├── .gitignore
├── CONTRIBUTING.md
├── README.Rmd
├── README.md
├── create-litr
└── index.Rmd
├── docs
├── 404.html
├── LICENSE-text.html
├── LICENSE.html
├── apple-touch-icon-120x120.png
├── apple-touch-icon-152x152.png
├── apple-touch-icon-180x180.png
├── apple-touch-icon-60x60.png
├── apple-touch-icon-76x76.png
├── apple-touch-icon.png
├── articles
│ ├── basic-example.html
│ ├── basic-example_files
│ │ └── figure-html
│ │ │ └── unnamed-chunk-5-1.png
│ ├── faqs.html
│ ├── index.html
│ ├── package-templates.html
│ ├── packages-in-the-wild.html
│ └── videos.html
├── authors.html
├── create
│ ├── 404.html
│ ├── adding-extras-to-an-r-package.html
│ ├── combining-.r-files.html
│ ├── document.html
│ ├── documenting-the-package-and-testing.html
│ ├── functionality-to-facilitate-workflow.html
│ ├── generating-package.html
│ ├── hash.html
│ ├── including-extras-for-litr.html
│ ├── including-templates.html
│ ├── index.html
│ ├── libs
│ │ ├── anchor-sections-1.1.0
│ │ │ ├── anchor-sections-hash.css
│ │ │ ├── anchor-sections.css
│ │ │ └── anchor-sections.js
│ │ ├── gitbook-2.6.7
│ │ │ ├── css
│ │ │ │ ├── fontawesome
│ │ │ │ │ └── fontawesome-webfont.ttf
│ │ │ │ ├── plugin-bookdown.css
│ │ │ │ ├── plugin-clipboard.css
│ │ │ │ ├── plugin-fontsettings.css
│ │ │ │ ├── plugin-highlight.css
│ │ │ │ ├── plugin-search.css
│ │ │ │ ├── plugin-table.css
│ │ │ │ └── style.css
│ │ │ └── js
│ │ │ │ ├── app.min.js
│ │ │ │ ├── clipboard.min.js
│ │ │ │ ├── jquery.highlight.js
│ │ │ │ ├── plugin-bookdown.js
│ │ │ │ ├── plugin-clipboard.js
│ │ │ │ ├── plugin-fontsettings.js
│ │ │ │ ├── plugin-search.js
│ │ │ │ └── plugin-sharing.js
│ │ └── jquery-3.6.0
│ │ │ └── jquery-3.6.0.min.js
│ ├── overview.html
│ ├── package-setup.html
│ ├── reference-keys.txt
│ ├── rendering.html
│ ├── search_index.json
│ └── tests.html
├── deps
│ ├── bootstrap-5.2.2
│ │ ├── bootstrap.bundle.min.js
│ │ ├── bootstrap.bundle.min.js.map
│ │ ├── bootstrap.min.css
│ │ ├── font.css
│ │ └── fonts
│ │ │ ├── 1Ptxg8zYS_SKggPN4iEgvnHyvveLxVs9pbCIPrc.woff
│ │ │ ├── 1Ptxg8zYS_SKggPN4iEgvnHyvveLxVvaorCIPrc.woff
│ │ │ ├── 1adeadb2fe618c5ed46221f15e12b9c8.woff
│ │ │ ├── 4iCs6KVjbNBYlgo6ew.woff
│ │ │ ├── 4iCs6KVjbNBYlgoKfw7w.woff
│ │ │ ├── 4iCv6KVjbNBYlgoCxCvTtA.woff
│ │ │ ├── 4iCv6KVjbNBYlgoCxCvjsGyL.woff
│ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7nsDQ.woff
│ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPa7j.woff
│ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3aPA.woff
│ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qOK7j.woff
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rAkw.woff
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vAkw.woff
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdo.woff
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zAkw.woff
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlxdo.woff
│ │ │ ├── CSR54z1Qlv-GDxkbKVQ_dFsvWNRevw.woff
│ │ │ ├── CSR54z1Qlv-GDxkbKVQ_dFsvaNA.woff
│ │ │ ├── CSR64z1Qlv-GDxkbKVQ_TOQ.woff
│ │ │ ├── CSR64z1Qlv-GDxkbKVQ_fOAKSw.woff
│ │ │ ├── HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DBKXhM0.woff
│ │ │ ├── HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DMyQhM0.woff
│ │ │ ├── HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTbI1rSg.woff
│ │ │ ├── HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTsoprSg.woff
│ │ │ ├── JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtZ6Ew9.woff
│ │ │ ├── JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtr6Ew9.woff
│ │ │ ├── JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCuM70w9.woff
│ │ │ ├── KFOlCnqEu92Fr1MmEU9fBBc-.woff
│ │ │ ├── KFOlCnqEu92Fr1MmEU9vAA.woff
│ │ │ ├── KFOlCnqEu92Fr1MmSU5fBBc-.woff
│ │ │ ├── KFOlCnqEu92Fr1MmSU5vAA.woff
│ │ │ ├── KFOlCnqEu92Fr1MmWUlfBBc-.woff
│ │ │ ├── KFOlCnqEu92Fr1MmWUlvAA.woff
│ │ │ ├── KFOmCnqEu92Fr1Me5g.woff
│ │ │ ├── KFOmCnqEu92Fr1Mu4mxM.woff
│ │ │ ├── QGYpz_kZZAGCONcK2A4bGOj8mNhL.woff
│ │ │ ├── S6u8w4BMUTPHjxsAXC-s.woff
│ │ │ ├── S6u8w4BMUTPHjxswWA.woff
│ │ │ ├── S6u9w4BMUTPHh6UVSwiPHw.woff
│ │ │ ├── S6u9w4BMUTPHh6UVeww.woff
│ │ │ ├── S6u9w4BMUTPHh7USSwiPHw.woff
│ │ │ ├── S6u9w4BMUTPHh7USeww.woff
│ │ │ ├── S6uyw4BMUTPHjx4wWA.woff
│ │ │ ├── S6uyw4BMUTPHvxo.woff
│ │ │ ├── UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuFuYMZs.woff
│ │ │ ├── UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuI6fMZs.woff
│ │ │ ├── UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuLyfMZs.woff
│ │ │ ├── XRXI3I6Li01BKofiOc5wtlZ2di8HDFwmRTA.woff
│ │ │ ├── XRXI3I6Li01BKofiOc5wtlZ2di8HDGUmRTA.woff
│ │ │ ├── XRXI3I6Li01BKofiOc5wtlZ2di8HDLshRTA.woff
│ │ │ ├── a98f7a7574819ba83bec6279a2cecd95.woff
│ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk0ZjaVQ.woff
│ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff
│ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff
│ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff
│ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff
│ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk_RkaVQ.woff
│ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkxhjaVQ.woff
│ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff
│ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff
│ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff
│ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff
│ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsgH1y4k.woff
│ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgshZ1y4k.woff
│ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff
│ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff
│ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff
│ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff
│ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjr0C4k.woff
│ │ │ └── q5uGsou0JOdh94bfvQlr.woff
│ ├── bootstrap-5.3.1
│ │ ├── bootstrap.bundle.min.js
│ │ ├── bootstrap.bundle.min.js.map
│ │ ├── bootstrap.min.css
│ │ ├── font.css
│ │ └── fonts
│ │ │ ├── 07d40e985ad7c747025dabb9f22142c4.woff2
│ │ │ ├── 1Ptug8zYS_SKggPNyC0ITw.woff2
│ │ │ ├── 1Ptug8zYS_SKggPNyCAIT5lu.woff2
│ │ │ ├── 1Ptug8zYS_SKggPNyCIIT5lu.woff2
│ │ │ ├── 1Ptug8zYS_SKggPNyCMIT5lu.woff2
│ │ │ ├── 1Ptug8zYS_SKggPNyCkIT5lu.woff2
│ │ │ ├── 1f5e011d6aae0d98fc0518e1a303e99a.woff2
│ │ │ ├── 4iCs6KVjbNBYlgoKcQ72j00.woff2
│ │ │ ├── 4iCs6KVjbNBYlgoKcg72j00.woff2
│ │ │ ├── 4iCs6KVjbNBYlgoKcw72j00.woff2
│ │ │ ├── 4iCs6KVjbNBYlgoKew72j00.woff2
│ │ │ ├── 4iCs6KVjbNBYlgoKfA72j00.woff2
│ │ │ ├── 4iCs6KVjbNBYlgoKfw72.woff2
│ │ │ ├── 4iCv6KVjbNBYlgoCxCvjs2yNL4U.woff2
│ │ │ ├── 4iCv6KVjbNBYlgoCxCvjsGyN.woff2
│ │ │ ├── 4iCv6KVjbNBYlgoCxCvjtGyNL4U.woff2
│ │ │ ├── 4iCv6KVjbNBYlgoCxCvjvGyNL4U.woff2
│ │ │ ├── 4iCv6KVjbNBYlgoCxCvjvWyNL4U.woff2
│ │ │ ├── 4iCv6KVjbNBYlgoCxCvjvmyNL4U.woff2
│ │ │ ├── 626330658504e338ee86aec8e957426b.woff2
│ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7jsDJT9g.woff2
│ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7ksDJT9g.woff2
│ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7nsDI.woff2
│ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7osDJT9g.woff2
│ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7psDJT9g.woff2
│ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7qsDJT9g.woff2
│ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7rsDJT9g.woff2
│ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qN67lqDY.woff2
│ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qNK7lqDY.woff2
│ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qNa7lqDY.woff2
│ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qNq7lqDY.woff2
│ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qO67lqDY.woff2
│ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qOK7l.woff2
│ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qPK7lqDY.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwkxduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwlBduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwlxdu.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmBduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmRduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmhduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmxduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwkxduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlBduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdu.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmBduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmRduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmhduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmxduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwkxduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlBduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlxdu.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmBduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmRduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmhduz8A.woff2
│ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmxduz8A.woff2
│ │ │ ├── CSR54z1Qlv-GDxkbKVQ_dFsvWNReuQ.woff2
│ │ │ ├── CSR54z1Qlv-GDxkbKVQ_dFsvWNpeudwk.woff2
│ │ │ ├── CSR64z1Qlv-GDxkbKVQ_fO4KTet_.woff2
│ │ │ ├── CSR64z1Qlv-GDxkbKVQ_fOAKTQ.woff2
│ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvQlMIXxw.woff2
│ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvUlMI.woff2
│ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvXlMIXxw.woff2
│ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvYlMIXxw.woff2
│ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvZlMIXxw.woff2
│ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvalMIXxw.woff2
│ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvblMIXxw.woff2
│ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlM-vWjMY.woff2
│ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlMOvWjMY.woff2
│ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlMevWjMY.woff2
│ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlMuvWjMY.woff2
│ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlOevWjMY.woff2
│ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlPevW.woff2
│ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlPuvWjMY.woff2
│ │ │ ├── JTUSjIg1_i6t8kCHKm459W1hyzbi.woff2
│ │ │ ├── JTUSjIg1_i6t8kCHKm459WRhyzbi.woff2
│ │ │ ├── JTUSjIg1_i6t8kCHKm459WZhyzbi.woff2
│ │ │ ├── JTUSjIg1_i6t8kCHKm459Wdhyzbi.woff2
│ │ │ ├── JTUSjIg1_i6t8kCHKm459Wlhyw.woff2
│ │ │ ├── QGYpz_kZZAGCONcK2A4bGOj8mNhN.woff2
│ │ │ ├── S6u8w4BMUTPHjxsAUi-qJCY.woff2
│ │ │ ├── S6u8w4BMUTPHjxsAXC-q.woff2
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│ │ │ ├── S6u9w4BMUTPHh6UVSwiPGQ.woff2
│ │ │ ├── S6u9w4BMUTPHh7USSwaPGR_p.woff2
│ │ │ ├── S6u9w4BMUTPHh7USSwiPGQ.woff2
│ │ │ ├── S6uyw4BMUTPHjx4wXg.woff2
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│ │ │ ├── c2f002b3a87d3f9bfeebb23d32cfd9f8.woff2
│ │ │ ├── ee91700cdbf7ce16c054c2bb8946c736.woff2
│ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqW106F15M.woff2
│ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWt06F15M.woff2
│ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtE6F15M.woff2
│ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtU6F15M.woff2
│ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtk6F15M.woff2
│ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWu06F15M.woff2
│ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuU6F.woff2
│ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuk6F15M.woff2
│ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWvU6F15M.woff2
│ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWxU6F15M.woff2
│ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS-muw.woff2
│ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS2mu1aB.woff2
│ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSCmu1aB.woff2
│ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSGmu1aB.woff2
│ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSKmu1aB.woff2
│ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSOmu1aB.woff2
│ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSumu1aB.woff2
│ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSymu1aB.woff2
│ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTUGmu1aB.woff2
│ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTVOmu1aB.woff2
│ │ │ ├── q5uGsou0JOdh94bfuQltOxU.woff2
│ │ │ └── q5uGsou0JOdh94bfvQlt.woff2
│ ├── bootstrap-toc-1.0.1
│ │ └── bootstrap-toc.min.js
│ ├── clipboard.js-2.0.11
│ │ └── clipboard.min.js
│ ├── data-deps.txt
│ ├── font-awesome-6.5.2
│ │ ├── css
│ │ │ ├── all.css
│ │ │ ├── all.min.css
│ │ │ ├── v4-shims.css
│ │ │ └── v4-shims.min.css
│ │ └── webfonts
│ │ │ ├── fa-brands-400.ttf
│ │ │ ├── fa-brands-400.woff2
│ │ │ ├── fa-regular-400.ttf
│ │ │ ├── fa-regular-400.woff2
│ │ │ ├── fa-solid-900.ttf
│ │ │ ├── fa-solid-900.woff2
│ │ │ ├── fa-v4compatibility.ttf
│ │ │ └── fa-v4compatibility.woff2
│ ├── headroom-0.11.0
│ │ ├── headroom.min.js
│ │ └── jQuery.headroom.min.js
│ ├── jquery-3.6.0
│ │ ├── jquery-3.6.0.js
│ │ ├── jquery-3.6.0.min.js
│ │ └── jquery-3.6.0.min.map
│ └── search-1.0.0
│ │ ├── autocomplete.jquery.min.js
│ │ ├── fuse.min.js
│ │ └── mark.min.js
├── favicon-16x16.png
├── favicon-32x32.png
├── favicon-96x96.png
├── favicon.ico
├── favicon.svg
├── index.html
├── katex-auto.js
├── lightswitch.js
├── link.svg
├── logo.png
├── pkgdown.js
├── pkgdown.yml
├── reference
│ ├── Rplot001.png
│ ├── add_chunk_label_hyperlinks.html
│ ├── add_function_hyperlinks.html
│ ├── add_hex_sticker.html
│ ├── add_pkgdown.html
│ ├── add_readme.html
│ ├── add_text_to_file.html
│ ├── add_vignettes.html
│ ├── check_unedited.html
│ ├── create_from_template.html
│ ├── description_litr_hash_field_name.html
│ ├── description_litr_version_field_name.html
│ ├── do_not_edit_message.html
│ ├── document.html
│ ├── draft.html
│ ├── draft_armadillo.html
│ ├── draft_bookdown.html
│ ├── draft_data.html
│ ├── draft_extras.html
│ ├── draft_rcpp.html
│ ├── figures
│ │ ├── diagram3.png
│ │ └── logo.png
│ ├── find_labels.html
│ ├── get_package_directory.html
│ ├── get_params_used.html
│ ├── hash_package_directory.html
│ ├── index.html
│ ├── insert_hrefs.html
│ ├── litr-package.html
│ ├── litr_gitbook.html
│ ├── litr_html_document.html
│ ├── litr_pdf_document.html
│ ├── litrify_output_format.html
│ ├── load_all.html
│ ├── make_noticeable.html
│ ├── read_hash_from_description.html
│ ├── remove_rstudio_extras.html
│ ├── render.html
│ ├── replace_ansi_sequences.html
│ ├── restore_knitr_objects.html
│ ├── send_to_package.html
│ ├── setup.html
│ ├── test_litr.html
│ ├── with_cleanup.html
│ ├── write_hash_to_description.html
│ └── write_version_to_description.html
├── search.json
├── site.webmanifest
├── sitemap.xml
├── web-app-manifest-192x192.png
└── web-app-manifest-512x512.png
├── examples
├── make-an-r-package-from-bookdown
│ ├── 1description.Rmd
│ ├── 2basics.Rmd
│ ├── 3more.Rmd
│ ├── 4end.Rmd
│ ├── _book
│ │ ├── 404.html
│ │ ├── conclude.html
│ │ ├── generalization-to-other-greetings.html
│ │ ├── index.html
│ │ ├── libs
│ │ │ ├── anchor-sections-1.1.0
│ │ │ │ ├── anchor-sections-hash.css
│ │ │ │ ├── anchor-sections.css
│ │ │ │ └── anchor-sections.js
│ │ │ ├── gitbook-2.6.7
│ │ │ │ ├── css
│ │ │ │ │ ├── fontawesome
│ │ │ │ │ │ └── fontawesome-webfont.ttf
│ │ │ │ │ ├── plugin-bookdown.css
│ │ │ │ │ ├── plugin-clipboard.css
│ │ │ │ │ ├── plugin-fontsettings.css
│ │ │ │ │ ├── plugin-highlight.css
│ │ │ │ │ ├── plugin-search.css
│ │ │ │ │ ├── plugin-table.css
│ │ │ │ │ └── style.css
│ │ │ │ └── js
│ │ │ │ │ ├── app.min.js
│ │ │ │ │ ├── clipboard.min.js
│ │ │ │ │ ├── jquery.highlight.js
│ │ │ │ │ ├── plugin-bookdown.js
│ │ │ │ │ ├── plugin-clipboard.js
│ │ │ │ │ ├── plugin-fontsettings.js
│ │ │ │ │ ├── plugin-search.js
│ │ │ │ │ └── plugin-sharing.js
│ │ │ └── jquery-3.6.0
│ │ │ │ └── jquery-3.6.0.min.js
│ │ ├── package-setup.html
│ │ ├── reference-keys.txt
│ │ ├── search_index.json
│ │ └── the-basics-of-saying-hello.html
│ ├── frombookdown
│ │ ├── .Rbuildignore
│ │ ├── DESCRIPTION
│ │ ├── LICENSE
│ │ ├── LICENSE.md
│ │ ├── NAMESPACE
│ │ ├── R
│ │ │ ├── frombookdown-package.R
│ │ │ └── say_hello.R
│ │ ├── man
│ │ │ ├── frombookdown-package.Rd
│ │ │ └── say_hello.Rd
│ │ └── tests
│ │ │ ├── testthat.R
│ │ │ └── testthat
│ │ │ └── tests.R
│ └── index.Rmd
├── make-an-r-package-with-armadillo
│ ├── create-witharmadillo.Rmd
│ ├── create-witharmadillo.html
│ └── witharmadillo
│ │ ├── .Rbuildignore
│ │ ├── DESCRIPTION
│ │ ├── LICENSE
│ │ ├── LICENSE.md
│ │ ├── NAMESPACE
│ │ ├── R
│ │ ├── RcppExports.R
│ │ └── witharmadillo-package.R
│ │ ├── man
│ │ ├── my_chol.Rd
│ │ └── witharmadillo-package.Rd
│ │ ├── src
│ │ ├── .gitignore
│ │ ├── Makevars
│ │ ├── Makevars.win
│ │ ├── RcppExports.cpp
│ │ └── code.cpp
│ │ └── tests
│ │ ├── testthat.R
│ │ └── testthat
│ │ └── tests.R
├── make-an-r-package-with-data
│ ├── create-rhasdata.Rmd
│ ├── create-rhasdata.html
│ └── rhasdata
│ │ ├── .Rbuildignore
│ │ ├── DESCRIPTION
│ │ ├── LICENSE
│ │ ├── LICENSE.md
│ │ ├── NAMESPACE
│ │ ├── R
│ │ └── mydata.R
│ │ ├── data
│ │ └── mydata.rda
│ │ └── man
│ │ └── mydata.Rd
├── make-an-r-package-with-extras
│ ├── create-withpkgdown.Rmd
│ ├── create-withpkgdown.html
│ ├── docs
│ │ ├── 404.html
│ │ ├── LICENSE-text.html
│ │ ├── LICENSE.html
│ │ ├── apple-touch-icon.png
│ │ ├── articles
│ │ │ ├── index.html
│ │ │ └── using-package.html
│ │ ├── authors.html
│ │ ├── deps
│ │ │ ├── bootstrap-5.3.1
│ │ │ │ ├── bootstrap.bundle.min.js
│ │ │ │ ├── bootstrap.bundle.min.js.map
│ │ │ │ └── bootstrap.min.css
│ │ │ ├── bootstrap-toc-1.0.1
│ │ │ │ └── bootstrap-toc.min.js
│ │ │ ├── clipboard.js-2.0.11
│ │ │ │ └── clipboard.min.js
│ │ │ ├── data-deps.txt
│ │ │ ├── font-awesome-6.5.2
│ │ │ │ ├── css
│ │ │ │ │ ├── all.css
│ │ │ │ │ ├── all.min.css
│ │ │ │ │ ├── v4-shims.css
│ │ │ │ │ └── v4-shims.min.css
│ │ │ │ └── webfonts
│ │ │ │ │ ├── fa-brands-400.ttf
│ │ │ │ │ ├── fa-brands-400.woff2
│ │ │ │ │ ├── fa-regular-400.ttf
│ │ │ │ │ ├── fa-regular-400.woff2
│ │ │ │ │ ├── fa-solid-900.ttf
│ │ │ │ │ ├── fa-solid-900.woff2
│ │ │ │ │ ├── fa-v4compatibility.ttf
│ │ │ │ │ └── fa-v4compatibility.woff2
│ │ │ ├── headroom-0.11.0
│ │ │ │ ├── headroom.min.js
│ │ │ │ └── jQuery.headroom.min.js
│ │ │ ├── jquery-3.6.0
│ │ │ │ ├── jquery-3.6.0.js
│ │ │ │ ├── jquery-3.6.0.min.js
│ │ │ │ └── jquery-3.6.0.min.map
│ │ │ └── search-1.0.0
│ │ │ │ ├── autocomplete.jquery.min.js
│ │ │ │ ├── fuse.min.js
│ │ │ │ └── mark.min.js
│ │ ├── favicon-96x96.png
│ │ ├── favicon.ico
│ │ ├── favicon.svg
│ │ ├── index.html
│ │ ├── katex-auto.js
│ │ ├── lightswitch.js
│ │ ├── link.svg
│ │ ├── logo.png
│ │ ├── pkgdown.js
│ │ ├── pkgdown.yml
│ │ ├── reference
│ │ │ ├── figures
│ │ │ │ └── logo.png
│ │ │ ├── index.html
│ │ │ ├── say_hello.html
│ │ │ └── say_hi.html
│ │ ├── search.json
│ │ ├── site.webmanifest
│ │ ├── sitemap.xml
│ │ ├── web-app-manifest-192x192.png
│ │ └── web-app-manifest-512x512.png
│ ├── source-files
│ │ ├── README.Rmd
│ │ ├── _pkgdown.yml
│ │ ├── litr-hex.png
│ │ └── using-package.Rmd
│ └── withpkgdown
│ │ ├── .Rbuildignore
│ │ ├── DESCRIPTION
│ │ ├── LICENSE
│ │ ├── LICENSE.md
│ │ ├── NAMESPACE
│ │ ├── R
│ │ └── say_hello.R
│ │ ├── README.Rmd
│ │ ├── README.md
│ │ ├── _pkgdown.yml
│ │ ├── man
│ │ ├── figures
│ │ │ └── logo.png
│ │ ├── say_hello.Rd
│ │ └── say_hi.Rd
│ │ ├── pkgdown
│ │ └── favicon
│ │ │ ├── apple-touch-icon.png
│ │ │ ├── favicon-96x96.png
│ │ │ ├── favicon.ico
│ │ │ ├── favicon.svg
│ │ │ ├── site.webmanifest
│ │ │ ├── web-app-manifest-192x192.png
│ │ │ └── web-app-manifest-512x512.png
│ │ └── vignettes
│ │ └── using-package.Rmd
├── make-an-r-package-with-rcpp
│ ├── create-withrcpp.Rmd
│ ├── create-withrcpp.html
│ └── withrcpp
│ │ ├── .Rbuildignore
│ │ ├── DESCRIPTION
│ │ ├── LICENSE
│ │ ├── LICENSE.md
│ │ ├── NAMESPACE
│ │ ├── R
│ │ ├── RcppExports.R
│ │ └── withrcpp-package.R
│ │ ├── man
│ │ ├── alternate_signs.Rd
│ │ └── withrcpp-package.Rd
│ │ ├── src
│ │ ├── .gitignore
│ │ ├── RcppExports.cpp
│ │ └── code.cpp
│ │ └── tests
│ │ ├── testthat.R
│ │ └── testthat
│ │ └── tests.R
└── make-an-r-package
│ ├── create-rhello.Rmd
│ ├── create-rhello.html
│ └── rhello
│ ├── .Rbuildignore
│ ├── DESCRIPTION
│ ├── LICENSE
│ ├── LICENSE.md
│ ├── NAMESPACE
│ ├── R
│ └── say_hello.R
│ ├── man
│ └── say_hello.Rd
│ └── tests
│ ├── testthat.R
│ └── testthat
│ └── tests.R
├── litr-project.Rproj
├── litr
├── .Rbuildignore
├── DESCRIPTION
├── LICENSE
├── LICENSE.md
├── NAMESPACE
├── R
│ ├── draft.R
│ ├── extras.R
│ ├── hash.R
│ ├── litr-package.R
│ ├── render.R
│ ├── setup.R
│ └── test_litr.R
├── README.Rmd
├── README.md
├── _pkgdown.yml
├── inst
│ └── rmarkdown
│ │ └── templates
│ │ ├── make-an-r-package-from-bookdown
│ │ ├── skeleton
│ │ │ ├── 1description.Rmd
│ │ │ ├── 2basics.Rmd
│ │ │ ├── 3more.Rmd
│ │ │ ├── 4end.Rmd
│ │ │ ├── index.Rmd
│ │ │ └── skeleton.Rmd
│ │ └── template.yaml
│ │ ├── make-an-r-package-with-armadillo
│ │ ├── skeleton
│ │ │ └── skeleton.Rmd
│ │ └── template.yaml
│ │ ├── make-an-r-package-with-data
│ │ ├── skeleton
│ │ │ └── skeleton.Rmd
│ │ └── template.yaml
│ │ ├── make-an-r-package-with-extras
│ │ ├── skeleton
│ │ │ ├── skeleton.Rmd
│ │ │ └── source-files
│ │ │ │ ├── README.Rmd
│ │ │ │ ├── _pkgdown.yml
│ │ │ │ ├── litr-hex.png
│ │ │ │ └── using-package.Rmd
│ │ └── template.yaml
│ │ ├── make-an-r-package-with-rcpp
│ │ ├── skeleton
│ │ │ └── skeleton.Rmd
│ │ └── template.yaml
│ │ └── make-an-r-package
│ │ ├── skeleton
│ │ └── skeleton.Rmd
│ │ └── template.yaml
├── man
│ ├── add_chunk_label_hyperlinks.Rd
│ ├── add_function_hyperlinks.Rd
│ ├── add_hex_sticker.Rd
│ ├── add_pkgdown.Rd
│ ├── add_readme.Rd
│ ├── add_text_to_file.Rd
│ ├── add_vignettes.Rd
│ ├── check_unedited.Rd
│ ├── create_from_template.Rd
│ ├── description_litr_hash_field_name.Rd
│ ├── description_litr_version_field_name.Rd
│ ├── do_not_edit_message.Rd
│ ├── document.Rd
│ ├── draft.Rd
│ ├── draft_armadillo.Rd
│ ├── draft_bookdown.Rd
│ ├── draft_data.Rd
│ ├── draft_extras.Rd
│ ├── draft_rcpp.Rd
│ ├── figures
│ │ ├── diagram3.png
│ │ └── logo.png
│ ├── find_labels.Rd
│ ├── get_package_directory.Rd
│ ├── get_params_used.Rd
│ ├── hash_package_directory.Rd
│ ├── insert_hrefs.Rd
│ ├── litr-package.Rd
│ ├── litr_gitbook.Rd
│ ├── litr_html_document.Rd
│ ├── litr_pdf_document.Rd
│ ├── litrify_output_format.Rd
│ ├── load_all.Rd
│ ├── make_noticeable.Rd
│ ├── read_hash_from_description.Rd
│ ├── remove_rstudio_extras.Rd
│ ├── render.Rd
│ ├── replace_ansi_sequences.Rd
│ ├── restore_knitr_objects.Rd
│ ├── send_to_package.Rd
│ ├── setup.Rd
│ ├── test_litr.Rd
│ ├── with_cleanup.Rd
│ ├── write_hash_to_description.Rd
│ └── write_version_to_description.Rd
├── pkgdown
│ └── favicon
│ │ ├── apple-touch-icon.png
│ │ ├── favicon-96x96.png
│ │ ├── favicon.ico
│ │ ├── favicon.svg
│ │ ├── site.webmanifest
│ │ ├── web-app-manifest-192x192.png
│ │ └── web-app-manifest-512x512.png
├── tests
│ ├── testthat.R
│ └── testthat
│ │ ├── create-pkg.Rmd
│ │ ├── create-rknuth.Rmd
│ │ └── tests.R
└── vignettes
│ ├── basic-example.Rmd
│ ├── faqs.Rmd
│ ├── package-templates.Rmd
│ ├── packages-in-the-wild.Rmd
│ └── videos.Rmd
└── source-files
├── README.Rmd
├── _pkgdown.yml
├── basic-example.Rmd
├── diagram3.png
├── faqs.Rmd
├── litr-hex.png
├── make-an-r-package-from-bookdown
├── 1description.Rmd
├── 2basics.Rmd
├── 3more.Rmd
├── 4end.Rmd
├── index.Rmd
└── skeleton.Rmd
├── make-an-r-package-with-armadillo
└── skeleton.Rmd
├── make-an-r-package-with-data
└── skeleton.Rmd
├── make-an-r-package-with-extras
├── skeleton.Rmd
└── source-files
│ ├── README.Rmd
│ ├── _pkgdown.yml
│ ├── litr-hex.png
│ └── using-package.Rmd
├── make-an-r-package-with-rcpp
└── skeleton.Rmd
├── make-an-r-package
└── skeleton.Rmd
├── package-templates.Rmd
├── packages-in-the-wild.Rmd
├── test-example-files
├── create-pkg.Rmd
└── create-rknuth.Rmd
└── videos.Rmd
/.gitignore:
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1 | .Rproj.user
2 | .Rhistory
3 | .RData
4 | .Ruserdata
5 | .DS_Store
6 |
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/CONTRIBUTING.md:
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1 | # Contributing to `litr`
2 |
3 | ## Debugging process
4 |
5 | Debugging issues with code run in `knitr` hooks can be tricky. We suggest the following workflow:
6 |
7 | 1. Temporarily modify the litr package (directly in a .R file, adding a browser call in the hook).
