Final tweaks to satisfy R CMD

graemeleehickey · Mar 27, 2017 · 182a47d · 182a47d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -16,7 +16,7 @@ Authors@R: c(
         role = "ctb"),
     person("Dimitris", "Rizopoulos", email = "[email protected]",
         role = c("ctb", "dtc"),
-        comment = "R/renal.R, R/hessian.R, R/vcov.R")
+        comment = "data/renal.rda, R/hessian.R, R/vcov.R")
     )
 Maintainer: Graeme L. Hickey <[email protected]>
 Date: 2017-03-25

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# joineRML 0.1.1.9000 (devel version).
+# joineRML 0.2.0
 
 ## New features
 

diff --git a/README.Rmd b/README.Rmd
@@ -17,8 +17,8 @@ knitr::opts_chunk$set(
 [![Travis-CI Build Status](https://travis-ci.org/graemeleehickey/joineRML.svg?branch=master)](https://travis-ci.org/graemeleehickey/joineRML)
 [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/graemeleehickey/joineRML?branch=master&svg=true)](https://ci.appveyor.com/project/graemeleehickey/joineRML)
 [![License](https://img.shields.io/badge/License-GPL%20%28%3E=%203%29-brightgreen.svg)](http://www.gnu.org/licenses/gpl-3.0.html)
-[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/joineRML)](https://cran.r-project.org/package=joineRML)
-[![](http://cranlogs.r-pkg.org/badges/joineRML)](http://cran.rstudio.com/web/packages/joineRML/index.html)
+[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/joineRML)](https://CRAN.R-project.org/package=joineRML)
+[![](http://cranlogs.r-pkg.org/badges/joineRML)](https://CRAN.R-project.org/package=joineRML)
 [![codecov](https://codecov.io/gh/graemeleehickey/joineRML/branch/master/graph/badge.svg)](https://codecov.io/gh/graemeleehickey/joineRML)
 
 `joineRML` is an extension of the joineR package for fitting joint models of time-to-event data and multivariate longitudinal data. The model fitted in joineRML is an extension of the Wulfsohn and Tsiatis (1997) and Henderson et al. (2000) models, which is comprised on $(K+1)$-sub-models: a Cox proportional hazards regression model (Cox, 1972) and a $K$-variate linear mixed-effects model - a direct extension of the Laird and Ware (1982) regression model. The model is fitted using a Monte Carlo Expectation-Maximization (MCEM) algorithm, which closely follows the methodology presented by Lin et al. (2002).

diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 joineRML
 ========
 
-[![Travis-CI Build Status](https://travis-ci.org/graemeleehickey/joineRML.svg?branch=master)](https://travis-ci.org/graemeleehickey/joineRML) [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/graemeleehickey/joineRML?branch=master&svg=true)](https://ci.appveyor.com/project/graemeleehickey/joineRML) [![License](https://img.shields.io/badge/License-GPL%20%28%3E=%203%29-brightgreen.svg)](http://www.gnu.org/licenses/gpl-3.0.html) [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/joineRML)](https://cran.r-project.org/package=joineRML) [![](http://cranlogs.r-pkg.org/badges/joineRML)](http://cran.rstudio.com/web/packages/joineRML/index.html) [![codecov](https://codecov.io/gh/graemeleehickey/joineRML/branch/master/graph/badge.svg)](https://codecov.io/gh/graemeleehickey/joineRML)
+[![Travis-CI Build Status](https://travis-ci.org/graemeleehickey/joineRML.svg?branch=master)](https://travis-ci.org/graemeleehickey/joineRML) [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/graemeleehickey/joineRML?branch=master&svg=true)](https://ci.appveyor.com/project/graemeleehickey/joineRML) [![License](https://img.shields.io/badge/License-GPL%20%28%3E=%203%29-brightgreen.svg)](http://www.gnu.org/licenses/gpl-3.0.html) [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/joineRML)](https://CRAN.R-project.org/package=joineRML) [![](http://cranlogs.r-pkg.org/badges/joineRML)](https://CRAN.R-project.org/package=joineRML) [![codecov](https://codecov.io/gh/graemeleehickey/joineRML/branch/master/graph/badge.svg)](https://codecov.io/gh/graemeleehickey/joineRML)
 
 `joineRML` is an extension of the joineR package for fitting joint models of time-to-event data and multivariate longitudinal data. The model fitted in joineRML is an extension of the Wulfsohn and Tsiatis (1997) and Henderson et al. (2000) models, which is comprised on (*K* + 1)-sub-models: a Cox proportional hazards regression model (Cox, 1972) and a *K*-variate linear mixed-effects model - a direct extension of the Laird and Ware (1982) regression model. The model is fitted using a Monte Carlo Expectation-Maximization (MCEM) algorithm, which closely follows the methodology presented by Lin et al. (2002).
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,23 +1,19 @@
-## Resubmission
-This is a resubmission owing to an installation ERROR reported by CRAN checks for r-oldrel-windows-ix86+x86_64. In this version I have:
-
-* Patched sigma.mjoint.R to reference S3 method for sigma depending on version number.
-
 ## Test environments
-* local OS X install, R 3.3.1
-* ubuntu 12.04 (on travis-ci), R 3.3.1
-* local Windows 7 Enterprise SP1 install, R 3.3.1 (via github_install)
-* win-builder (devel and release)
-* r-oldrel-windows (via R-hub)
+* local OS X install, R 3.3.3
+* ubuntu 12.04 (on travis-ci), R 3.3.2 (+ devel, oldrel)
+* windows (on appveyor)
+* win-builder (devel, release)
+* tested on several R-hub platforms
 
 ## R CMD check results
 
-0 errors | 0 warnings | 0 notes
+0 errors | 0 warnings | 1 notes
 
 ## Reverse dependencies
 
 There are no reverse dependencies.
 
 ## Other notes
 
-The vignette code can take about 15-20 minutes to run due to the Monte Carlo simulation example.
+* win-builder NOTE refers to a spelling error, but word (covariates) is correct.
+* The vignette code can take about 15-20 minutes to run due to the Monte Carlo simulation example.