From 85f07b39c0f244829f8c30a57763fbf0683e1de1 Mon Sep 17 00:00:00 2001 From: kaz-yos Date: Sat, 17 Jun 2017 06:13:48 -0400 Subject: [PATCH 1/9] Quote package names --- DESCRIPTION | 10 +++++----- NEWS | 8 ++++++-- 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index bddb7f2..3f5c378 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,17 +1,17 @@ Package: tableone Type: Package -Title: Create "Table 1" to Describe Baseline Characteristics +Title: Create 'Table 1' to Describe Baseline Characteristics Version: 0.8.1 Date: 2017-06-16 Author: Kazuki Yoshida, Justin Bohn. Maintainer: Kazuki Yoshida -Description: Creates "Table 1", i.e., description of baseline patient +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 + 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: diff --git a/NEWS b/NEWS index 9f0c8d4..0daf499 100644 --- a/NEWS +++ b/NEWS @@ -1,11 +1,15 @@ -tableone 0.8.1 (2017-06-16) +tableone 0.8.1 (2017-06-17) ---------------------------------------------------------------- -BUG FIX +BUG FIXES * Fix alignment issue with the Missing column. Note currently the percentage is shown with 1 decimal and this is hard-coded. +* Change vignetteBuilder to knitr to form the index correctly. + +* Single-quote package names in DESCRIPTION. + tableone 0.8.0 (2017-06-15) ---------------------------------------------------------------- From 92a437a13929b54eed3bc4e3d184e9327fa22c4d Mon Sep 17 00:00:00 2001 From: kaz-yos Date: Sat, 17 Jun 2017 06:26:49 -0400 Subject: [PATCH 2/9] Change to knitr from rmarkdown package This populates inst/doc with - introduction.R - introduction.Rmd - introduction.html - smd.R - smd.Rmd - smd.html It also added build/vignette.rds file. References http://r-pkgs.had.co.nz/vignettes.html#vignette-workflow https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Non_002dSweave-vignettes --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3f5c378..c9c08ff 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -29,9 +29,9 @@ Suggests: Matching, reshape2, ggplot2, - rmarkdown, + knitr, geepack, lme4 URL: https://github.com/kaz-yos/tableone -VignetteBuilder: rmarkdown +VignetteBuilder: knitr RoxygenNote: 6.0.1 From 600ae016469081d9579f84f69a942aea80bad90a Mon Sep 17 00:00:00 2001 From: kaz-yos Date: Sat, 17 Jun 2017 06:48:42 -0400 Subject: [PATCH 3/9] Add vignettes to Makefile --- Makefile | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 0d68c74..378035a 100644 --- a/Makefile +++ b/Makefile @@ -23,7 +23,7 @@ PKG_FILES := DESCRIPTION NAMESPACE NEWS $(R_FILES) $(TST_FILES) $(SRC_FILES) $(V ## .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: test build_win build check revdep install clean +.PHONY: test build_win vignettes build check revdep install clean ### Define targets @@ -38,6 +38,9 @@ build_win: Rscript -e "devtools::build_win(version = 'R-devel')" Rscript -e "devtools::build_win(version = 'R-release')" +vignettes: + Rscript -e "devtools::build_vignettes()" + ## 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 @@ -45,7 +48,6 @@ build: $(PKG_NAME)_$(PKG_VERSION).tar.gz ## (file target) The *.tar.gz file depends on package files including NAMESPACE, ## and build *.tar.gz file from these. $(PKG_NAME)_$(PKG_VERSION).tar.gz: $(PKG_FILES) - cp -a ${VIG_FILES} inst/doc/ Rscript -e "devtools::build(pkg = '.', path = '.', manual = TRUE)" ## (file target) NAMESPACE depends on *.R files, and excecute roxygen2 on these. From 935531b7e78b6eaadc015af8483b238b05a58155 Mon Sep 17 00:00:00 2001 From: kaz-yos Date: Sat, 17 Jun 2017 06:57:19 -0400 Subject: [PATCH 4/9] Fix spelling in DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index c9c08ff..e124018 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,7 +9,7 @@ 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. + supported via the 'survey' package. See 'github' for a screen cast. '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. From 85ccd0b0faa69197c2611c0aa99e78c94fe5a4c0 Mon Sep 17 00:00:00 2001 From: kaz-yos Date: Sat, 17 Jun 2017 07:03:05 -0400 Subject: [PATCH 5/9] Fix vignettes for bad links Fix CRAN links in vignettes Drop a broken link to MW paper Ignore resulting files in inst/doc --- .gitignore | 4 ++++ inst/doc/introduction.Rmd | 2 +- inst/doc/smd.Rmd | 4 ++-- vignettes/introduction.Rmd | 2 +- vignettes/smd.Rmd | 4 ++-- 5 files changed, 10 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 8df890f..5e5f663 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,7 @@ *.tar.gz *.Rcheck revdep +/inst/doc/introduction.R +/inst/doc/introduction.html +/inst/doc/smd.R +/inst/doc/smd.html diff --git a/inst/doc/introduction.Rmd b/inst/doc/introduction.Rmd index 1471697..65b9d5c 