %\VignetteIndexEntry{Using standardized mean differences}
   %\VignetteEngine{knitr::rmarkdown}
   \usepackage[utf8]{inputenc}
 ---