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| # 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: [develop] | ||
| pull_request: | ||
| branches: [develop] | ||
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|
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| name: Dev_R-CMD-check | ||
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| jobs: | ||
| R-CMD-check: | ||
| runs-on: ${{ matrix.config.os }} | ||
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| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
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| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - {os: ubuntu-latest, r: 'release'} | ||
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| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| NOT_CRAN: true | ||
| TAR_NOT_CRAN: true | ||
| R_KEEP_PKG_SOURCE: yes | ||
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: false | ||
| TORCH_INSTALL: 1 | ||
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| steps: | ||
| - uses: actions/checkout@v3 | ||
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| - uses: r-lib/actions/setup-pandoc@v2 | ||
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| - name: Install Mac system dependencies | ||
| if: runner.os == 'macOS' | ||
| run: brew install zeromq | ||
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| - name: Install Linux system dependencies | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install libglpk-dev libglpk40 | ||
| - 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 | ||
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| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: any::rcmdcheck | ||
| needs: check | ||
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| - uses: r-lib/actions/check-r-package@v2 | ||
| with: | ||
| upload-snapshots: true |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,6 @@ | ||
| #' @keywords internal | ||
| "_PACKAGE" | ||
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| ## usethis namespace: start | ||
| ## usethis namespace: end | ||
| NULL |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,64 +1,43 @@ | ||
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| <!-- README.md is generated from README.Rmd. Please edit that file --> | ||
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| # laims.analysis <img src='man/figures/logo.png' align="right" height="120" /> | ||
| # biorecur | ||
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| <!-- badges: start --> | ||
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| [](https://lifecycle.r-lib.org/articles/stages.html#experimental) | ||
| [](https://app.codecov.io/gh/UBESP-DCTV/laims.analysis?branch=master) | ||
| [](https://github.com/UBESP-DCTV/laims.analysis/actions/workflows/check-release.yaml) | ||
| [](https://github.com/UBESP-DCTV/laims.analysis/actions) | ||
| [](https://github.com/UBESP-DCTV/biorecur/actions/workflows/R-CMD-check.yaml) | ||
| [](https://github.com/UBESP-DCTV/biorecur/actions/workflows/R-CMD-check-dev.yaml) | ||
| [](https://github.com/UBESP-DCTV/biorecur/actions/workflows/test-coverage.yaml) | ||
| [](https://github.com/UBESP-DCTV/biorecur/actions/workflows/lint.yaml) | ||
| <!-- badges: end --> | ||
|
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| This project would represent the template for the analyses conducted | ||
| within the Laboratory of Artificial Intelligence from the Medical | ||
| Sciences (LAIMS) at the Unit of Biostatistics, Epidemiology, and Public | ||
| health (UBEP) within the Department of Cardiac, Thoracic, Vascular | ||
| Sciences, and Public Health (DSCTVPH) of the University of Padova | ||
| (UniPD). | ||
| The goal of `{biorecur}` is to implement marginalized mixed and SPARE | ||
| models on GWAS data. | ||
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| The aim is to provide a ready-to-use robust, reproducible infrastructure | ||
| for complex to quick analyses. | ||
| ## Installation | ||
|
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| When you create a new project based on this template, name it (i.e., | ||
| it’s folder) accordingly with your project’s name (possibly without | ||
| spaces). Next, you can open the `01-FIRST_RUN.R`script, and execute the | ||
| code and instructions within it. There, you will have the opportunity to | ||
| set the very first and basic pieces of information for your project, and | ||
| activate all its functionalities. After that, you can start to develop | ||
| your project, defining its `targets` (i.e., it’s main object outputs) in | ||
| the `_targets.R` file, which define the concept DAG of your project | ||
| tracking all it’s dependencies. | ||
| You can install the development version of `{biorecur}` from | ||
| [GitHub](https://github.com/) with: | ||
|
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||
| In the `dev/` folder, you will find also the `02-dev_cycle.R` and the | ||
| `03-run_cycle.R` helping you across the development and execution/update | ||
| of the project. | ||
| ``` r | ||
| # install.packages("devtools") | ||
| devtools::install_github("UBESP-DCTV/biorecur") | ||
| ``` | ||
|
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| ## Functionalities | ||
| ## Example | ||
|
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||
| - A dedicated packages’ **project-level library** powered by `{renv}` | ||
| - All the **documentation** for functions and the project itself powered | ||
| by `{roxygen2}` | ||
| - A **test-driven environment** powered by `{testthat}`, `{checkmate}`, | ||
| and `{covr}`. | ||
| - Systems for grammar and static code checking powered by `{spelling}` | ||
| and `{lintr}`, respectively | ||
| - Continuous Integration and Development is activated and powered by | ||
| GitHub actions, automating linters and checks execution, and coverage | ||
| assessment. | ||
| - A full environment enforcing reproducibility by the execution, caching | ||
| and invalidation of a structured project’s pipeline powered by | ||
| `{targets}` and `{tarchetypes}` in conjunction and synergy with | ||
| Rmarkdown scientifically flavored documents powered by `{distill}` | ||
| (with options for connections with Zotero as citation manager, linked | ||
| with local or remote libraries) | ||
| This is a basic example which shows you how to solve a common problem: | ||
|
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| ``` r | ||
| library(biorecur) | ||
| ## basic example code | ||
| ``` | ||
|
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| ## Code of Conduct | ||
|
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| Please note that the `laims.analysis` project is released with a | ||
| [Contributor Code of | ||
| Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). | ||
| Please note that the biorecur project is released with a [Contributor | ||
| Code of | ||
| Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). | ||
| By contributing to this project, you agree to abide by its terms. |
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| main: | ||
| store: C:/Users/corrado.lanera/Documents/GitHub/ubep/laims.analysis/_targets | ||
| store: C:/Users/Luca/Unit of Biostatistics Epidemiology and Public Health/LeSEXP | ||
| - biorecur/_targets |
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