100644 --- a/inst/doc/introduction.Rmd +++ b/inst/doc/introduction.Rmd @@ -162,5 +162,5 @@ print(tab3$ContTable, nonnormal = biomarkers) -------------------- - Authored by Kazuki Yoshida -- CRAN page: http://cran.r-project.org/package=tableone +- CRAN page: https://cran.r-project.org/package=tableone - github page: https://github.com/kaz-yos/tableone diff --git a/inst/doc/smd.Rmd b/inst/doc/smd.Rmd index f01f177..e5cd31c 100644 --- a/inst/doc/smd.Rmd +++ b/inst/doc/smd.Rmd @@ -152,7 +152,7 @@ addmargins(table(ExtractSmd(tabMatched) > 0.1)) ## Propensity score matching weight -The matching weight method is a weighting analogue to the 1:1 pairwise algorithmic matching (http://www.ncbi.nlm.nih.gov/pubmed/23902694 ). An earlier version of the paper is available free (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.359.4724&rep=rep1&type=pdf ). The matching weight is defined as the smaller of the predicted probabilities of receiving or not receiving the treatment over the predicted probability of being assigned to the arm the patient is actually in. After weighting, all the standardized mean differences are below 0.1. The standardized mean differences in weighted data are explained in http://onlinelibrary.wiley.com/doi/10.1002/sim.6607/full . +The matching weight method is a weighting analogue to the 1:1 pairwise algorithmic matching (http://www.ncbi.nlm.nih.gov/pubmed/23902694 ). The matching weight is defined as the smaller of the predicted probabilities of receiving or not receiving the treatment over the predicted probability of being assigned to the arm the patient is actually in. After weighting, all the standardized mean differences are below 0.1. The standardized mean differences in weighted data are explained in http://onlinelibrary.wiley.com/doi/10.1002/sim.6607/full . ```{r} @@ -254,5 +254,5 @@ print(resTogether, quote = FALSE) -------------------- - Authored by Kazuki Yoshida -- CRAN page: http://cran.r-project.org/package=tableone +- CRAN page: https://cran.r-project.org/package=tableone - github page: https://github.com/kaz-yos/tableone diff --git a/vignettes/introduction.Rmd b/vignettes/introduction.Rmd index 1471697..65b9d5c 100644 --- a/vignettes/introduction.Rmd +++ b/vignettes/introduction.Rmd @@ -162,5 +162,5 @@ print(tab3$ContTable, nonnormal = biomarkers) -------------------- - Authored by Kazuki Yoshida -- CRAN page: http://cran.r-project.org/package=tableone +- CRAN page: https://cran.r-project.org/package=tableone - github page: https://github.com/kaz-yos/tableone diff --git a/vignettes/smd.Rmd b/vignettes/smd.Rmd index f01f177..e5cd31c 100644 --- a/vignettes/smd.Rmd +++ b/vignettes/smd.Rmd @@ -152,7 +152,7 @@ addmargins(table(ExtractSmd(tabMatched) > 0.1)) ## Propensity score matching weight -The matching weight method is a weighting analogue to the 1:1 pairwise algorithmic matching (http://www.ncbi.nlm.nih.gov/pubmed/23902694 ). An earlier version of the paper is available free (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.359.4724&rep=rep1&type=pdf ). The matching weight is defined as the smaller of the predicted probabilities of receiving or not receiving the treatment over the predicted probability of being assigned to the arm the patient is actually in. After weighting, all the standardized mean differences are below 0.1. The standardized mean differences in weighted data are explained in http://onlinelibrary.wiley.com/doi/10.1002/sim.6607/full . +The matching weight method is a weighting analogue to the 1:1 pairwise algorithmic matching (http://www.ncbi.nlm.nih.gov/pubmed/23902694 ). The matching weight is defined as the smaller of the predicted probabilities of receiving or not receiving the treatment over the predicted probability of being assigned to the arm the patient is actually in. After weighting, all the standardized mean differences are below 0.1. The standardized mean differences in weighted data are explained in http://onlinelibrary.wiley.com/doi/10.1002/sim.6607/full . ```{r} @@ -254,5 +254,5 @@ print(resTogether, quote = FALSE) -------------------- - Authored by Kazuki Yoshida -- CRAN page: http://cran.r-project.org/package=tableone +- CRAN page: https://cran.r-project.org/package=tableone - github page: https://github.com/kaz-yos/tableone From ed624860a3a06c51eaef43793c213357682ada08 Mon Sep 17 00:00:00 2001 From: kaz-yos Date: Sat, 17 Jun 2017 07:14:11 -0400 Subject: [PATCH 6/9] Clean Makefile Comment appropriately Revert check in Makefile Add check_devtools for devtools::check() --- Makefile | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/Makefile b/Makefile index 378035a..09afff9 100644 --- a/Makefile +++ b/Makefile @@ -23,7 +23,7 @@ PKG_FILES := DESCRIPTION NAMESPACE NEWS $(R_FILES) $(TST_FILES) $(SRC_FILES) $(V ## .