8 | 2. Then install that version of litr with `devtools::install('litr', dependencies=False)` assuming you're at the root of the project directory. Using `dependencies=False` helps ensure you're not prompted about updating packages each time you install the package.
9 | 3. Once you're installed this modified version of litr and have restarted your R session, then call `litr::render()` on the file you are working on with `fresh_session=FALSE` to make sure the debugger hits the breakpoint as desired.
10 |
11 | Repeat this process until you (hopefully) find a fix for the issue.
12 |
13 | ## Github API Rate Limiting
14 |
15 | Knitting `create-litr/index.Rmd` makes quite a few calls to the GitHub API and it is easy to quickly reach the GitHub rate limit knitting `index.Rmd` repeatedly in a short period of time. To increase your GitHub API rate limit
16 | - Use `usethis::create_github_token()` to create a Personal Access Token.
17 | - Use `usethis::edit_r_environ()` and add the token as `GITHUB_PAT`.
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/docs/create/libs/anchor-sections-1.1.0/anchor-sections-hash.css:
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1 | /* Styles for section anchors */
2 | a.anchor-section::before {content: '#';font-size: 80%;}
3 |
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1 | /* Styles for section anchors */
2 | a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
3 | .hasAnchor:hover a.anchor-section {visibility: visible;}
4 | ul > li > .anchor-section {display: none;}
5 |
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1 | document.addEventListener('DOMContentLoaded', function () {
2 | // If section divs is used, we need to put the anchor in the child header
3 | const headers = document.querySelectorAll("div.hasAnchor.section[class*='level'] > :first-child")
4 |
5 | headers.forEach(function (x) {
6 | // Add to the header node
7 | if (!x.classList.contains('hasAnchor')) x.classList.add('hasAnchor')
8 | // Remove from the section or div created by Pandoc
9 | x.parentElement.classList.remove('hasAnchor')
10 | })
11 | })
12 |
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1 | div.sourceCode {
2 | position: relative;
3 | }
4 |
5 | .copy-to-clipboard-button {
6 | position: absolute;
7 | right: 0;
8 | top: 0;
9 | visibility: hidden;
10 | }
11 |
12 | .copy-to-clipboard-button:focus {
13 | outline: 0;
14 | }
15 |
16 | div.sourceCode:hover > .copy-to-clipboard-button {
17 | visibility: visible;
18 | }
19 |
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/docs/create/libs/gitbook-2.6.7/css/plugin-search.css:
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1 | .book .book-summary .book-search {
2 | padding: 6px;
3 | background: transparent;
4 | position: absolute;
5 | top: -50px;
6 | left: 0px;
7 | right: 0px;
8 | transition: top 0.5s ease;
9 | }
10 | .book .book-summary .book-search input,
11 | .book .book-summary .book-search input:focus,
12 | .book .book-summary .book-search input:hover {
13 | width: 100%;
14 | background: transparent;
15 | border: 1px solid #ccc;
16 | box-shadow: none;
17 | outline: none;
18 | line-height: 22px;
19 | padding: 7px 4px;
20 | color: inherit;
21 | box-sizing: border-box;
22 | }
23 | .book.with-search .book-summary .book-search {
24 | top: 0px;
25 | }
26 | .book.with-search .book-summary ul.summary {
27 | top: 50px;
28 | }
29 | .with-search .summary li[data-level] a[href*=".html#"] {
30 | display: none;
31 | }
32 |
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/docs/create/libs/gitbook-2.6.7/css/plugin-table.css:
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1 | .book .book-body .page-wrapper .page-inner section.normal table{display:table;width:100%;border-collapse:collapse;border-spacing:0;overflow:auto}.book .book-body .page-wrapper .page-inner section.normal table td,.book .book-body .page-wrapper .page-inner section.normal table th{padding:6px 13px;border:1px solid #ddd}.book .book-body .page-wrapper .page-inner section.normal table tr{background-color:#fff;border-top:1px solid #ccc}.book .book-body .page-wrapper .page-inner section.normal table tr:nth-child(2n){background-color:#f8f8f8}.book .book-body .page-wrapper .page-inner section.normal table th{font-weight:700}
2 |
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/docs/create/libs/gitbook-2.6.7/js/plugin-clipboard.js:
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1 | gitbook.require(["gitbook", "jQuery"], function(gitbook, $) {
2 |
3 | var copyButton = '';
4 | var clipboard;
5 |
6 | gitbook.events.bind("page.change", function() {
7 |
8 | if (!ClipboardJS.isSupported()) return;
9 |
10 | // the page.change event is thrown twice: before and after the page changes
11 | if (clipboard) {
12 | // clipboard is already defined but we are on the same page
13 | if (clipboard._prevPage === window.location.pathname) return;
14 | // clipboard is already defined and url path change
15 | // we can deduct that we are before page changes
16 | clipboard.destroy(); // destroy the previous events listeners
17 | clipboard = undefined; // reset the clipboard object
18 | return;
19 | }
20 |
21 | $(copyButton).prependTo("div.sourceCode");
22 |
23 | clipboard = new ClipboardJS(".copy-to-clipboard-button", {
24 | text: function(trigger) {
25 | return trigger.parentNode.textContent;
26 | }
27 | });
28 |
29 | clipboard._prevPage = window.location.pathname
30 |
31 | });
32 |
33 | });
34 |
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/docs/create/reference-keys.txt:
--------------------------------------------------------------------------------
1 | preamble
2 | overview
3 | package-setup
4 | a-note-on-circularity
5 | generating-package
6 | sending-code-chunks-to-the-package
7 | setting-up-the-r-package-creation
8 | hash
9 | document
10 | rendering
11 | output-format
12 | pdf-output-format
13 | html-output-format
14 | bookdown-output-format
15 | render
16 | functionality-to-facilitate-workflow
17 | load-all
18 | templates
19 | including-template-files-in-package
20 | draft-functions-for-working-from-template
21 | adding-extras-to-an-r-package
22 | adding-a-readme
23 | adding-a-hex-sticker
24 | adding-vignettes
25 | add-a-pkgdown-site
26 | tests
27 | test-check-unedited
28 | testing-get_params_used
29 | testing-chunk-referencing
30 | testing-different-ways-of-rendering
31 | testing-other-templates
32 | documenting-the-package-and-testing
33 | add-examples-folder-with-the-output-of-knitting-each-example
34 | including-extras-for-litr
35 | readme-with-hex-sticker
36 | vignettes
37 | a-pkgdown-site
38 |
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/docs/deps/bootstrap-5.2.2/font.css:
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1 | @font-face {
2 | font-family: 'Source Sans Pro';
3 | font-style: normal;
4 | font-weight: 300;
5 | font-display: swap;
6 | src: url(fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zAkw.woff) format('woff');
7 | }
8 | @font-face {
9 | font-family: 'Source Sans Pro';
10 | font-style: normal;
11 | font-weight: 400;
12 | font-display: swap;
13 | src: url(fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3aPA.woff) format('woff');
14 | }
15 | @font-face {
16 | font-family: 'Source Sans Pro';
17 | font-style: normal;
18 | font-weight: 700;
19 | font-display: swap;
20 | src: url(fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vAkw.woff) format('woff');
21 | }
22 |
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1 | /*!
2 | * headroom.js v0.9.4 - Give your page some headroom. Hide your header until you need it
3 | * Copyright (c) 2017 Nick Williams - http://wicky.nillia.ms/headroom.js
4 | * License: MIT
5 | */
6 |
7 | !function(a){a&&(a.fn.headroom=function(b){return this.each(function(){var c=a(this),d=c.data("headroom"),e="object"==typeof b&&b;e=a.extend(!0,{},Headroom.options,e),d||(d=new Headroom(this,e),d.init(),c.data("headroom",d)),"string"==typeof b&&(d[b](),"destroy"===b&&c.removeData("headroom"))})},a("[data-headroom]").each(function(){var b=a(this);b.headroom(b.data())}))}(window.Zepto||window.jQuery);
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2 | document.addEventListener("DOMContentLoaded", function () {
3 | var mathElements = document.getElementsByClassName("math");
4 | var macros = [];
5 | for (var i = 0; i < mathElements.length; i++) {
6 | var texText = mathElements[i].firstChild;
7 | if (mathElements[i].tagName == "SPAN") {
8 | katex.render(texText.data, mathElements[i], {
9 | displayMode: mathElements[i].classList.contains("display"),
10 | throwOnError: false,
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1 | pandoc: '3.2'
2 | pkgdown: 2.1.2
3 | pkgdown_sha: ~
4 | articles:
5 | basic-example: basic-example.html
6 | faqs: faqs.html
7 | package-templates: package-templates.html
8 | packages-in-the-wild: packages-in-the-wild.html
9 | videos: videos.html
10 | last_built: 2025-05-23T15:47Z
11 |
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3 | "short_name": "",
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7 | "sizes": "192x192",
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10 | },
11 | {
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1 | # Package setup
2 |
3 | Every R package needs a DESCRIPTION file, so we start by specifying this information:
4 |
5 | ```{r package-setup, message=FALSE, results='hide'}
6 | usethis::create_package(
7 | path = ".",
8 | fields = list(
9 | Package = params$package_name,
10 | Version = "0.0.0.9000",
11 | Title = "A Package Defined in a Bookdown",
12 | Description = "This package uses litr to define an R package through writing a bookdown.",
13 | `Authors@R` = person(
14 | given = "First",
15 | family = "Last",
16 | email = "you@gmail.com",
17 | role = c("aut", "cre")
18 | )
19 | )
20 | )
21 | usethis::use_mit_license(copyright_holder = "F. Last")
22 | ```
23 |
24 | Although it's not required, it can be nice to add some package-level documentation. This is what will show up when someone types `package?` in the console.
25 |
26 | ```{package_doc}
27 | #' A Package Defined in a Bookdown
28 | #'
29 | #' This package uses `litr` to define an R package through writing a `bookdown`.
30 | #'
31 | #' @docType package
32 | ```
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/examples/make-an-r-package-from-bookdown/2basics.Rmd:
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1 | # The basics of saying hello
2 |
3 | Let's define a function for our R package:
4 |
5 | ```{r}
6 | #' Say hello to someone
7 | #'
8 | #' @param name Name of a person
9 | #' @param exclamation Whether to include an exclamation mark
10 | #' @export
11 | say_hello <- function(name, exclamation = TRUE) {
12 | paste0("Hello ", name, ifelse(exclamation, "!", "."))
13 | }
14 | ```
15 |
16 | Code chunks whose first line starts with `#'` are added to the package.
17 |
18 | We can try running it.
19 |
20 | ```{r}
21 | say_hello("Jacob")
22 | ```
23 |
24 | That code chunk does not start with `#'`, so it is not added to the package.
25 |
26 | Let's write some tests to make sure the function behaves as desired:
27 |
28 | ```{r}
29 | testthat::test_that("say_hello works", {
30 | testthat::expect_equal(say_hello("Jacob"), "Hello Jacob!")
31 | testthat::expect_equal(say_hello("Jacob", exclamation = FALSE), "Hello Jacob.")
32 | })
33 | ```
34 |
35 | Code chunks that have one or more lines starting with `test_that(` (or `testthat::test_that(`) are added to the package as tests.
36 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/3more.Rmd:
--------------------------------------------------------------------------------
1 | # Generalization to other greetings
2 |
3 | We can now get fancier and define more functions across as many .Rmd files as we like. Hyperlinks work across different .Rmd files. For example, you can click on `say_hello()` and it will bring you to the definition in the previous chapter.
