From 0892a79e6f8d0e767a76cab8177e7ea6b087d0e8 Mon Sep 17 00:00:00 2001 From: markean Date: Tue, 26 Dec 2023 15:28:57 +0900 Subject: [PATCH] package metadata and structure updated --- .Rbuildignore | 5 + .github/.gitignore | 1 + .github/workflows/R-CMD-check.yaml | 49 +++ DESCRIPTION | 29 +- LICENSE.md | 595 +++++++++++++++++++++++++++++ NEWS.md | 5 + README.Rmd | 35 ++ README.md | 39 +- codemeta.json | 95 +++++ data-raw/DATASET.R | 3 + inst/WORDLIST | 2 + man/figures/README-pressure-1.png | Bin 0 -> 17067 bytes tests/spelling.R | 3 + 13 files changed, 853 insertions(+), 8 deletions(-) create mode 100644 .github/.gitignore create mode 100644 .github/workflows/R-CMD-check.yaml create mode 100644 LICENSE.md create mode 100644 NEWS.md create mode 100644 README.Rmd create mode 100644 codemeta.json create mode 100644 data-raw/DATASET.R create mode 100644 inst/WORDLIST create mode 100644 man/figures/README-pressure-1.png create mode 100644 tests/spelling.R diff --git a/.Rbuildignore b/.Rbuildignore index d821302..cd1d2ab 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -2,3 +2,8 @@ ^renv\.lock$ ^.*\.Rproj$ ^\.Rproj\.user$ +^LICENSE\.md$ +^README\.Rmd$ +^data-raw$ +^\.github$ +^codemeta\.json$ diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..a3ac618 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,49 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + +name: R-CMD-check + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macos-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + + steps: + - uses: actions/checkout@v3 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true diff --git a/DESCRIPTION b/DESCRIPTION index 0bb8e02..70b077e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,11 +1,26 @@ Package: retel Type: Package -Title: What the Package Does (Title Case) -Version: 0.1.0 -Author: Who wrote it -Maintainer: The package maintainer -Description: More about what it does (maybe more than one line) - Use four spaces when indenting paragraphs within the Description. -License: What license is it under? +Title: Regularized Exponentially Tilted Empirical Likelihood +Version: 0.1.0.9000 +Authors@R: c( + person("Eunseop", "Kim", email = "markean@pm.me", + role = c("aut", "cre")), + person("Steven", "MacEachern", role = c("ctb", "ths")), + person("Mario", "Peruggia", role = c("ctb", "ths")) + ) +Description: Computes regularized exponentially tilted empirical likelihood for + Bayesian inference. Details of the methods are given in Kim, MacEachern, and + Peruggia (2023) . This work was supported + by the U.S. National Science Foundation under Grants No. SES-1921523 and + DMS-2015552. +License: GPL (>= 3) +URL: https://github.com/markean/retel +BugReports: https://github.com/markean/retel/issues +Depends: + R (>= 4.1.0) +Suggests: + melt, + spelling Encoding: UTF-8 +Language: en-US LazyData: true diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..175443c --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,595 @@ +GNU General Public License +========================== + +_Version 3, 29 June 2007_ +_Copyright © 2007 Free Software Foundation, Inc. <>_ + +Everyone is permitted to copy and distribute verbatim copies of this license +document, but changing it is not allowed. + +## Preamble + +The GNU General Public License is a free, copyleft license for software and other +kinds of works. + +The licenses for most software and other practical works are designed to take away +your freedom to share and change the works. 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Disclaimer of Warranty + +THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. +EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES +PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER +EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE +QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE +DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + +### 16. Limitation of Liability + +IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY +COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS +PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, +INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE +PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE +OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE +WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE +POSSIBILITY OF SUCH DAMAGES. + +### 17. Interpretation of Sections 15 and 16 + +If the disclaimer of warranty and limitation of liability provided above cannot be +given local legal effect according to their terms, reviewing courts shall apply local +law that most closely approximates an absolute waiver of all civil liability in +connection with the Program, unless a warranty or assumption of liability accompanies +a copy of the Program in return for a fee. + +_END OF TERMS AND CONDITIONS_ + +## How to Apply These Terms to Your New Programs + +If you develop a new program, and you want it to be of the greatest possible use to +the public, the best way to achieve this is to make it free software which everyone +can redistribute and change under these terms. + +To do so, attach the following notices to the program. It is safest to attach them +to the start of each source file to most effectively state the exclusion of warranty; +and each file should have at least the “copyright” line and a pointer to +where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + +If the program does terminal interaction, make it output a short notice like this +when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type 'show c' for details. + +The hypothetical commands `show w` and `show c` should show the appropriate parts of +the General Public License. Of course, your program's commands might be different; +for a GUI interface, you would use an “about box”. + +You should also get your employer (if you work as a programmer) or school, if any, to +sign a “copyright disclaimer” for the program, if necessary. For more +information on this, and how to apply and follow the GNU GPL, see +<>. + +The GNU General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may consider it +more useful to permit linking proprietary applications with