From 1d062449f6ff60267c3b92d50d37f16a00c0a0ab Mon Sep 17 00:00:00 2001 From: kaz-yos Date: Mon, 17 Feb 2014 22:22:24 -0500 Subject: [PATCH 1/5] NEWS fixed --- NEWS | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/NEWS b/NEWS index 309f756..aa69389 100644 --- a/NEWS +++ b/NEWS @@ -1,4 +1,4 @@ -tableone 0.3.0 (2014-02-16) +tableone 0.3.0 (2014-02-17) ---------------------------------------------------------------- NEW FEATURES @@ -10,6 +10,11 @@ NEW FEATURES new minMax argument, a logical value specifying whether to show median [min, max] instead of median [IQR] for nonnormal variables +* The print method for the TableOne/CatTable class object has a + new cramVars argument, a character vector to specify which + 2-level factors to should have both levels presented in one row. + + BUG FIXES * Documentations were fixed to represent the current version. From 547d5e3682196f608230bae0b1bc9e60c75e49b4 Mon Sep 17 00:00:00 2001 From: kaz-yos Date: Mon, 17 Feb 2014 23:15:21 -0500 Subject: [PATCH 2/5] README.md example changed --- README.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 125d137..95edd6e 100644 --- a/README.md +++ b/README.md @@ -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 From 7bcbbc76b749843e134b4a643ed20b333cf2977e Mon Sep 17 00:00:00 2001 From: kaz-yos Date: Tue, 18 Feb 2014 09:24:01 -0500 Subject: [PATCH 3/5] typo fixed --- DESCRIPTION | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 46a4e78..cf1426d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,7 +9,7 @@ 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 diff --git a/README.md b/README.md index 95edd6e..2e90254 100644 --- 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 From d9bc992fec6c5bd520c8602d92f127b9cebe126f Mon Sep 17 00:00:00 2001 From: kaz-yos Date: Tue, 18 Feb 2014 10:27:03 -0500 Subject: [PATCH 4/5] imports e1071 gmodels; suggests survival, instead of Depends --- DESCRIPTION | 9 +++++---- NAMESPACE | 2 ++ R/print.CatTable.R | 2 +- R/tableone-package.R | 1 + 4 files changed, 9 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index cf1426d..65ae4e5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ 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 Description: This package creates "Table 1", i.e., description of baseline @@ -13,8 +13,9 @@ Description: This package creates "Table 1", i.e., description of baseline 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 index 9cfa0bc..9b6b5ea 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -8,3 +8,5 @@ export(CreateCatTable) export(CreateContTable) export(CreateTableOne) export(ShowRegTable) +import(e1071) +import(gmodels) diff --git a/R/print.CatTable.R b/R/print.CatTable.R index fd59144..4bd80c0 100644 --- 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 index 1961439..1c45db2 100644 --- 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. From 2e1dc365305bf83dab3d06ea1c651f89980ba6be Mon Sep 17 00:00:00 2001 From: kaz-yos Date: Tue, 18 Feb 2014 10:44:35 -0500 Subject: [PATCH 5/5] NEWS updated for 0.3.1 --- NEWS | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/NEWS b/NEWS index aa69389..2f734a2 100644 --- 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