4 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/4end.Rmd:
--------------------------------------------------------------------------------
1 | # Conclusion {#conclude}
2 |
3 | When you are done defining the package, it remains to convert the Roxygen to documentation.
4 |
5 | ```{r}
6 | litr::document() # <-- use instead of devtools::document()
7 | ```
8 |
9 | You can also add some extra things to your package here if you like, such as a README, some vignettes, a [pkgdown](https://pkgdown.r-lib.org/) site, etc. See [here](https://github.com/jacobbien/litr-project/tree/main/examples/make-an-r-package-with-extras) for an example of how to do this with `litr`.
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/_book/libs/anchor-sections-1.1.0/anchor-sections-hash.css:
--------------------------------------------------------------------------------
1 | /* Styles for section anchors */
2 | a.anchor-section::before {content: '#';font-size: 80%;}
3 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/_book/libs/anchor-sections-1.1.0/anchor-sections.css:
--------------------------------------------------------------------------------
1 | /* Styles for section anchors */
2 | a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
3 | .hasAnchor:hover a.anchor-section {visibility: visible;}
4 | ul > li > .anchor-section {display: none;}
5 |
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/examples/make-an-r-package-from-bookdown/_book/libs/anchor-sections-1.1.0/anchor-sections.js:
--------------------------------------------------------------------------------
1 | document.addEventListener('DOMContentLoaded', function () {
2 | // If section divs is used, we need to put the anchor in the child header
3 | const headers = document.querySelectorAll("div.hasAnchor.section[class*='level'] > :first-child")
4 |
5 | headers.forEach(function (x) {
6 | // Add to the header node
7 | if (!x.classList.contains('hasAnchor')) x.classList.add('hasAnchor')
8 | // Remove from the section or div created by Pandoc
9 | x.parentElement.classList.remove('hasAnchor')
10 | })
11 | })
12 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/_book/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/jacobbien/litr-project/2dbd65959376a6318fd96342a14a60ca59a1e6a3/examples/make-an-r-package-from-bookdown/_book/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/_book/libs/gitbook-2.6.7/css/plugin-clipboard.css:
--------------------------------------------------------------------------------
1 | div.sourceCode {
2 | position: relative;
3 | }
4 |
5 | .copy-to-clipboard-button {
6 | position: absolute;
7 | right: 0;
8 | top: 0;
9 | visibility: hidden;
10 | }
11 |
12 | .copy-to-clipboard-button:focus {
13 | outline: 0;
14 | }
15 |
16 | div.sourceCode:hover > .copy-to-clipboard-button {
17 | visibility: visible;
18 | }
19 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/_book/libs/gitbook-2.6.7/css/plugin-search.css:
--------------------------------------------------------------------------------
1 | .book .book-summary .book-search {
2 | padding: 6px;
3 | background: transparent;
4 | position: absolute;
5 | top: -50px;
6 | left: 0px;
7 | right: 0px;
8 | transition: top 0.5s ease;
9 | }
10 | .book .book-summary .book-search input,
11 | .book .book-summary .book-search input:focus,
12 | .book .book-summary .book-search input:hover {
13 | width: 100%;
14 | background: transparent;
15 | border: 1px solid #ccc;
16 | box-shadow: none;
17 | outline: none;
18 | line-height: 22px;
19 | padding: 7px 4px;
20 | color: inherit;
21 | box-sizing: border-box;
22 | }
23 | .book.with-search .book-summary .book-search {
24 | top: 0px;
25 | }
26 | .book.with-search .book-summary ul.summary {
27 | top: 50px;
28 | }
29 | .with-search .summary li[data-level] a[href*=".html#"] {
30 | display: none;
31 | }
32 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/_book/libs/gitbook-2.6.7/css/plugin-table.css:
--------------------------------------------------------------------------------
1 | .book .book-body .page-wrapper .page-inner section.normal table{display:table;width:100%;border-collapse:collapse;border-spacing:0;overflow:auto}.book .book-body .page-wrapper .page-inner section.normal table td,.book .book-body .page-wrapper .page-inner section.normal table th{padding:6px 13px;border:1px solid #ddd}.book .book-body .page-wrapper .page-inner section.normal table tr{background-color:#fff;border-top:1px solid #ccc}.book .book-body .page-wrapper .page-inner section.normal table tr:nth-child(2n){background-color:#f8f8f8}.book .book-body .page-wrapper .page-inner section.normal table th{font-weight:700}
2 |
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/examples/make-an-r-package-from-bookdown/_book/libs/gitbook-2.6.7/js/plugin-clipboard.js:
--------------------------------------------------------------------------------
1 | gitbook.require(["gitbook", "jQuery"], function(gitbook, $) {
2 |
3 | var copyButton = '';
4 | var clipboard;
5 |
6 | gitbook.events.bind("page.change", function() {
7 |
8 | if (!ClipboardJS.isSupported()) return;
9 |
10 | // the page.change event is thrown twice: before and after the page changes
11 | if (clipboard) {
12 | // clipboard is already defined but we are on the same page
13 | if (clipboard._prevPage === window.location.pathname) return;
14 | // clipboard is already defined and url path change
15 | // we can deduct that we are before page changes
16 | clipboard.destroy(); // destroy the previous events listeners
17 | clipboard = undefined; // reset the clipboard object
18 | return;
19 | }
20 |
21 | $(copyButton).prependTo("div.sourceCode");
22 |
23 | clipboard = new ClipboardJS(".copy-to-clipboard-button", {
24 | text: function(trigger) {
25 | return trigger.parentNode.textContent;
26 | }
27 | });
28 |
29 | clipboard._prevPage = window.location.pathname
30 |
31 | });
32 |
33 | });
34 |
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/examples/make-an-r-package-from-bookdown/_book/reference-keys.txt:
--------------------------------------------------------------------------------
1 | introduction
2 | package-setup
3 | the-basics-of-saying-hello
4 | generalization-to-other-greetings
5 | conclude
6 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/frombookdown/.Rbuildignore:
--------------------------------------------------------------------------------
1 | ^LICENSE\.md$
2 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/frombookdown/DESCRIPTION:
--------------------------------------------------------------------------------
1 | Package: frombookdown
2 | Title: A Package Defined in a Bookdown
3 | Version: 0.0.0.9000
4 | Authors@R:
5 | person("First", "Last", , "you@gmail.com", role = c("aut", "cre"))
6 | Description: This package uses litr to define an R package through writing
7 | a bookdown.
8 | License: MIT + file LICENSE
9 | Encoding: UTF-8
10 | Roxygen: list(markdown = TRUE)
11 | RoxygenNote: 7.3.2
12 | Suggests:
13 | testthat (>= 3.0.0)
14 | Config/testthat/edition: 3
15 | LitrVersionUsed: 0.9.3
16 | LitrId: 045a8c3c8552188e0f9fa30cdd298363
17 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/frombookdown/LICENSE:
--------------------------------------------------------------------------------
1 | YEAR: 2025
2 | COPYRIGHT HOLDER: F. Last
3 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/frombookdown/LICENSE.md:
--------------------------------------------------------------------------------
1 | # MIT License
2 |
3 | Copyright (c) 2025 F. Last
4 |
5 | Permission is hereby granted, free of charge, to any person obtaining a copy
6 | of this software and associated documentation files (the "Software"), to deal
7 | in the Software without restriction, including without limitation the rights
8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 |
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 |
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/frombookdown/NAMESPACE:
--------------------------------------------------------------------------------
1 | # Generated by roxygen2: do not edit by hand
2 |
3 | export(say_hello)
4 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/frombookdown/R/frombookdown-package.R:
--------------------------------------------------------------------------------
1 | #' A Package Defined in a Bookdown
2 | #'
3 | #' This package uses `litr` to define an R package through writing a `bookdown`.
4 | #'
5 | #' @docType package
6 | #' @keywords internal
7 | "_PACKAGE"
8 |
9 | ## usethis namespace: start
10 | ## usethis namespace: end
11 | NULL
12 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/frombookdown/R/say_hello.R:
--------------------------------------------------------------------------------
1 | # Generated from _main.Rmd: do not edit by hand
2 |
3 | #' Say hello to someone
4 | #'
5 | #' @param name Name of a person
6 | #' @param exclamation Whether to include an exclamation mark
7 | #' @export
8 | say_hello <- function(name, exclamation = TRUE) {
9 | paste0("Hello ", name, ifelse(exclamation, "!", "."))
10 | }
11 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/frombookdown/man/frombookdown-package.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \docType{package}
4 | \name{frombookdown-package}
5 | \alias{frombookdown}
6 | \alias{frombookdown-package}
7 | \title{A Package Defined in a Bookdown}
8 | \description{
9 | This package uses \code{litr} to define an R package through writing a \code{bookdown}.
10 | }
11 | \author{
12 | \strong{Maintainer}: First Last \email{you@gmail.com}
13 |
14 | }
15 | \keyword{internal}
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/frombookdown/man/say_hello.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{say_hello}
4 | \alias{say_hello}
5 | \title{Say hello to someone}
6 | \usage{
7 | say_hello(name, exclamation = TRUE)
8 | }
9 | \arguments{
10 | \item{name}{Name of a person}
11 |
12 | \item{exclamation}{Whether to include an exclamation mark}
13 | }
14 | \description{
15 | Say hello to someone
16 | }
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/frombookdown/tests/testthat.R:
--------------------------------------------------------------------------------
1 | # This file is part of the standard setup for testthat.
2 | # It is recommended that you do not modify it.
3 | #
4 | # Where should you do additional test configuration?
5 | # Learn more about the roles of various files in:
6 | # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
7 | # * https://testthat.r-lib.org/articles/special-files.html
8 |
9 | library(testthat)
10 | library(frombookdown)
11 |
12 | test_check("frombookdown")
13 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/frombookdown/tests/testthat/tests.R:
--------------------------------------------------------------------------------
1 | # Generated from _main.Rmd: do not edit by hand
2 | testthat::test_that("say_hello works", {
3 | testthat::expect_equal(say_hello("Jacob"), "Hello Jacob!")
4 | testthat::expect_equal(say_hello("Jacob", exclamation = FALSE), "Hello Jacob.")
5 | })
6 |
7 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-from-bookdown/index.Rmd:
--------------------------------------------------------------------------------
1 | ---
2 | title: "Creating the ``r params$package_name`` R package"
3 | author: "Jacob Bien"
4 | date: "`r Sys.Date()`"
5 | site: bookdown::bookdown_site
6 | knit: litr::render
7 | output: litr::litr_gitbook
8 | params:
9 | package_name: "frombookdown" # <-- change this to your package name
10 | package_parent_dir: "." # <-- relative to this file's location
11 | documentclass: book
12 | ---
13 |
14 | # Introduction
15 |
16 | You can introduce what your R package does here.
17 |
18 | **Note:** If you are working in RStudio, you can simply press "Knit" to render this bookdown (and open `_book/index.html` to see the result). More generally, in a console you can run the following:
19 |
20 | ```{r, eval = FALSE}
21 | litr::render("index.Rmd", output_format = litr::litr_gitbook())
22 | ```
23 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/.Rbuildignore:
--------------------------------------------------------------------------------
1 | ^LICENSE\.md$
2 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/DESCRIPTION:
--------------------------------------------------------------------------------
1 | Package: witharmadillo
2 | Title: A Package That Uses RcppArmadillo Code
3 | Version: 0.0.0.9000
4 | Authors@R:
5 | person("First", "Last", , "you@gmail.com", role = c("aut", "cre"))
6 | Description: This package uses RcppArmadillo.
7 | License: MIT + file LICENSE
8 | Encoding: UTF-8
9 | Roxygen: list(markdown = TRUE)
10 | RoxygenNote: 7.3.2
11 | LinkingTo:
12 | Rcpp,
13 | RcppArmadillo
14 | Imports:
15 | Rcpp
16 | Suggests:
17 | testthat (>= 3.0.0)
18 | Config/testthat/edition: 3
19 | LitrVersionUsed: 0.9.3
20 | LitrId: 82f28ae9f3cf7083ad248dfd793d37f4
21 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/LICENSE:
--------------------------------------------------------------------------------
1 | YEAR: 2025
2 | COPYRIGHT HOLDER: F. Last
3 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/LICENSE.md:
--------------------------------------------------------------------------------
1 | # MIT License
2 |
3 | Copyright (c) 2025 F. Last
4 |
5 | Permission is hereby granted, free of charge, to any person obtaining a copy
6 | of this software and associated documentation files (the "Software"), to deal
7 | in the Software without restriction, including without limitation the rights
8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 |
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 |
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/NAMESPACE:
--------------------------------------------------------------------------------
1 | # Generated by roxygen2: do not edit by hand
2 |
3 | export(my_chol)
4 | importFrom(Rcpp,sourceCpp)
5 | useDynLib(witharmadillo, .registration = TRUE)
6 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/R/RcppExports.R:
--------------------------------------------------------------------------------
1 | # Generated by using Rcpp::compileAttributes() -> do not edit by hand
2 | # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
3 |
4 | #' Cholesky decomposition
5 | #'
6 | #' @param X A positive definite matrix
7 | #' @export
8 | my_chol <- function(X) {
9 | .Call(`_witharmadillo_my_chol`, X)
10 | }
11 |
12 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/R/witharmadillo-package.R:
--------------------------------------------------------------------------------
1 | #' @keywords internal
2 | "_PACKAGE"
3 |
4 | ## usethis namespace: start
5 | #' @importFrom Rcpp sourceCpp
6 | #' @useDynLib witharmadillo, .registration = TRUE
7 | ## usethis namespace: end
8 | NULL
9 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/man/my_chol.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in create-witharmadillo.Rmd.
3 | \name{my_chol}
4 | \alias{my_chol}
5 | \title{Cholesky decomposition}
6 | \usage{
7 | my_chol(X)
8 | }
9 | \arguments{
10 | \item{X}{A positive definite matrix}
11 | }
12 | \description{
13 | Cholesky decomposition
14 | }
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/man/witharmadillo-package.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in create-witharmadillo.Rmd.
3 | \docType{package}
4 | \name{witharmadillo-package}
5 | \alias{witharmadillo}
6 | \alias{witharmadillo-package}
7 | \title{witharmadillo: A Package That Uses RcppArmadillo Code}
8 | \description{
9 | This package uses RcppArmadillo.
