Merge branch 'rc-0.7.0'

See NEWS for details
* Weighted data support via survey
* SMD support along with vignette and ExtractSmd()
* includeNA option for constructors
* ShowRegTable() can use custom confint function
* print.TableOne() aligns sample size

.Rbuildignore

@@ -4,9 +4,20 @@
 ## Avoid git(hub) related files
 \.git/*
 README.md
+cran-comment.md
 
 ## Avoid Makefile, testing-related files, and archives
 Makefile
+revdep_check.txt
 tableone.Rcheck
 .*.tar.gz
 .*.gif
+
+## unit testing
+test-all.txt
+tests/testthat/ref-*
+
+## CRAN compatibility check
+cran-check.txt
+## Travis-CI
+^\.travis\.yml$

.gitignore

@@ -0,0 +1,7 @@
+*~
+*.DS_Store
+*.zip
+*.pdf
+*.Rhistory
+*.tar.gz
+*.Rcheck

.travis.yml

@@ -0,0 +1,14 @@
+# Sample .travis.yml for R projects
+
+language: r
+warnings_are_errors: true
+sudo: required
+
+env:
+ global:
+   - CRAN: http://cran.rstudio.com
+
+notifications:
+  email:
+    on_success: change
+    on_failure: change

DESCRIPTION

@@ -1,24 +1,33 @@
 Package: tableone
 Type: Package
-Title: Create "Table 1" to describe baseline characteristics
-Version: 0.6.3
-Date: 2014-12-28
+Title: Create "Table 1" to Describe Baseline Characteristics
+Version: 0.7.0
+Date: 2015-08-10
 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 subgroup comparisons. 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 command-line users.
+Description: Creates "Table 1", i.e., description of baseline patient
+    characteristics, which is essential in every medical research.
+    Supports both continuous and categorical variables, as well as
+    p-values and standardized mean differences. Weighted data are
+    supported via the survey package. See github for a screencast.
+    tableone was inspired by descriptive statistics functions in
+    Deducer , a Java-based GUI package by Ian Fellows. This package
+    does not require GUI or Java, and intended for command-line users.
 License: GPL-2
 Imports:
+    survey,
+    MASS,
     e1071,
+    zoo,
     gmodels
 Suggests:
     survival,
     testthat,
+    Matrix,
+    dummies,
+    Matching,
+    reshape2,
+    ggplot2,
     knitr
 URL: https://github.com/kaz-yos/tableone
 VignetteBuilder: knitr

Makefile

@@ -15,18 +15,29 @@ PKG_VERSION=$(shell grep -i ^version: DESCRIPTION | cut -d : -d \  -f 2)
 
 ## Define files to check for updates
 R_FILES   := $(wildcard R/*.R)
+TST_FILES := $(wildcard tests/testthat/*.R)
 SRC_FILES := $(wildcard src/*) $(addprefix src/, $(COPY_SRC))
 VIG_FILES := $(wildcard vignettes/*)
-PKG_FILES := DESCRIPTION NAMESPACE NEWS $(R_FILES) $(SRC_FILES) $(VIG_FILES)
+PKG_FILES := DESCRIPTION NAMESPACE NEWS $(R_FILES) $(TST_FILES) $(SRC_FILES) $(VIG_FILES)
 
 
 ## .PHONY to allow non-file targets (file targets should not be here)
 ## https://www.gnu.org/software/make/manual/html_node/Phony-Targets.html
-.PHONY: build check install clean
+.PHONY: test build_win build check revdep install clean
 
 
 ### Define targets
 
+## test just runs testthat scripts. No dependencies.
+test:
+	Rscript -e "devtools::test()" | tee test-all.txt
+
+## build_win always build regardless of file update status
+## Links to results e-mailed (no useful output locally)
+build_win:
+	Rscript -e "devtools::build_win(version = 'R-devel')"
+	Rscript -e "devtools::build_win(version = 'R-release')"
+
 ## build depends on the *.tar.gz file, i.e., its own product.
 ## *.tar.gz file is defined seprately to prevent build execution on every invocation.
 build: $(PKG_NAME)_$(PKG_VERSION).tar.gz
@@ -43,7 +54,11 @@ NAMESPACE: $(R_FILES)
 
