Merge pull request #22 from ACCLAB/v0.1.0

add badges, update install instructions

.Rbuildignore

@@ -1,3 +1,4 @@
+^CRAN-RELEASE$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.travis\.yml$

CRAN-RELEASE

@@ -0,0 +1,2 @@
+This package was submitted to CRAN on 2018-11-13.
+Once it is accepted, delete this file and tag the release (commit 6908c51c3e).

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dabestr
 Type: Package
-Title: Data Analysis using Bootstrap-Coupled Estimation in R
+Title: Data Analysis using Bootstrap-Coupled Estimation
 Version: 0.1.0
 Authors@R: c(
     person("Joses W.", "Ho", 
@@ -9,7 +9,7 @@ Authors@R: c(
           role = c("aut"))
           )
 Maintainer: Joses W. Ho <[email protected]>
-Description: Data Analysis using Bootstrap-Coupled ESTimation in R.
+Description: Data Analysis using Bootstrap-Coupled ESTimation.
     Estimation statistics is a simple framework that avoids the pitfalls of 
     significance testing. It uses familiar statistical concepts: means, 
     mean differences, and error bars. More importantly, it focuses on the 
@@ -20,6 +20,7 @@ Description: Data Analysis using Bootstrap-Coupled ESTimation in R.
     display the underlying distribution.
     2. It presents the effect size as a bootstrap 95% confidence interval on a 
     separate but aligned axes.
+    Estimation plots are introduced in Ho et al (2018) <doi:10.1101/377978>.
 License: file LICENSE
 Encoding: UTF-8
 LazyData: true

LICENSE

@@ -1,21 +1,21 @@
-Copyright (c) 2016-2018 Joses W. Ho and Tayfun Tumkaya
+Copyright (c) 2016-2018, Joses W. Ho and Tayfun Tumkaya
 All rights reserved.
 
-`dabestr` is licensed under the Clear BSD License.
 Redistribution and use in source and binary forms, with or without
-modification, are permitted (subject to the limitations in the disclaimer
-below) provided that the following conditions are met:
+modification, are permitted provided that the following conditions are
+met:
 
-* Redistributions of source code must retain the above copyright notice,
-this list of conditions and the following disclaimer.
+    Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
 
-* Redistributions in binary form must reproduce the above copyright
-notice, this list of conditions and the following disclaimer in the
-documentation and/or other materials provided with the distribution.
+    Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in
+    the documentation and/or other materials provided with the
+    distribution.
 
-* Neither the name of the copyright holder nor the names of its
-contributors may be used to endorse or promote products derived from this
-software without specific prior written permission.
+    Neither the name of the copyright holders nor the names of its
+    contributors may be used to endorse or promote products derived
+    from this software without specific prior written permission.
 
 NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
 THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
@@ -29,28 +29,3 @@ BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
 IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGE.
-
-
-
-
-This package contains the file `flat_violin.R`, copyright (c) 2018 David
-Robinson, Micah Allen, Davide Poggiali, Kirstie Whitaker, Tom Rhys Marshall and
-Rogier Kievit. It is licensed under the MIT License.
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of `flat_violin.R` (the "Software"), to deal in the Software without restriction,
-including without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to permit
-persons to whom the Software is furnished to do so, subject to the following
-conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

README.Rmd

@@ -2,7 +2,6 @@
 output: github_document
 ---
 
-<!-- README.md is generated from README.Rmd. Please edit that file -->
 
 ```{r, echo = FALSE}
 knitr::opts_chunk$set(
@@ -14,10 +13,9 @@ knitr::opts_chunk$set(
 
 # dabestr
 
-[![Travis CI build status](https://img.shields.io/travis/com/ACCLAB/dabestr/master.svg)](https://travis-ci.com/ACCLAB/dabestr/)
+[![minimal R version](https://img.shields.io/badge/R%3E%3D-3.5.0-6666ff.svg)](https://cran.r-project.org/) [![CRAN Status Badge](https://www.r-pkg.org/badges/version-last-release/dabestr?color=orange)](https://cran.r-project.org/package=dabestr) [![Travis CI build status](https://img.shields.io/travis/com/ACCLAB/dabestr/master.svg)](https://travis-ci.com/ACCLAB/dabestr/) [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 
-
-dabestr is a package for **D**ata **A**nalysis using **B**ootstrap-Coupled **EST**imation in R.
+dabestr is a package for **D**ata **A**nalysis using **B**ootstrap-Coupled **EST**imation.
 
 ## About
 
@@ -139,13 +137,13 @@ plot(shared.control, theme = custom.theme,color.column = Gender)
 
 ## Installation
 
-Currently, this package is only available on Github. A CRAN version is forthcoming.
-
 Your version of R must be 3.5.0 or higher.
 