10 | }
11 | \author{
12 | \strong{Maintainer}: First Last \email{you@gmail.com}
13 |
14 | }
15 | \keyword{internal}
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/src/.gitignore:
--------------------------------------------------------------------------------
1 | *.o
2 | *.so
3 | *.dll
4 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/src/Makevars:
--------------------------------------------------------------------------------
1 | CXX_STD = CXX11
2 | PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
3 | PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
4 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/src/Makevars.win:
--------------------------------------------------------------------------------
1 | CXX_STD = CXX11
2 | PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
3 | PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
4 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/src/RcppExports.cpp:
--------------------------------------------------------------------------------
1 | // Generated by using Rcpp::compileAttributes() -> do not edit by hand
2 | // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
3 |
4 | #include
5 | #include
6 |
7 | using namespace Rcpp;
8 |
9 | #ifdef RCPP_USE_GLOBAL_ROSTREAM
10 | Rcpp::Rostream& Rcpp::Rcout = Rcpp::Rcpp_cout_get();
11 | Rcpp::Rostream& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
12 | #endif
13 |
14 | // my_chol
15 | arma::mat my_chol(arma::mat& X);
16 | RcppExport SEXP _witharmadillo_my_chol(SEXP XSEXP) {
17 | BEGIN_RCPP
18 | Rcpp::RObject rcpp_result_gen;
19 | Rcpp::RNGScope rcpp_rngScope_gen;
20 | Rcpp::traits::input_parameter< arma::mat& >::type X(XSEXP);
21 | rcpp_result_gen = Rcpp::wrap(my_chol(X));
22 | return rcpp_result_gen;
23 | END_RCPP
24 | }
25 |
26 | static const R_CallMethodDef CallEntries[] = {
27 | {"_witharmadillo_my_chol", (DL_FUNC) &_witharmadillo_my_chol, 1},
28 | {NULL, NULL, 0}
29 | };
30 |
31 | RcppExport void R_init_witharmadillo(DllInfo *dll) {
32 | R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
33 | R_useDynamicSymbols(dll, FALSE);
34 | }
35 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/src/code.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 | using namespace Rcpp;
4 | // Generated from create-witharmadillo.Rmd: do not edit by hand
5 | // [[Rcpp::depends(RcppArmadillo)]]
6 | using namespace arma;
7 |
8 | //' Cholesky decomposition
9 | //'
10 | //' @param X A positive definite matrix
11 | //' @export
12 | // [[Rcpp::export]]
13 | arma::mat my_chol(arma::mat& X) {
14 | return arma::chol(X);
15 | }
16 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/tests/testthat.R:
--------------------------------------------------------------------------------
1 | # This file is part of the standard setup for testthat.
2 | # It is recommended that you do not modify it.
3 | #
4 | # Where should you do additional test configuration?
5 | # Learn more about the roles of various files in:
6 | # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
7 | # * https://testthat.r-lib.org/articles/special-files.html
8 |
9 | library(testthat)
10 | library(witharmadillo)
11 |
12 | test_check("witharmadillo")
13 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-armadillo/witharmadillo/tests/testthat/tests.R:
--------------------------------------------------------------------------------
1 | # Generated from create-witharmadillo.Rmd: do not edit by hand
2 | testthat::test_that("my_chol works", {
3 | x <- matrix(0, 3, 3)
4 | x[upper.tri(x, diag = TRUE)] <- 1:6
5 | xchol <- my_chol(crossprod(x))
6 | testthat::expect_equal(crossprod(xchol), crossprod(x))
7 | testthat::expect_true(all(xchol[lower.tri(xchol)] == 0))
8 | })
9 |
10 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-data/rhasdata/.Rbuildignore:
--------------------------------------------------------------------------------
1 | ^LICENSE\.md$
2 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-data/rhasdata/DESCRIPTION:
--------------------------------------------------------------------------------
1 | Package: rhasdata
2 | Title: A Package That Has Data
3 | Version: 0.0.0.9000
4 | Authors@R:
5 | person("First", "Last", , "you@gmail.com", role = c("aut", "cre"))
6 | Description: This package has a dataset. It could also have some
7 | functions, but for now all it has is some data.
8 | License: MIT + file LICENSE
9 | Encoding: UTF-8
10 | Roxygen: list(markdown = TRUE)
11 | RoxygenNote: 7.3.2
12 | Depends:
13 | R (>= 3.5)
14 | LazyData: true
15 | LitrVersionUsed: 0.9.3
16 | LitrId: ee85c6aad6ff32c1145329613a7a9c7f
17 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-data/rhasdata/LICENSE:
--------------------------------------------------------------------------------
1 | YEAR: 2025
2 | COPYRIGHT HOLDER: F. Last
3 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-data/rhasdata/LICENSE.md:
--------------------------------------------------------------------------------
1 | # MIT License
2 |
3 | Copyright (c) 2025 F. Last
4 |
5 | Permission is hereby granted, free of charge, to any person obtaining a copy
6 | of this software and associated documentation files (the "Software"), to deal
7 | in the Software without restriction, including without limitation the rights
8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 |
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 |
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 |
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1 | # Generated by roxygen2: do not edit by hand
2 |
3 |
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1 | # Generated from create-rhasdata.Rmd: do not edit by hand
2 |
3 | #' A regression data set
4 | #'
5 | #' @format A data frame with 100 rows and 2 variables:
6 | #' \describe{
7 | #' \item{x}{a predictor variable}
8 | #' \item{y}{a response variable}
9 | #' }
10 | #' @source This data was simulated. But usually we might cite a source here.
11 | "mydata"
12 |
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in create-rhasdata.Rmd.
3 | \docType{data}
4 | \name{mydata}
5 | \alias{mydata}
6 | \title{A regression data set}
7 | \format{
8 | A data frame with 100 rows and 2 variables:
9 | \describe{
10 | \item{x}{a predictor variable}
11 | \item{y}{a response variable}
12 | }
13 | }
14 | \source{
15 | This data was simulated. But usually we might cite a source here.
16 | }
17 | \usage{
18 | mydata
19 | }
20 | \description{
21 | A regression data set
22 | }
23 | \keyword{datasets}
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1 | /*!
2 | * headroom.js v0.9.4 - Give your page some headroom. Hide your header until you need it
3 | * Copyright (c) 2017 Nick Williams - http://wicky.nillia.ms/headroom.js
4 | * License: MIT
5 | */
6 |
7 | !function(a){a&&(a.fn.headroom=function(b){return this.each(function(){var c=a(this),d=c.data("headroom"),e="object"==typeof b&&b;e=a.extend(!0,{},Headroom.options,e),d||(d=new Headroom(this,e),d.init(),c.data("headroom",d)),"string"==typeof b&&(d[b](),"destroy"===b&&c.removeData("headroom"))})},a("[data-headroom]").each(function(){var b=a(this);b.headroom(b.data())}))}(window.Zepto||window.jQuery);
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2 | document.addEventListener("DOMContentLoaded", function () {
3 | var mathElements = document.getElementsByClassName("math");
4 | var macros = [];
5 | for (var i = 0; i < mathElements.length; i++) {
6 | var texText = mathElements[i].firstChild;
7 | if (mathElements[i].tagName == "SPAN") {
8 | katex.render(texText.data, mathElements[i], {
9 | displayMode: mathElements[i].classList.contains("display"),
10 | throwOnError: false,
11 | macros: macros,
12 | fleqn: false
13 | });
14 | }}});
15 |
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1 |
2 |
3 |
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1 | pandoc: '3.2'
2 | pkgdown: 2.1.2
3 | pkgdown_sha: ~
4 | articles:
5 | using-package: using-package.html
6 | last_built: 2025-05-23T15:47Z
7 |
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1 | {
2 | "name": "",
3 | "short_name": "",
4 | "icons": [
5 | {
6 | "src": "/web-app-manifest-192x192.png",
7 | "sizes": "192x192",
8 | "type": "image/png",
9 | "purpose": "maskable"
10 | },
11 | {
12 | "src": "/web-app-manifest-512x512.png",
13 | "sizes": "512x512",
14 | "type": "image/png",
15 | "purpose": "maskable"
16 | }
17 | ],
18 | "theme_color": "#ffffff",
19 | "background_color": "#ffffff",
20 | "display": "standalone"
21 | }
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1 |
2 | /404.html
3 | /LICENSE-text.html
4 | /LICENSE.html
5 | /articles/index.html
6 | /articles/using-package.html
7 | /authors.html
8 | /index.html
9 | /reference/index.html
10 | /reference/say_hello.html
11 | /reference/say_hi.html
12 |
13 |
14 |
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/examples/make-an-r-package-with-extras/source-files/README.Rmd:
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1 | ---
2 | output: github_document
3 | ---
4 |
5 |
6 |
7 | ```{r, include = FALSE}
8 | knitr::opts_chunk$set(
9 | collapse = TRUE,
10 | eval = FALSE,
11 | comment = "#>",
12 | fig.path = "man/figures/README-",
13 | out.width = "100%"
14 | )
15 | ```
16 |
17 | # withpkgdown: An Example Package
18 |
19 |
20 |
21 |
22 | This package's purpose is to show how to use [litr](https://github.com/jacobbien/litr-project/tree/main/litr) to create a package with a README, a vignette, a pkgdown site, and (of course) a hex sticker. We can see the result of all of that at this package's website [here](https://jacobbien.github.io/withpkgdown-project/).
23 |
24 | ## Getting started
25 |
26 | Put instructions here for how to install your package:
27 |
28 | ```{r}
29 | # [change "jacobbien" to your github username]
30 | # remotes::install_github("jacobbien/withpkgdown-project", subdir = "withpkgdown")
31 | ```
32 |
33 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-extras/source-files/_pkgdown.yml:
--------------------------------------------------------------------------------
1 | destination: ../docs/
2 |
3 | url: ~
4 | template:
5 | bootstrap: 5
6 |
7 | navbar:
8 | structure:
9 | left: [reference, articles, search]
10 | right: [github]
11 |
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/examples/make-an-r-package-with-extras/source-files/using-package.Rmd:
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1 | ---
2 | title: "Using withpkgdown Package"
3 | author: "Your Name"
4 | date: "`r Sys.Date()`"
5 | output: rmarkdown::html_vignette
6 | vignette: >
7 | %\VignetteIndexEntry{Using withpkgdown Package}
8 | %\VignetteEngine{knitr::rmarkdown}
9 | %\VignetteEncoding{UTF-8}
10 | ---
11 |
12 | This vignette describes how to use this package. You start by loading the package.
13 |
14 | ```{r}
15 | library(withpkgdown)
16 | ```
17 |
18 | ### Saying hello
19 |
20 | To say hello, you use the `say_hello()` function:
21 |
22 | For example, to say hello to someone named Jacob, you'd do the following:
23 |
24 | ```{r}
25 | say_hello("Jacob")
26 | ```
27 |
28 | ### Saying hi
29 |
30 | To say hi to someone, one would use the following:
31 |
32 | ```{r}
33 | say_hi("Jacob")
34 | ```
35 |
36 | ### More advanced use
37 |
38 | You can control the punctuation by using the `exclamation` argument:
39 |
40 | ```{r}
41 | say_hello("Jacob", exclamation=FALSE)
42 | ```
43 |
44 |
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/examples/make-an-r-package-with-extras/withpkgdown/.Rbuildignore:
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1 | ^LICENSE\.md$
2 | ^README\.Rmd$
3 | ^_pkgdown\.yml$
4 | ^docs$
5 | ^pkgdown$
6 |
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/examples/make-an-r-package-with-extras/withpkgdown/DESCRIPTION:
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1 | Package: withpkgdown
2 | Title: A Package With a README, Vignette, and Pkgdown Site
3 | Version: 0.0.0.9000
4 | Authors@R:
5 | person("First", "Last", , "you@gmail.com", role = c("aut", "cre"))
6 | Description: This package's purpose is to show how to have a README,
7 | vignette, and a pkgdown website using litr.
8 | License: MIT + file LICENSE
9 | Encoding: UTF-8
10 | Roxygen: list(markdown = TRUE)
11 | RoxygenNote: 7.3.2
12 | Suggests:
13 | knitr,
14 | rmarkdown
15 | VignetteBuilder: knitr
16 | URL: https://github.com/jacobbien/litr-project/tree/main/examples/make-an-r-package-with-extras/withpkgdown
17 | LitrVersionUsed: 0.9.3
18 | LitrId: 96b38e0a25a89fbb9a4c27c943d76bb5
19 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-extras/withpkgdown/LICENSE:
--------------------------------------------------------------------------------
1 | YEAR: 2025
2 | COPYRIGHT HOLDER: F. Last
3 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-extras/withpkgdown/LICENSE.md:
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1 | # MIT License
2 |
3 | Copyright (c) 2025 F. Last
4 |
5 | Permission is hereby granted, free of charge, to any person obtaining a copy
6 | of this software and associated documentation files (the "Software"), to deal
7 | in the Software without restriction, including without limitation the rights
8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 |
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 |
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 |
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/examples/make-an-r-package-with-extras/withpkgdown/NAMESPACE:
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1 | # Generated by roxygen2: do not edit by hand
2 |
3 | export(say_hello)
4 | export(say_hi)
5 |
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/examples/make-an-r-package-with-extras/withpkgdown/R/say_hello.R:
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1 | # Generated from create-withpkgdown.Rmd: do not edit by hand
2 |
3 | #' Say hello to someone
4 | #'
5 | #' @param name Name of a person
6 | #' @param exclamation Whether to include an exclamation mark
7 | #' @export
8 | say_hello <- function(name, exclamation = TRUE) {
9 | paste0("Hello ", name, ifelse(exclamation, "!", "."))
10 | }
11 |
12 | #' Say hi to someone
13 | #'
14 | #' @param name Name of a person
15 | #' @param exclamation Whether to include an exclamation mark
16 | #' @export
17 | say_hi <- function(name, exclamation = TRUE) {
18 | paste0("Hi ", name, ifelse(exclamation, "!", "."))
