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Update GitHub Actions
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‎.github/workflows/GitHub_Actions_CI.yaml renamed to ‎.github/workflows/R-CMD-check.yaml

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@@ -1,36 +1,46 @@
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# CI GitHub Action ... adapted from usethis::use_github_actions()
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [master]
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branches: [main, master]
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pull_request:
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branches: [master, new_feature]
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branches: [main, master]
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name: GitHub Actions CI
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name: R-CMD-check.yaml
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## change if caches needs to be refreshed
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env:
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cache-version: v4
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permissions: read-all
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: windows-latest, r: 'release', not_cran: 'true'}
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- {os: macos-12, r: 'release', not_cran: 'true'}
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- {os: ubuntu-latest, r: 'devel', not_cran: 'true'}
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- {os: ubuntu-latest, r: 'release', not_cran: 'true'}
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- {os: ubuntu-latest, r: 'oldrel', not_cran: 'true'}
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- {os: macos-12, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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env:
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_R_CHECK_FORCE_SUGGESTS_: true
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- name: Install JAGS on macOS
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if: runner.os == 'macOS'
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run: brew install jags
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curl --progress-bar -s -o 'C:\JAGS-4.3.1.exe' -L 'https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/JAGS-4.3.1.exe'
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C:\JAGS-4.3.1.exe /S
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: |
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any::rcmdcheck
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any::XML
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any::covr
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extra-packages: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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with:
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upload-snapshots: true
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- name: Test coverage
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run: |
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covr::codecov()
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shell: Rscript {0}
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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

‎.github/workflows/test-coverage.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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name: test-coverage.yaml
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permissions: read-all
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jobs:
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test-coverage:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::covr, any::xml2
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needs: coverage
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- name: Test coverage
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run: |
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cov <- covr::package_coverage(
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quiet = FALSE,
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clean = FALSE,
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install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
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)
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covr::to_cobertura(cov)
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shell: Rscript {0}
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- uses: codecov/codecov-action@v4
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with:
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fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
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file: ./cobertura.xml
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plugin: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
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run: |
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## --------------------------------------------------------------------
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v4
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

‎README.Rmd

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@@ -18,7 +18,7 @@ library(BayLum)
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# BayLum <img width=120px src="man/figures/logo_BayLum.png" align="right" />
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<!-- badges: start -->
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[![R-CMD-check](https://github.com/crp2a/BayLum/actions/workflows/GitHub_Actions_CI.yaml/badge.svg)](https://github.com/crp2a/BayLum/actions/workflows/GitHub_Actions_CI.yaml)
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[![R-CMD-check](https://github.com/crp2a/BayLum/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/crp2a/BayLum/actions/workflows/R-CMD-check.yaml)
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[![codecov](https://codecov.io/gh/crp2a/BayLum/graph/badge.svg?token=cOdZr6imKX)](https://app.codecov.io/gh/crp2a/BayLum)
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[![r-universe](https://crp2a.r-universe.dev/badges/BayLum)](https://crp2a.r-universe.dev/BayLum)
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## Installation
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To install the latest development builds directly from GitHub, run
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**You need to have [JAGS](https://mcmc-jags.sourceforge.io) installed on your computer.**
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```{r gh-installation, eval = FALSE}
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if(!require("devtools"))
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install.packages("devtools")
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devtools::install_github("crp2a/BayLum@master")
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```
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To install a developer build other than 'master', replace the term 'master' in the codeline by the name
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of the wanted developer build.
54-
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**Please note that you need to have [JAGS](https://mcmc-jags.sourceforge.io) installed on your computer**
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## Note
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You can install the released version of **BayLum** from [CRAN](https://CRAN.R-project.org) with:
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**The package comes without any guarantee!**
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```{r cran-installation, eval=FALSE}
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install.packages("BayLum")
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```
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Please further note that this version is a development version and may change day by day. For stable branches please visit
62-
the package on [CRAN 'BayLum'](https://CRAN.R-project.org/package=BayLum ).
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And the development version from [GitHub](https://github.com/) with:
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## Funding
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```{r gh-installation, eval=FALSE}
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# install.packages("remotes")
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remotes::install_github("crp2a/BayLum")
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```
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The development of `'BayLum'` received a state financial support managed by the Agence Nationale de la Recherche (France) through the program *Investissements d'avenir* (ref. [ANR-10-LABX-52](https://lascarbx.labex.u-bordeaux.fr)) between 2015 and 2018.
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Please note that development versions may change day by day.
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## License
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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 any later version.
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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](https://github.com/crp2a/BayLum/blob/master/LICENSE) for more details.
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## Acknowledgements
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The development of **BayLum** received a state financial support managed by the Agence Nationale de la Recherche (France) through the program *Investissements d'avenir* (ref. [ANR-10-LABX-52](https://lascarbx.labex.u-bordeaux.fr)) between 2015 and 2018.

‎README.md

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<!-- badges: start -->
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[![R-CMD-check](https://github.com/crp2a/BayLum/actions/workflows/GitHub_Actions_CI.yaml/badge.svg)](https://github.com/crp2a/BayLum/actions/workflows/GitHub_Actions_CI.yaml)
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[![R-CMD-check](https://github.com/crp2a/BayLum/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/crp2a/BayLum/actions/workflows/R-CMD-check.yaml)
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[![codecov](https://codecov.io/gh/crp2a/BayLum/graph/badge.svg?token=cOdZr6imKX)](https://app.codecov.io/gh/crp2a/BayLum)
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[![r-universe](https://crp2a.r-universe.dev/badges/BayLum)](https://crp2a.r-universe.dev/BayLum)
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## Installation
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To install the latest development builds directly from GitHub, run
52+
**You need to have [JAGS](https://mcmc-jags.sourceforge.io) installed on
53+
your computer.**
54+
55+
You can install the released version of **BayLum** from
56+
[CRAN](https://CRAN.R-project.org) with:
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``` r
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if(!require("devtools"))
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install.packages("devtools")
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devtools::install_github("crp2a/BayLum@master")
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install.packages("BayLum")
5860
```
5961

60-
To install a developer build other than ‘master’, replace the term
61-
‘master’ in the codeline by the name of the wanted developer build.
62-
63-
**Please note that you need to have
64-
[JAGS](https://mcmc-jags.sourceforge.io) installed on your computer**
65-
66-
## Note
62+
And the development version from [GitHub](https://github.com/) with:
6763

68-
**The package comes without any guarantee!**
69-
70-
Please further note that this version is a development version and may
71-
change day by day. For stable branches please visit the package on [CRAN
72-
‘BayLum’](https://CRAN.R-project.org/package=BayLum).
64+
``` r
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# install.packages("remotes")
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remotes::install_github("crp2a/BayLum")
67+
```
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## Funding
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The development of `'BayLum'` received a state financial support managed
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by the Agence Nationale de la Recherche (France) through the program
78-
*Investissements d’avenir* (ref.
79-
[ANR-10-LABX-52](https://lascarbx.labex.u-bordeaux.fr)) between 2015 and
80-
2018.
69+
Please note that development versions may change day by day.
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## License
8372

@@ -92,3 +81,11 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the [GNU
9281
General Public
9382
License](https://github.com/crp2a/BayLum/blob/master/LICENSE) for more
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details.
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## Acknowledgements
86+
87+
The development of **BayLum** received a state financial support managed
88+
by the Agence Nationale de la Recherche (France) through the program
89+
*Investissements d’avenir* (ref.
90+
[ANR-10-LABX-52](https://lascarbx.labex.u-bordeaux.fr)) between 2015 and
91+
2018.

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