 ```{r demo.install, eval=FALSE}
-# install.packages("dabestr") ## Does not work; awaiting CRAN acceptance.
+install.packages("dabestr")
 
+# To install the latest development version on Github,
+# use the line below.
 devtools::install_github("ACCLAB/dabestr")
 ```
 

README.md

@@ -1,11 +1,10 @@
 
-<!-- README.md is generated from README.Rmd. Please edit that file -->
 dabestr
 =======
 
-[![Travis CI build status](https://img.shields.io/travis/com/ACCLAB/dabestr/master.svg)](https://travis-ci.com/ACCLAB/dabestr/)
+[![minimal R version](https://img.shields.io/badge/R%3E%3D-3.5.0-6666ff.svg)](https://cran.r-project.org/) [![CRAN Status Badge](https://www.r-pkg.org/badges/version-last-release/dabestr?color=orange)](https://cran.r-project.org/package=dabestr) [![Travis CI build status](https://img.shields.io/travis/com/ACCLAB/dabestr/master.svg)](https://travis-ci.com/ACCLAB/dabestr/) [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 
-dabestr is a package for **D**ata **A**nalysis using **B**ootstrap-Coupled **EST**imation in R.
+dabestr is a package for **D**ata **A**nalysis using **B**ootstrap-Coupled **EST**imation.
 
 About
 -----
@@ -25,13 +24,13 @@ An estimation plot has two key features.
 Installation
 ------------
 
-Currently, this package is only available on Github. A CRAN version is forthcoming.
-
 Your version of R must be 3.5.0 or higher.
 
 ``` r
-# install.packages("dabestr") ## Does not work; awaiting CRAN acceptance.
+install.packages("dabestr")
 
+# To install the latest development version on Github,
+# use the line below.
 devtools::install_github("ACCLAB/dabestr")
 ```
 

cran-comments.md

@@ -1,30 +1,30 @@
+## Resubmission
+This is a resubmission. In this version I have:
+
+* Cleaned the LICENSE file. Note that the package is licensed under 
+the BSD 3-Clause Clear License, which is a variant of the BSD 3-Clause 
+License that explicitly does not grant any patent rights
+<https://choosealicense.com/licenses/bsd-3-clause-clear/>. 
+It does not seem to be listed in the license templates on CRAN
+<https://cran.r-project.org/web/licenses/>.
+
+* Fixed the DOI markup.
+
+* Removed the redundant "in R" from the title.
+
+* Added reference about the plots and methods in the Description field 
+of DESCRIPTION.
+
+
 ## Test environments
 * local OS X install, R 3.5.0
+* local debian install, R 3.5.1
 * ubuntu 14.04.5 (on travis-ci, devel and release)
 * win-builder (devel and release)
 
 
 ## R CMD check results
-There were no ERRORs or WARNINGs.
-
-There were 3 NOTEs:
-
-* The installed package size is over 5 MB because the vignettes have a large number of plots. Future releases will progressively reduce the filesize of the vignettes.
-
-* Non-FOSS package license (file LICENSE)
-  The LICENSE does not match a FOSS template license because it contains the original copyright license for "flat_violin.R".
-
-* Found the following (possibly) invalid URLs:
-    URL: https://www.jstor.org/stable/2246110
-      From: man/dabest.Rd
-      Status: 403
-      Message: Forbidden
-
-    DOI: https://doi.org/10.1101/377978
-      From: inst/CITATION
-      Message: Invalid DOI
-
-  Both the DOI and URL are valid, and can be accessed by modern browsers.
+There were no ERRORs, WARNINGs, or NOTEs.
 
 
 ## Downstream dependencies

dabestr.Rproj

@@ -18,4 +18,5 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace

inst/CITATION

@@ -9,7 +9,7 @@ citEntry(entry       = "Misc",
                         as.person("Adam Claridge-Chang")
                         ),
          year        = "2018",
-         doi         = "https://doi.org/10.1101/377978",
+         doi         = "10.1101/377978",
          url         = "https://www.biorxiv.org/content/early/2018/07/26/377978.full.pdf",
          textVersion = "Moving beyond P values: Everyday data analysis with estimation plots. (2018) Joses Ho, Tayfun Tumkaya, Sameer Aryal, Hyungwon Choi, Adam Claridge-Chang. bioRxiv doi: https://doi.org/10.1101/377978"
          )