19 | }
20 |
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/examples/make-an-r-package-with-extras/withpkgdown/README.Rmd:
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1 | ---
2 | output: github_document
3 | ---
4 |
5 |
6 |
7 | ```{r, include = FALSE}
8 | knitr::opts_chunk$set(
9 | collapse = TRUE,
10 | eval = FALSE,
11 | comment = "#>",
12 | fig.path = "man/figures/README-",
13 | out.width = "100%"
14 | )
15 | ```
16 |
17 | # withpkgdown: An Example Package
18 |
19 |
20 |
21 |
22 | This package's purpose is to show how to use [litr](https://github.com/jacobbien/litr-project/tree/main/litr) to create a package with a README, a vignette, a pkgdown site, and (of course) a hex sticker. We can see the result of all of that at this package's website [here](https://jacobbien.github.io/withpkgdown-project/).
23 |
24 | ## Getting started
25 |
26 | Put instructions here for how to install your package:
27 |
28 | ```{r}
29 | # [change "jacobbien" to your github username]
30 | # remotes::install_github("jacobbien/withpkgdown-project", subdir = "withpkgdown")
31 | ```
32 |
33 |
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/examples/make-an-r-package-with-extras/withpkgdown/README.md:
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1 |
2 |
3 |
4 | # withpkgdown: An Example Package
5 |
6 |
7 |
8 |
9 | This package’s purpose is to show how to use
10 | [litr](https://github.com/jacobbien/litr-project/tree/main/litr) to
11 | create a package with a README, a vignette, a pkgdown site, and (of
12 | course) a hex sticker. We can see the result of all of that at this
13 | package’s website
14 | [here](https://jacobbien.github.io/withpkgdown-project/).
15 |
16 | ## Getting started
17 |
18 | Put instructions here for how to install your package:
19 |
20 | ``` r
21 | # [change "jacobbien" to your github username]
22 | # remotes::install_github("jacobbien/withpkgdown-project", subdir = "withpkgdown")
23 | ```
24 |
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/examples/make-an-r-package-with-extras/withpkgdown/_pkgdown.yml:
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1 | destination: ../docs/
2 |
3 | url: ~
4 | template:
5 | bootstrap: 5
6 |
7 | navbar:
8 | structure:
9 | left: [reference, articles, search]
10 | right: [github]
11 |
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/examples/make-an-r-package-with-extras/withpkgdown/man/say_hello.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in create-withpkgdown.Rmd.
3 | \name{say_hello}
4 | \alias{say_hello}
5 | \title{Say hello to someone}
6 | \usage{
7 | say_hello(name, exclamation = TRUE)
8 | }
9 | \arguments{
10 | \item{name}{Name of a person}
11 |
12 | \item{exclamation}{Whether to include an exclamation mark}
13 | }
14 | \description{
15 | Say hello to someone
16 | }
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/examples/make-an-r-package-with-extras/withpkgdown/man/say_hi.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in create-withpkgdown.Rmd.
3 | \name{say_hi}
4 | \alias{say_hi}
5 | \title{Say hi to someone}
6 | \usage{
7 | say_hi(name, exclamation = TRUE)
8 | }
9 | \arguments{
10 | \item{name}{Name of a person}
11 |
12 | \item{exclamation}{Whether to include an exclamation mark}
13 | }
14 | \description{
15 | Say hi to someone
16 | }
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1 | {
2 | "name": "",
3 | "short_name": "",
4 | "icons": [
5 | {
6 | "src": "/web-app-manifest-192x192.png",
7 | "sizes": "192x192",
8 | "type": "image/png",
9 | "purpose": "maskable"
10 | },
11 | {
12 | "src": "/web-app-manifest-512x512.png",
13 | "sizes": "512x512",
14 | "type": "image/png",
15 | "purpose": "maskable"
16 | }
17 | ],
18 | "theme_color": "#ffffff",
19 | "background_color": "#ffffff",
20 | "display": "standalone"
21 | }
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/examples/make-an-r-package-with-extras/withpkgdown/vignettes/using-package.Rmd:
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1 | ---
2 | title: "Using withpkgdown Package"
3 | author: "Your Name"
4 | date: "`r Sys.Date()`"
5 | output: rmarkdown::html_vignette
6 | vignette: >
7 | %\VignetteIndexEntry{Using withpkgdown Package}
8 | %\VignetteEngine{knitr::rmarkdown}
9 | %\VignetteEncoding{UTF-8}
10 | ---
11 |
12 | This vignette describes how to use this package. You start by loading the package.
13 |
14 | ```{r}
15 | library(withpkgdown)
16 | ```
17 |
18 | ### Saying hello
19 |
20 | To say hello, you use the `say_hello()` function:
21 |
22 | For example, to say hello to someone named Jacob, you'd do the following:
23 |
24 | ```{r}
25 | say_hello("Jacob")
26 | ```
27 |
28 | ### Saying hi
29 |
30 | To say hi to someone, one would use the following:
31 |
32 | ```{r}
33 | say_hi("Jacob")
34 | ```
35 |
36 | ### More advanced use
37 |
38 | You can control the punctuation by using the `exclamation` argument:
39 |
40 | ```{r}
41 | say_hello("Jacob", exclamation=FALSE)
42 | ```
43 |
44 |
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/examples/make-an-r-package-with-rcpp/withrcpp/.Rbuildignore:
--------------------------------------------------------------------------------
1 | ^LICENSE\.md$
2 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-rcpp/withrcpp/DESCRIPTION:
--------------------------------------------------------------------------------
1 | Package: withrcpp
2 | Title: A Package That Uses Rcpp Code
3 | Version: 0.0.0.9000
4 | Authors@R:
5 | person("First", "Last", , "you@gmail.com", role = c("aut", "cre"))
6 | Description: This package uses Rcpp.
7 | License: MIT + file LICENSE
8 | Encoding: UTF-8
9 | Roxygen: list(markdown = TRUE)
10 | RoxygenNote: 7.3.2
11 | LinkingTo:
12 | Rcpp
13 | Imports:
14 | Rcpp
15 | Suggests:
16 | testthat (>= 3.0.0)
17 | Config/testthat/edition: 3
18 | LitrVersionUsed: 0.9.3
19 | LitrId: 60aa4f185c1e54b6b72b5c0868087e24
20 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-rcpp/withrcpp/LICENSE:
--------------------------------------------------------------------------------
1 | YEAR: 2025
2 | COPYRIGHT HOLDER: F. Last
3 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-rcpp/withrcpp/LICENSE.md:
--------------------------------------------------------------------------------
1 | # MIT License
2 |
3 | Copyright (c) 2025 F. Last
4 |
5 | Permission is hereby granted, free of charge, to any person obtaining a copy
6 | of this software and associated documentation files (the "Software"), to deal
7 | in the Software without restriction, including without limitation the rights
8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 |
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 |
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-rcpp/withrcpp/NAMESPACE:
--------------------------------------------------------------------------------
1 | # Generated by roxygen2: do not edit by hand
2 |
3 | export(alternate_signs)
4 | importFrom(Rcpp,sourceCpp)
5 | useDynLib(withrcpp, .registration = TRUE)
6 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-rcpp/withrcpp/R/RcppExports.R:
--------------------------------------------------------------------------------
1 | # Generated by using Rcpp::compileAttributes() -> do not edit by hand
2 | # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
3 |
4 | #' Alternately flip the signs of elements of a vector
5 | #'
6 | #' @param v A numerical vector
7 | #' @export
8 | alternate_signs <- function(v) {
9 | .Call(`_withrcpp_alternate_signs`, v)
10 | }
11 |
12 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-rcpp/withrcpp/R/withrcpp-package.R:
--------------------------------------------------------------------------------
1 | #' My great package
2 | #'
3 | #' Here's an overview of the package.
4 | #'
5 | #' @docType package
6 | #' @seealso \code{\link{alternate_signs}}
7 | #' @keywords internal
8 | "_PACKAGE"
9 |
10 | ## usethis namespace: start
11 | #' @importFrom Rcpp sourceCpp
12 | #' @useDynLib withrcpp, .registration = TRUE
13 | ## usethis namespace: end
14 | NULL
15 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-rcpp/withrcpp/man/alternate_signs.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in create-withrcpp.Rmd.
3 | \name{alternate_signs}
4 | \alias{alternate_signs}
5 | \title{Alternately flip the signs of elements of a vector}
6 | \usage{
7 | alternate_signs(v)
8 | }
9 | \arguments{
10 | \item{v}{A numerical vector}
11 | }
12 | \description{
13 | Alternately flip the signs of elements of a vector
14 | }
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-rcpp/withrcpp/man/withrcpp-package.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in create-withrcpp.Rmd.
3 | \docType{package}
4 | \name{withrcpp-package}
5 | \alias{withrcpp}
6 | \alias{withrcpp-package}
7 | \title{My great package}
8 | \description{
9 | Here's an overview of the package.
10 | }
11 | \seealso{
12 | \code{\link{alternate_signs}}
13 | }
14 | \author{
15 | \strong{Maintainer}: First Last \email{you@gmail.com}
16 |
17 | }
18 | \keyword{internal}
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-rcpp/withrcpp/src/.gitignore:
--------------------------------------------------------------------------------
1 | *.o
2 | *.so
3 | *.dll
4 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-rcpp/withrcpp/src/RcppExports.cpp:
--------------------------------------------------------------------------------
1 | // Generated by using Rcpp::compileAttributes() -> do not edit by hand
2 | // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
3 |
4 | #include
5 |
6 | using namespace Rcpp;
7 |
8 | #ifdef RCPP_USE_GLOBAL_ROSTREAM
9 | Rcpp::Rostream& Rcpp::Rcout = Rcpp::Rcpp_cout_get();
10 | Rcpp::Rostream& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
11 | #endif
12 |
13 | // alternate_signs
14 | NumericVector alternate_signs(NumericVector v);
15 | RcppExport SEXP _withrcpp_alternate_signs(SEXP vSEXP) {
16 | BEGIN_RCPP
17 | Rcpp::RObject rcpp_result_gen;
18 | Rcpp::RNGScope rcpp_rngScope_gen;
19 | Rcpp::traits::input_parameter< NumericVector >::type v(vSEXP);
20 | rcpp_result_gen = Rcpp::wrap(alternate_signs(v));
21 | return rcpp_result_gen;
22 | END_RCPP
23 | }
24 |
25 | static const R_CallMethodDef CallEntries[] = {
26 | {"_withrcpp_alternate_signs", (DL_FUNC) &_withrcpp_alternate_signs, 1},
27 | {NULL, NULL, 0}
28 | };
29 |
30 | RcppExport void R_init_withrcpp(DllInfo *dll) {
31 | R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
32 | R_useDynamicSymbols(dll, FALSE);
33 | }
34 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-rcpp/withrcpp/src/code.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | using namespace Rcpp;
3 | // Generated from create-withrcpp.Rmd: do not edit by hand
4 |
5 | //' Alternately flip the signs of elements of a vector
6 | //'
7 | //' @param v A numerical vector
8 | //' @export
9 | // [[Rcpp::export]]
10 | NumericVector alternate_signs(NumericVector v) {
11 | int n = v.size();
12 | NumericVector out(n);
13 | for(int i = 0; i < n; i++) {
14 | if (i % 2 == 0) {
15 | out[i] = v[i];
16 | }
17 | else {
18 | out[i] = -v[i];
19 | }
20 | }
21 | return out;
22 | }
23 |
--------------------------------------------------------------------------------
/examples/make-an-r-package-with-rcpp/withrcpp/tests/testthat.R:
--------------------------------------------------------------------------------
1 | # This file is part of the standard setup for testthat.
2 | # It is recommended that you do not modify it.
3 | #
4 | # Where should you do additional test configuration?
5 | # Learn more about the roles of various files in:
6 | # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
7 | # * https://testthat.r-lib.org/articles/special-files.html
8 |
9 | library(testthat)
10 | library(withrcpp)
11 |
12 | test_check("withrcpp")
13 |
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/examples/make-an-r-package-with-rcpp/withrcpp/tests/testthat/tests.R:
--------------------------------------------------------------------------------
1 | # Generated from create-withrcpp.Rmd: do not edit by hand
2 | testthat::test_that("alternate_signs works", {
3 | testthat::expect_equal(alternate_signs(1:3), c(1, -2, 3))
4 | testthat::expect_equal(alternate_signs(c(-4, 2)), c(-4, -2))
5 | })
6 |
7 |
--------------------------------------------------------------------------------
/examples/make-an-r-package/rhello/.Rbuildignore:
--------------------------------------------------------------------------------
1 | ^LICENSE\.md$
2 |
--------------------------------------------------------------------------------
/examples/make-an-r-package/rhello/DESCRIPTION:
--------------------------------------------------------------------------------
1 | Package: rhello
2 | Title: A Package That Says Hello
3 | Version: 0.0.0.9000
4 | Authors@R:
5 | person("First", "Last", , "you@gmail.com", role = c("aut", "cre"))
6 | Description: This package says hello. But its actual purpose is to show
7 | how an R package can be completely coded in a single R markdown file.
8 | License: MIT + file LICENSE
9 | Encoding: UTF-8
10 | Roxygen: list(markdown = TRUE)
11 | RoxygenNote: 7.3.2
12 | Suggests:
13 | testthat (>= 3.0.0)
14 | Config/testthat/edition: 3
15 | LitrVersionUsed: 0.9.3
16 | LitrId: 5a4ba5a52b04676010a24fd8bc26d039
17 |
--------------------------------------------------------------------------------
/examples/make-an-r-package/rhello/LICENSE:
--------------------------------------------------------------------------------
1 | YEAR: 2025
2 | COPYRIGHT HOLDER: F. Last
3 |
--------------------------------------------------------------------------------
/examples/make-an-r-package/rhello/LICENSE.md:
--------------------------------------------------------------------------------
1 | # MIT License
2 |
3 | Copyright (c) 2025 F. Last
4 |
5 | Permission is hereby granted, free of charge, to any person obtaining a copy
6 | of this software and associated documentation files (the "Software"), to deal
7 | in the Software without restriction, including without limitation the rights
8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 |
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 |
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 |
--------------------------------------------------------------------------------
/examples/make-an-r-package/rhello/NAMESPACE:
--------------------------------------------------------------------------------
1 | # Generated by roxygen2: do not edit by hand
2 |
3 | export(say_hello)
4 |
--------------------------------------------------------------------------------
/examples/make-an-r-package/rhello/R/say_hello.R:
--------------------------------------------------------------------------------
1 | # Generated from create-rhello.Rmd: do not edit by hand
2 |
3 | #' Say hello to someone
4 | #'
5 | #' @param name Name of a person
6 | #' @param exclamation Whether to include an exclamation mark
7 | #' @export
8 | say_hello <- function(name, exclamation = TRUE) {
9 | paste0("Hello ", name, ifelse(exclamation, "!", "."))