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: test build_win vignettes build check revdep install clean +.PHONY: test winbuild vignettes build check check_devtools revdep install clean ### Define targets @@ -32,12 +32,13 @@ PKG_FILES := DESCRIPTION NAMESPACE NEWS $(R_FILES) $(TST_FILES) $(SRC_FILES) $(V test: NAMESPACE Rscript -e "options(width = 120); devtools::test()" | tee test-all.txt -## build_win always build regardless of file update status +## winbuild always build regardless of file update status ## Links to results e-mailed (no useful output locally) -build_win: +winbuild: Rscript -e "devtools::build_win(version = 'R-devel')" Rscript -e "devtools::build_win(version = 'R-release')" +## Build vignettes in inst/doc vignettes: Rscript -e "devtools::build_vignettes()" @@ -57,6 +58,9 @@ 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 | tee cran-check.txt + +check_devtools: $(PKG_NAME)_$(PKG_VERSION).tar.gz Rscript -e "options(width = 120); devtools::check(pkg = '.', check_dir = '.', manual = TRUE)" | tee cran-check.txt ## revdep requires the *.tar.gz file, and execute strict tests on it. From ca23289df9cc67332edd900cfe709f3d22b968c5 Mon Sep 17 00:00:00 2001 From: kaz-yos Date: Sat, 17 Jun 2017 07:29:29 -0400 Subject: [PATCH 7/9] Update CRAN check results with direct R CMD check invocation --- cran-check.txt | 14 +++++++------- tableone.Rcheck/tableone-Ex.Rout | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/cran-check.txt b/cran-check.txt index 81e7fc7..58d77f9 100644 --- a/cran-check.txt +++ b/cran-check.txt @@ -1,9 +1,3 @@ -* checking for file ‘/Users/kazuki/Documents/programming/r/tableone/DESCRIPTION’ ... OK -* preparing ‘tableone’: -* checking DESCRIPTION meta-information ... OK -* checking for LF line-endings in source and make files -* checking for empty or unneeded directories -* building ‘tableone_0.8.1.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) @@ -12,6 +6,8 @@ * checking for file ‘tableone/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tableone’ version ‘0.8.1’ +* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers +Maintainer: ‘Kazuki Yoshida ’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK @@ -23,6 +19,7 @@ * checking whether package ‘tableone’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK +* checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK @@ -35,6 +32,7 @@ * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK +* checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK @@ -55,7 +53,9 @@ * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK - diff --git a/tableone.Rcheck/tableone-Ex.Rout b/tableone.Rcheck/tableone-Ex.Rout index 5f89362..d53cdb1 100644 --- 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: 7.4 0.285 8.882 0.005 0.005 +Time elapsed: 9.407 0.276 9.755 0.006 0.005 > grDevices::dev.off() null device 1 From a0d37ccdbd128f324c13e550596b25a5c91e873c Mon Sep 17 00:00:00 2001 From: kaz-yos Date: Sat, 17 Jun 2017 07:30:12 -0400 Subject: [PATCH 8/9] Update cran note for 0.8.1 --- cran-comment.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/cran-comment.md b/cran-comment.md index a3b5af0..40990a5 100644 --- a/cran-comment.md +++ b/cran-comment.md @@ -1,22 +1,26 @@ ## What's new The following changes are included. -tableone 0.8.1 (2017-06-16) +tableone 0.8.1 (2017-06-17) ---------------------------------------------------------------- BUG FIX * Fix alignment issue with the Missing column. Note currently the percentage is shown with 1 decimal and this is hard-coded. +* Change vignetteBuilder to knitr to form the index correctly. +* Single-quote package names in DESCRIPTION. + ## Test environments * Local OS X 10.12.5, R 3.4.0 * Ubuntu Linux on Travis-CI (oldrel, release, and devel) * win-builder (release and devel) + ## R CMD check results * ERRORs: None * WARNINGs: None -* NOTEs: - - Author e-mail check +* NOTEs: None + ## Downstream dependencies RcmdrPlugin.EZR GUI frontend: No change was made to APIs. From d05e3b7f8b347bf323c5908e28f0b236fef722fd Mon Sep 17 00:00:00 2001 From: kaz-yos Date: Sat, 17 Jun 2017 07:37:20 -0400 Subject: [PATCH 9/9] Add revdep results --- cran-comment.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/cran-comment.md b/cran-comment.md index 40990a5..9b0d5c5 100644 --- a/cran-comment.md +++ b/cran-comment.md @@ -23,4 +23,5 @@ BUG FIX ## Downstream dependencies -RcmdrPlugin.EZR GUI frontend: No change was made to APIs. +Checked RcmdrPlugin.EZR: 0 errors | 0 warnings | 0 notes +Checked rpsftm : 0 errors | 0 warnings | 0 notes