 ## check requires the *.tar.gz file, and execute strict tests on it.
 check: $(PKG_NAME)_$(PKG_VERSION).tar.gz
-	R CMD check --as-cran ./$(PKG_NAME)_$(PKG_VERSION).tar.gz
+	R CMD check --as-cran ./$(PKG_NAME)_$(PKG_VERSION).tar.gz | tee cran-check.txt
+
+## revdep requires the *.tar.gz file, and execute strict tests on it.
+revdep: $(PKG_NAME)_$(PKG_VERSION).tar.gz
+	Rscript -e "devtools::revdep_check()" | tee revdep_check.txt
 
 ## install requires the *.tar.gz file, and execute installation using it.
 install: $(PKG_NAME)_$(PKG_VERSION).tar.gz
@@ -64,6 +79,9 @@ list:
 	@echo "R files:"
 	@echo $(R_FILES)
 	@echo
+	@echo "Test files:"
+	@echo $(TST_FILES)
+	@echo
 	@echo "Source files:"
 	@echo $(SRC_FILES)
 	@echo

NAMESPACE

@@ -1,14 +1,34 @@
-# Generated by roxygen2 (4.1.0): do not edit by hand
+# Generated by roxygen2 (4.1.1): do not edit by hand
 
 S3method(print,CatTable)
 S3method(print,ContTable)
 S3method(print,TableOne)
+S3method(print,svyCatTable)
+S3method(print,svyContTable)
 S3method(summary,CatTable)
 S3method(summary,ContTable)
 S3method(summary,TableOne)
+S3method(summary,svyCatTable)
+S3method(summary,svyContTable)
 export(CreateCatTable)
 export(CreateContTable)
 export(CreateTableOne)
+export(ExtractSmd)
 export(ShowRegTable)
-import(e1071)
-import(gmodels)
+export(svyCreateCatTable)
+export(svyCreateContTable)
+export(svyCreateTableOne)
+import(survey)
+importFrom(stats,as.formula)
+importFrom(stats,chisq.test)
+importFrom(stats,coef)
+importFrom(stats,confint)
+importFrom(stats,fisher.test)
+importFrom(stats,kruskal.test)
+importFrom(stats,median)
+importFrom(stats,oneway.test)
+importFrom(stats,quantile)
+importFrom(stats,sd)
+importFrom(stats,var)
+importFrom(stats,xtabs)
+importFrom(utils,combn)

NEWS

@@ -1,3 +1,60 @@
+tableone 0.7.0 (2015-08-10)
+----------------------------------------------------------------
+
+NEW FEATURES
+
+* Weighted data are now supported via the survey package.
+  svydesign() should be used to create a survey design object,
+  and this object should be used for svyCreateTableOne() instead
+  of a data frame. Other options are essentially the same. All
+  results will be weighted results.
+
+* Standardized mean differences are calculated. print() methods
+  include smd option, which defaults to FALSE for backward
+  compatibility. If TRUE, SMD is shown on the right side of the
+  table. To suppress p-values, use test = FALSE option.
+  summary() methods also print SMDs. If there are more than two
+  strata, all possible pairwise contrasts are shown along with the
+  average SMD across all contrats. In this case, print methods only
+  prints the average SMD for brevity. For categorical variables
+  Yang and Dalton's suggested method (A unified approach to
+  measuring the effect size between two groups using SAS.
+  SAS Paper 335-2012) is used. SMDs for weighted data are
+  experimental.
+
+* ExtractSmd() function can be used to extract SMD values as a
+  numeric matrix, which then can be used for plotting, etc.
+
+* An new RMarkdown vignette explains the use of standardized
+  mean differences.
+
+* The includeNA option for CreateTableOne() and svyCreateTableOne()
+  make NA's in factors treated as a regular level.
+
+* ShowRegTable() now has ciFun option, which allows use of
+  the confint.default function if calculation is too slow for
+  glm results.
+
+* print.TableOne() aligns the sample size with other summaries.
+
+
+OTHER CHANGES
+
+* ShowRegTable() uses coef to refer to coefficients.
+
+* Unit tests were extended to cover more functions.
+
+* CreateTableOne() was refactored to avoid redundant calculation.
+
+* New dependencies: survey, MASS, and zoo
+
+
+BUG FIXES
+
+* Fixed pDigits option in print.ContTable(), which was not correctly
+  functional as advertised.
+
+
 tableone 0.6.3 (2014-12-28)
 ----------------------------------------------------------------