10 | }
11 |
--------------------------------------------------------------------------------
/examples/make-an-r-package/rhello/man/say_hello.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in create-rhello.Rmd.
3 | \name{say_hello}
4 | \alias{say_hello}
5 | \title{Say hello to someone}
6 | \usage{
7 | say_hello(name, exclamation = TRUE)
8 | }
9 | \arguments{
10 | \item{name}{Name of a person}
11 |
12 | \item{exclamation}{Whether to include an exclamation mark}
13 | }
14 | \description{
15 | Say hello to someone
16 | }
--------------------------------------------------------------------------------
/examples/make-an-r-package/rhello/tests/testthat.R:
--------------------------------------------------------------------------------
1 | # This file is part of the standard setup for testthat.
2 | # It is recommended that you do not modify it.
3 | #
4 | # Where should you do additional test configuration?
5 | # Learn more about the roles of various files in:
6 | # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
7 | # * https://testthat.r-lib.org/articles/special-files.html
8 |
9 | library(testthat)
10 | library(rhello)
11 |
12 | test_check("rhello")
13 |
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/examples/make-an-r-package/rhello/tests/testthat/tests.R:
--------------------------------------------------------------------------------
1 | # Generated from create-rhello.Rmd: do not edit by hand
2 | testthat::test_that("say_hello works", {
3 | testthat::expect_equal(say_hello("Jacob"), "Hello Jacob!")
4 | testthat::expect_equal(say_hello("Jacob", exclamation = FALSE), "Hello Jacob.")
5 | })
6 |
7 |
--------------------------------------------------------------------------------
/litr-project.Rproj:
--------------------------------------------------------------------------------
1 | Version: 1.0
2 |
3 | RestoreWorkspace: Default
4 | SaveWorkspace: Default
5 | AlwaysSaveHistory: Default
6 |
7 | EnableCodeIndexing: Yes
8 | UseSpacesForTab: Yes
9 | NumSpacesForTab: 2
10 | Encoding: UTF-8
11 |
12 | RnwWeave: Sweave
13 | LaTeX: pdfLaTeX
14 |
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/litr/.Rbuildignore:
--------------------------------------------------------------------------------
1 | ^LICENSE\.md$
2 | ^README\.Rmd$
3 | ^_pkgdown\.yml$
4 | ^docs$
5 | ^pkgdown$
6 |
--------------------------------------------------------------------------------
/litr/DESCRIPTION:
--------------------------------------------------------------------------------
1 | Package: litr
2 | Title: Literate Programming for Writing R Packages
3 | Version: 0.9.3
4 | Authors@R: c(
5 | person("Jacob", "Bien", , "jbien@usc.edu", role = c("aut", "cre")),
6 | person("Patrick Vossler", role = "aut")
7 | )
8 | Description: Allows one to fully create an R package in a single .Rmd
9 | file. Includes functionality and .Rmd templates for a literate
10 | programming approach to R package development.
11 | License: MIT + file LICENSE
12 | Encoding: UTF-8
13 | Roxygen: list(markdown = TRUE)
14 | RoxygenNote: 7.3.2
15 | Imports:
16 | bookdown,
17 | desc,
18 | devtools,
19 | digest,
20 | fansi,
21 | fs,
22 | knitr,
23 | pkgdown,
24 | rmarkdown,
25 | stringr,
26 | usethis,
27 | xfun,
28 | xml2,
29 | yaml
30 | Suggests:
31 | dplyr,
32 | Rcpp,
33 | testthat (>= 3.0.0)
34 | Config/testthat/edition: 3
35 | VignetteBuilder: knitr
36 | URL: https://github.com/jacobbien/litr-project/tree/main/litr
37 | LitrVersionUsed: 0.9.3
38 | LitrId: 1dc557ee5a7ae434b13c5b61d3d3f530
39 |
--------------------------------------------------------------------------------
/litr/LICENSE:
--------------------------------------------------------------------------------
1 | YEAR: 2025
2 | COPYRIGHT HOLDER: J. Bien
3 |
--------------------------------------------------------------------------------
/litr/LICENSE.md:
--------------------------------------------------------------------------------
1 | # MIT License
2 |
3 | Copyright (c) 2025 J. Bien
4 |
5 | Permission is hereby granted, free of charge, to any person obtaining a copy
6 | of this software and associated documentation files (the "Software"), to deal
7 | in the Software without restriction, including without limitation the rights
8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 |
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 |
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 |
--------------------------------------------------------------------------------
/litr/NAMESPACE:
--------------------------------------------------------------------------------
1 | # Generated by roxygen2: do not edit by hand
2 |
3 | export(add_hex_sticker)
4 | export(add_pkgdown)
5 | export(add_readme)
6 | export(add_vignettes)
7 | export(document)
8 | export(draft)
9 | export(draft_armadillo)
10 | export(draft_bookdown)
11 | export(draft_data)
12 | export(draft_extras)
13 | export(draft_rcpp)
14 | export(litr_gitbook)
15 | export(litr_html_document)
16 | export(litr_pdf_document)
17 | export(litrify_output_format)
18 | export(load_all)
19 | export(render)
20 |
--------------------------------------------------------------------------------
/litr/R/litr-package.R:
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1 | #' Literate Programming for Writing R Packages
2 | #'
3 | #' Allows one to fully create an R package in a single .Rmd file. Includes
4 | #' functionality and .Rmd templates for a literate programming approach to R
5 | #' package development.
6 | #'
7 | #' @examples
8 | #' \dontrun{
9 | #' # Make a file create-rhello.Rmd based on a template
10 | #' litr::draft("rhello")
11 | #' # Now call litr::render (or press Knit if in RStudio) to generate not just
12 | #' # create-rhello.html, but also an R package called `rhello`.
13 | #' litr::render("create-rhello.Rmd")
14 | #' }
15 | #' @docType package
16 | #' @seealso \code{\link{render}}
17 | #' @keywords internal
18 | "_PACKAGE"
19 |
20 | ## usethis namespace: start
21 | ## usethis namespace: end
22 | NULL
23 |
--------------------------------------------------------------------------------
/litr/R/test_litr.R:
--------------------------------------------------------------------------------
1 | # Generated from _main.Rmd: do not edit by hand
2 |
3 | #' Run tests for `litr` itself
4 | #'
5 | #' Special function for testing `litr`. The trick is to temporarily install
6 | #' the new version of `litr`, run the test, and then put things back how it was
7 | #' before.
8 | #'
9 | #' Typical values for `install_old` could be
10 | #' - `function() devtools::install("[location of old version]")`
11 | #' - `function() remotes::install_github("jacobbien/litr-project@*release", subdir = "litr")`.
12 | #'
13 | #' @param install_old A function that when run will install the old version
14 | #' @param location_of_new Path to the new package directory
15 | #' @keywords internal
16 | test_litr <- function(install_old, location_of_new) {
17 | devtools::unload(params$package_name)
18 | devtools::install(location_of_new)
19 | out <- devtools::test(location_of_new)
20 | install_old()
21 | return(out)
22 | }
23 |
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/litr/inst/rmarkdown/templates/make-an-r-package-from-bookdown/skeleton/1description.Rmd:
--------------------------------------------------------------------------------
1 | # Package setup
2 |
3 | Every R package needs a DESCRIPTION file, so we start by specifying this information:
4 |
5 | ```{r package-setup, message=FALSE, results='hide'}
6 | usethis::create_package(
7 | path = ".",
8 | fields = list(
9 | Package = params$package_name,
10 | Version = "0.0.0.9000",
11 | Title = "A Package Defined in a Bookdown",
12 | Description = "This package uses litr to define an R package through writing a bookdown.",
13 | `Authors@R` = person(
14 | given = "First",
15 | family = "Last",
16 | email = "you@gmail.com",
17 | role = c("aut", "cre")
18 | )
19 | )
20 | )
21 | usethis::use_mit_license(copyright_holder = "F. Last")
22 | ```
23 |
24 | Although it's not required, it can be nice to add some package-level documentation. This is what will show up when someone types `package?` in the console.
25 |
26 | ```{package_doc}
27 | #' A Package Defined in a Bookdown
28 | #'
29 | #' This package uses `litr` to define an R package through writing a `bookdown`.
30 | #'
31 | #' @docType package
32 | ```
--------------------------------------------------------------------------------
/litr/inst/rmarkdown/templates/make-an-r-package-from-bookdown/skeleton/2basics.Rmd:
--------------------------------------------------------------------------------
1 | # The basics of saying hello
2 |
3 | Let's define a function for our R package:
4 |
5 | ```{r}
6 | #' Say hello to someone
7 | #'
8 | #' @param name Name of a person
9 | #' @param exclamation Whether to include an exclamation mark
10 | #' @export
11 | say_hello <- function(name, exclamation = TRUE) {
12 | paste0("Hello ", name, ifelse(exclamation, "!", "."))
13 | }
14 | ```
15 |
16 | Code chunks whose first line starts with `#'` are added to the package.
17 |
18 | We can try running it.
19 |
20 | ```{r}
21 | say_hello("Jacob")
22 | ```
23 |
24 | That code chunk does not start with `#'`, so it is not added to the package.
25 |
26 | Let's write some tests to make sure the function behaves as desired:
27 |
28 | ```{r}
29 | testthat::test_that("say_hello works", {
30 | testthat::expect_equal(say_hello("Jacob"), "Hello Jacob!")
31 | testthat::expect_equal(say_hello("Jacob", exclamation = FALSE), "Hello Jacob.")
32 | })
33 | ```
34 |
35 | Code chunks that have one or more lines starting with `test_that(` (or `testthat::test_that(`) are added to the package as tests.
36 |
--------------------------------------------------------------------------------
/litr/inst/rmarkdown/templates/make-an-r-package-from-bookdown/skeleton/3more.Rmd:
--------------------------------------------------------------------------------
1 | # Generalization to other greetings
2 |
3 | We can now get fancier and define more functions across as many .Rmd files as we like. Hyperlinks work across different .Rmd files. For example, you can click on `say_hello()` and it will bring you to the definition in the previous chapter.
4 |
--------------------------------------------------------------------------------
/litr/inst/rmarkdown/templates/make-an-r-package-from-bookdown/skeleton/4end.Rmd:
--------------------------------------------------------------------------------
1 | # Conclusion {#conclude}
2 |
3 | When you are done defining the package, it remains to convert the Roxygen to documentation.
4 |
5 | ```{r}
6 | litr::document() # <-- use instead of devtools::document()
7 | ```
8 |
9 | You can also add some extra things to your package here if you like, such as a README, some vignettes, a [pkgdown](https://pkgdown.r-lib.org/) site, etc. See [here](https://github.com/jacobbien/litr-project/tree/main/examples/make-an-r-package-with-extras) for an example of how to do this with `litr`.
--------------------------------------------------------------------------------
/litr/inst/rmarkdown/templates/make-an-r-package-from-bookdown/skeleton/index.Rmd:
--------------------------------------------------------------------------------
1 | ---
2 | title: "Creating the ``r params$package_name`` R package"
3 | author: "Jacob Bien"
4 | date: "`r Sys.Date()`"
5 | site: bookdown::bookdown_site
6 | knit: litr::render
7 | output: litr::litr_gitbook
8 | params:
9 | package_name: "frombookdown" # <-- change this to your package name
10 | package_parent_dir: "." # <-- relative to this file's location
11 | documentclass: book
12 | ---
13 |
14 | # Introduction
15 |
16 | You can introduce what your R package does here.
17 |
18 | **Note:** If you are working in RStudio, you can simply press "Knit" to render this bookdown (and open `_book/index.html` to see the result). More generally, in a console you can run the following:
19 |
20 | ```{r, eval = FALSE}
21 | litr::render("index.Rmd", output_format = litr::litr_gitbook())
22 | ```
23 |
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/litr/inst/rmarkdown/templates/make-an-r-package-from-bookdown/skeleton/skeleton.Rmd:
--------------------------------------------------------------------------------
1 |
--------------------------------------------------------------------------------
/litr/inst/rmarkdown/templates/make-an-r-package-from-bookdown/template.yaml:
--------------------------------------------------------------------------------
1 | name: Template To Make an R Package From a Bookdown
2 | description: >
3 | Template for a bookdown that defines an R package using literate programming.
4 | create_dir: TRUE
5 |
--------------------------------------------------------------------------------
/litr/inst/rmarkdown/templates/make-an-r-package-with-armadillo/template.yaml:
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1 | name: Template To Make an R Package With RcppArmadillo
2 | description: >
3 | Template for an Rmd file for writing an R package that makes use of RcppArmadillo while using literate programming.
4 | create_dir: FALSE
5 |
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/litr/inst/rmarkdown/templates/make-an-r-package-with-data/template.yaml:
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1 | name: Template To Make an R Package With a Dataset
2 | description: >
3 | Template for an Rmd file for writing an R package with a dataset using literate programming.
4 | create_dir: FALSE
5 |
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/litr/inst/rmarkdown/templates/make-an-r-package-with-extras/skeleton/source-files/README.Rmd:
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1 | ---
2 | output: github_document
3 | ---
4 |
5 |
6 |
7 | ```{r, include = FALSE}
8 | knitr::opts_chunk$set(
9 | collapse = TRUE,
10 | eval = FALSE,
11 | comment = "#>",
12 | fig.path = "man/figures/README-",
13 | out.width = "100%"
14 | )
15 | ```
16 |
17 | # withpkgdown: An Example Package
18 |
19 |
20 |
21 |
22 | This package's purpose is to show how to use [litr](https://github.com/jacobbien/litr-project/tree/main/litr) to create a package with a README, a vignette, a pkgdown site, and (of course) a hex sticker. We can see the result of all of that at this package's website [here](https://jacobbien.github.io/withpkgdown-project/).