the library. If this is +what you want to do, use the GNU Lesser General Public License instead of this +License. But first, please read +<>. diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..8ac919d --- /dev/null +++ b/NEWS.md @@ -0,0 +1,5 @@ +# retel (development version) + + +# retel 0.1.0 +* Initial release. diff --git a/README.Rmd b/README.Rmd new file mode 100644 index 0000000..107d0c9 --- /dev/null +++ b/README.Rmd @@ -0,0 +1,35 @@ +--- +output: github_document +--- + + + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>", + fig.path = "man/figures/README-", + out.width = "100%" +) +``` + +# retel + +[![Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept) +[![R-CMD-check](https://github.com/markean/retel/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/markean/retel/actions/workflows/R-CMD-check.yaml) + + +## Overview +Computes regularized exponentially tilted empirical likelihood for Bayesian inference. + +This repository accompanies the research paper titled 'Regularized Exponentially Tilted Empirical Likelihood for Bayesian Inference,' available on [arXiv](https://arxiv.org/abs/2112.09206). +The `retel-paper` folder contains code and additional resources related to the paper. +This work was supported by the U.S. National Science Foundation under Grants No. [SES-1921523](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1921523) and [DMS-2015552](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2015552). + + +## Installation +You can install the development version of retel from [GitHub](https://github.com/) with: +``` r +# install.packages("devtools") +devtools::install_github("markean/retel") +``` diff --git a/README.md b/README.md index 61cd0ce..6bd7f31 100644 --- a/README.md +++ b/README.md @@ -1 +1,38 @@ -# retel - Regularized Exponentially Tilted Empirical Likelihood + + + +# retel + + + +[![Project Status: Concept – Minimal or no implementation has been done +yet, or the repository is only intended to be a limited example, demo, +or +proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept) +[![R-CMD-check](https://github.com/markean/retel/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/markean/retel/actions/workflows/R-CMD-check.yaml) + + +## Overview + +Computes regularized exponentially tilted empirical likelihood for +Bayesian inference. + +This repository accompanies the research paper titled ‘Regularized +Exponentially Tilted Empirical Likelihood for Bayesian Inference,’ +available on [arXiv](https://arxiv.org/abs/2112.09206). The +`retel-paper` folder contains code and additional resources related to +the paper. This work was supported by the U.S. National Science +Foundation under Grants +No. [SES-1921523](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1921523) +and +[DMS-2015552](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2015552). + +## Installation + +You can install the development version of retel from +[GitHub](https://github.com/) with: + +``` r +# install.packages("devtools") +devtools::install_github("markean/retel") +``` diff --git a/codemeta.json b/codemeta.json new file mode 100644 index 0000000..ee68393 --- /dev/null +++ b/codemeta.json @@ -0,0 +1,95 @@ +{ + "@context": "https://doi.org/10.5063/schema/codemeta-2.0", + "@type": "SoftwareSourceCode", + "identifier": "retel", + "description": "Computes regularized exponentially tilted empirical likelihood for Bayesian inference. Details of the methods are given in Kim, MacEachern, and Peruggia (2023) . This work was supported by the U.S. National Science Foundation under Grants No. SES-1921523 and DMS-2015552.", + "name": "retel: Regularized Exponentially Tilted Empirical Likelihood", + "codeRepository": "https://github.com/markean/retel", + "issueTracker": "https://github.com/markean/retel/issues", + "license": "https://spdx.org/licenses/GPL-3.0", + "version": "0.1.0.9000", + "programmingLanguage": { + "@type": "ComputerLanguage", + "name": "R", + "url": "https://r-project.org" + }, + "runtimePlatform": "R version 4.3.2 (2023-10-31)", + "author": [ + { + "@type": "Person", + "givenName": "Eunseop", + "familyName": "Kim", + "email": "markean@pm.me" + } + ], + "contributor": [ + { + "@type": "Person", + "givenName": "Steven", + "familyName": "MacEachern" + }, + { + "@type": "Person", + "givenName": "Mario", + "familyName": "Peruggia" + }, + { + "@type": "Person", + "givenName": "Steven", + "familyName": "MacEachern" + }, + { + "@type": "Person", + "givenName": "Mario", + "familyName": "Peruggia" + } + ], + "maintainer": [ + { + "@type": "Person", + "givenName": "Eunseop", + "familyName": "Kim", + "email": "markean@pm.me" + } + ], + "softwareSuggestions": [ + { + "@type": "SoftwareApplication", + "identifier": "melt", + "name": "melt", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=melt" + }, + { + "@type": "SoftwareApplication", + "identifier": "spelling", + "name": "spelling", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=spelling" + } + ], + "softwareRequirements": { + "1": { + "@type": "SoftwareApplication", + "identifier": "R", + "name": "R", + "version": ">= 4.1.0" + }, + "SystemRequirements": null + }, + "fileSize": "2481.81KB", + "readme": "https://github.com/markean/retel/blob/main/README.md", + "contIntegration": "https://github.com/markean/retel/actions/workflows/R-CMD-check.yaml", + "developmentStatus": "https://www.repostatus.org/#concept", + "keywords": ["r", "r-package", "rstats"] +} diff --git a/data-raw/DATASET.R b/data-raw/DATASET.R new file mode 100644 index 0000000..6514a94 --- /dev/null +++ b/data-raw/DATASET.R @@ -0,0 +1,3 @@ +## code to prepare `DATASET` dataset goes here + +usethis::use_data(DATASET, overwrite = TRUE) diff --git a/inst/WORDLIST b/inst/WORDLIST new file mode 100644 index 0000000..8a8e204 --- /dev/null +++ b/inst/WORDLIST @@ -0,0 +1,2 @@ +arXiv +’ diff --git a/man/figures/README-pressure-1.png b/man/figures/README-pressure-1.png new file mode 100644 index 0000000000000000000000000000000000000000..cfd45c5f63d0101b91154ec9601ac5e71ebe3d64 GIT binary patch literal 17067 zcmeIa2T+tN#wtz6 zf#aU3K7Z$3dpvF`UlPWWWJ@8UzOj$$Ryn6?TxvZriK^N;Ii|6ddI@HBv%2>_vMw3l 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