23 |
24 | ## Getting started
25 |
26 | Put instructions here for how to install your package:
27 |
28 | ```{r}
29 | # [change "jacobbien" to your github username]
30 | # remotes::install_github("jacobbien/withpkgdown-project", subdir = "withpkgdown")
31 | ```
32 |
33 |
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/litr/inst/rmarkdown/templates/make-an-r-package-with-extras/skeleton/source-files/_pkgdown.yml:
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1 | destination: ../docs/
2 |
3 | url: ~
4 | template:
5 | bootstrap: 5
6 |
7 | navbar:
8 | structure:
9 | left: [reference, articles, search]
10 | right: [github]
11 |
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/litr/inst/rmarkdown/templates/make-an-r-package-with-extras/skeleton/source-files/litr-hex.png:
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/litr/inst/rmarkdown/templates/make-an-r-package-with-extras/skeleton/source-files/using-package.Rmd:
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1 | ---
2 | title: "Using withpkgdown Package"
3 | author: "Your Name"
4 | date: "`r Sys.Date()`"
5 | output: rmarkdown::html_vignette
6 | vignette: >
7 | %\VignetteIndexEntry{Using withpkgdown Package}
8 | %\VignetteEngine{knitr::rmarkdown}
9 | %\VignetteEncoding{UTF-8}
10 | ---
11 |
12 | This vignette describes how to use this package. You start by loading the package.
13 |
14 | ```{r}
15 | library(withpkgdown)
16 | ```
17 |
18 | ### Saying hello
19 |
20 | To say hello, you use the `say_hello()` function:
21 |
22 | For example, to say hello to someone named Jacob, you'd do the following:
23 |
24 | ```{r}
25 | say_hello("Jacob")
26 | ```
27 |
28 | ### Saying hi
29 |
30 | To say hi to someone, one would use the following:
31 |
32 | ```{r}
33 | say_hi("Jacob")
34 | ```
35 |
36 | ### More advanced use
37 |
38 | You can control the punctuation by using the `exclamation` argument:
39 |
40 | ```{r}
41 | say_hello("Jacob", exclamation=FALSE)
42 | ```
43 |
44 |
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/litr/inst/rmarkdown/templates/make-an-r-package-with-extras/template.yaml:
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1 | name: Template To Make an R Package With a README, Vignette, and Pkgdown Site
2 | description: >
3 | Template for an Rmd file for writing an R package that has a README, vignette, and pkgdown site while using literate programming.
4 | create_dir: FALSE
5 |
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/litr/inst/rmarkdown/templates/make-an-r-package-with-rcpp/template.yaml:
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1 | name: Template To Make an R Package With Rcpp
2 | description: >
3 | Template for an Rmd file for writing an R package that makes use of Rcpp while using literate programming.
4 | create_dir: FALSE
5 |
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/litr/inst/rmarkdown/templates/make-an-r-package/template.yaml:
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1 | name: Template To Make an R Package
2 | description: >
3 | Template for an Rmd file for writing an R package using literate programming.
4 | create_dir: FALSE
5 |
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/litr/man/add_chunk_label_hyperlinks.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{add_chunk_label_hyperlinks}
4 | \alias{add_chunk_label_hyperlinks}
5 | \title{Add hyperlinks to embedded chunks}
6 | \usage{
7 | add_chunk_label_hyperlinks(
8 | html_files,
9 | reference_start = "<<",
10 | reference_end = ">>"
11 | )
12 | }
13 | \arguments{
14 | \item{html_files}{Character vector of file names of html files that were created
15 | from Rmd files}
16 |
17 | \item{reference_start}{The delimiter used to indicate the start of a chunk label}
18 |
19 | \item{reference_end}{The delimiter used to indicate the end of a chunk label}
20 | }
21 | \description{
22 | Finds chunks that are referenced in the html file(s) by looking for comments
23 | of the form \verb{###"foo"###} and then wraps \code{foo} in a \code{span} tag with \code{id="foo"}
24 | and then whenever the chunk label \verb{<>} is found it wraps it in a
25 | \verb{a href="file.html#foo"} tag so that it will be a hyperlink to \code{foo}'s
26 | definition.
27 | }
28 | \keyword{internal}
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/litr/man/add_function_hyperlinks.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{add_function_hyperlinks}
4 | \alias{add_function_hyperlinks}
5 | \title{Add hyperlinks to function definitions}
6 | \usage{
7 | add_function_hyperlinks(html_files, pkg_name)
8 | }
9 | \arguments{
10 | \item{html_files}{Character vector of file names of html files that were created
11 | from Rmd files}
12 |
13 | \item{pkg_name}{Name of the package created by litr. Taken from YAML front matter}
14 | }
15 | \description{
16 | Finds functions that are defined in the html file(s) by looking for text of the
17 | form \verb{foo <- function(} and then wraps \code{foo} in a \code{span} tag with \code{id="foo"}
18 | and then whenever \code{foo} is found it wraps a \verb{a href="file.html#foo"} tag so
19 | that it will be a hyperlink to \code{foo}'s definition.
20 | }
21 | \keyword{internal}
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/litr/man/add_hex_sticker.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{add_hex_sticker}
4 | \alias{add_hex_sticker}
5 | \title{Add a hex sticker to package}
6 | \usage{
7 | add_hex_sticker(hex_png_file)
8 | }
9 | \arguments{
10 | \item{hex_png_file}{The .png file with your package's hex sticker}
11 | }
12 | \description{
13 | In addition to calling this function, you should add to your README.Rmd something like this:
14 | }
15 | \details{
16 | \verb{# your-title
}
17 |
18 | See \href{https://pkgdown.r-lib.org/reference/build_home.html#package-logo}{here}
19 | for more.
20 | }
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/litr/man/add_pkgdown.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{add_pkgdown}
4 | \alias{add_pkgdown}
5 | \title{Add a pkgdown site}
6 | \usage{
7 | add_pkgdown(config_path = NULL)
8 | }
9 | \arguments{
10 | \item{config_path}{The _pkgdown.yml file that lives somewhere outside of your package. If NULL, then a basic default will be used.}
11 | }
12 | \description{
13 | This function creates a website for your package. You can see it locally by
14 | opening \code{docs/index.html} in your package. To get it online you can copy the
15 | \code{docs} directory to your website's server.
16 | }
17 | \details{
18 | Be sure that in the generating .Rmd file this is called \emph{after}
19 | \code{litr::document()} has been called. To customize the site, you may pass a
20 | customized \verb{_pkgdown.yml} file as described in \href{https://pkgdown.r-lib.org/articles/customise.html}{this \code{pkgdown} vignette}.
21 | }
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/litr/man/add_readme.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{add_readme}
4 | \alias{add_readme}
5 | \title{Add README to package}
6 | \usage{
7 | add_readme(rmd_file)
8 | }
9 | \arguments{
10 | \item{rmd_file}{The path to a .Rmd file.}
11 | }
12 | \description{
13 | This function takes a README.Rmd file, copies it into the package, and then
14 | renders it to a README.md file. It also adds these two files to the
15 | .Rbuildignore.
16 | }
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/litr/man/add_text_to_file.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{add_text_to_file}
4 | \alias{add_text_to_file}
5 | \title{Add Some Text to a File}
6 | \usage{
7 | add_text_to_file(
8 | txt,
9 | filename,
10 | location = NULL,
11 | req_exist = FALSE,
12 | pad = FALSE,
13 | msg = NULL
14 | )
15 | }
16 | \arguments{
17 | \item{txt}{Character vector to add to file}
18 |
19 | \item{filename}{Name of file}
20 |
21 | \item{location}{Specifies where text should be added. See description for more.}
22 |
23 | \item{req_exist}{If TRUE, then throws an error if file doesn't exist}
24 |
25 | \item{pad}{If TRUE, then when text is being added to a preexisting file, it adds a newline}
26 |
27 | \item{msg}{An optional message to put at top of file if this is a new file}
28 | }
29 | \description{
30 | The text will be added to the file at a particular line specified by
31 | \code{location}. The first line of \code{txt} will be on line \code{location} of the
32 | modified file. If \code{location} is NULL, then text is added to end of file.
33 | If file does not exist, it is created and \code{location} is ignored (unless
34 | \code{req_exist} is \code{TRUE}, in which case an error is thrown).
35 | }
36 | \keyword{internal}
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/litr/man/add_vignettes.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{add_vignettes}
4 | \alias{add_vignettes}
5 | \title{Add one or more vignettes to package}
6 | \usage{
7 | add_vignettes(rmd_files, other_files = NULL)
8 | }
9 | \arguments{
10 | \item{rmd_files}{A character vector of .Rmd files, each corresponding to
11 | a vignette}
12 |
13 | \item{other_files}{A character vector of any other files needed in the
14 | vignettes directory (.bib file, images, etc.)}
15 | }
16 | \description{
17 | Add one or more vignettes to package
18 | }
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/litr/man/check_unedited.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{check_unedited}
4 | \alias{check_unedited}
5 | \title{Check if package directory is the unedited output of litr::render()}
6 | \usage{
7 | check_unedited(package_dir)
8 | }
9 | \arguments{
10 | \item{package_dir}{Path to package}
11 | }
12 | \description{
13 | Uses hash stored in a special \code{litr} field of DESCRIPTION file to check that
14 | the current state of the R package directory is identical to its state at the
15 | time that it was created by \code{litr::render()}.
16 | }
17 | \keyword{internal}
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/litr/man/create_from_template.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{create_from_template}
4 | \alias{create_from_template}
5 | \title{Internal function for creating a .Rmd file from template}
6 | \usage{
7 | create_from_template(pkg_name, dir, template_name)
8 | }
9 | \arguments{
10 | \item{pkg_name}{Name of package to be created.}
11 |
12 | \item{dir}{(Optional) Directory where .Rmd file should be created}
13 |
14 | \item{template_name}{Name of template}
15 | }
16 | \description{
17 | Internal function for creating a .Rmd file from template
18 | }
19 | \keyword{internal}
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/litr/man/description_litr_hash_field_name.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{description_litr_hash_field_name}
4 | \alias{description_litr_hash_field_name}
5 | \title{Generate litr hash field name for DESCRIPTION file}
6 | \usage{
7 | description_litr_hash_field_name()
8 | }
9 | \description{
10 | Generate litr hash field name for DESCRIPTION file
11 | }
12 | \keyword{internal}
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/litr/man/description_litr_version_field_name.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{description_litr_version_field_name}
4 | \alias{description_litr_version_field_name}
5 | \title{Generate litr version field name for DESCRIPTION file}
6 | \usage{
7 | description_litr_version_field_name()
8 | }
9 | \description{
10 | Generate litr version field name for DESCRIPTION file
11 | }
12 | \keyword{internal}
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/litr/man/do_not_edit_message.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{do_not_edit_message}
4 | \alias{do_not_edit_message}
5 | \title{Generate do-not-edit message to put at top of file}
6 | \usage{
7 | do_not_edit_message(rmd_file, type = c("R", "man", "c"))
8 | }
9 | \arguments{
10 | \item{rmd_file}{Name of the Rmd file to mention}
11 |
12 | \item{type}{Whether this is a R/ file, man/ file, or a c file}
13 | }
14 | \description{
15 | Generate do-not-edit message to put at top of file
16 | }
17 | \keyword{internal}
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/litr/man/document.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{document}
4 | \alias{document}
5 | \title{Use roxygen to document a package from within a Rmd file}
6 | \usage{
7 | document(...)
8 | }
9 | \arguments{
10 | \item{...}{Arguments to be passed to \code{devtools::document()}}
11 | }
12 | \description{
13 | This is a wrapper for the \code{devtools::document()} function, which in turn is a
14 | wrapper for the \code{roxygen2::roxygenize()} function. It is written assuming that
15 | it is being called from within a generating Rmd file. The purpose for \code{litr}
16 | having this wrapper is two-fold. First, it ensures that the first line
17 | in the outputted \code{Rd} files should not say "Please edit documentation in
18 | R/file.R" but instead should refer to the Rmd file that generates everything.
19 | Second, in the case that Rcpp is being used, it makes some adjustments to ensure
20 | that the compiling of the C++ code should be successful.
21 | }
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/litr/man/draft.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{draft}
4 | \alias{draft}
5 | \title{Create a new litr .Rmd document for creating an R package}
6 | \usage{
7 | draft(pkg_name = "rhello", dir = ".")
8 | }
9 | \arguments{
10 | \item{pkg_name}{Name of package to be created.}
11 |
12 | \item{dir}{(Optional) Directory where .Rmd file should be created}
13 | }
14 | \description{
15 | This creates \verb{create-[pkg_name].Rmd} that when knitted (i.e., when passed to
16 | \code{litr::render()}) will create an R package called \code{pkg_name}.
17 | }
18 | \details{
19 | This is the most basic R package template, with one function and one test
20 | function.
21 | }
22 | \seealso{
23 | \code{\link{draft_bookdown}} \code{\link{draft_data}} \code{\link{draft_rcpp}} \code{\link{draft_extras}} \code{\link{draft_armadillo}}
24 | }
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/litr/man/draft_armadillo.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{draft_armadillo}
4 | \alias{draft_armadillo}
5 | \title{Create a new litr .Rmd document for creating an R package that uses \code{RcppArmadillo}}
6 | \usage{
7 | draft_armadillo(pkg_name = "witharmadillo", dir = ".")
8 | }
9 | \arguments{
10 | \item{pkg_name}{Name of package to be created.}
11 |
12 | \item{dir}{(Optional) Directory where .Rmd file should be created}
13 | }
14 | \description{
15 | This creates \verb{create-[pkg_name].Rmd} that when knitted (i.e., when passed to
16 | \code{litr::render()}) will create an R package called \code{pkg_name}.
17 | This template shows how to make an R package that uses \code{RcppArmadillo}.
18 | }
19 | \seealso{
20 | \code{\link{draft}} \code{\link{draft_bookdown}} \code{\link{draft_data}} \code{\link{draft_rcpp}} \code{\link{draft_extras}}
21 | }
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/litr/man/draft_bookdown.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{draft_bookdown}
4 | \alias{draft_bookdown}
5 | \title{Create a new litr .Rmd document for creating an R package from \code{bookdown}}
6 | \usage{
7 | draft_bookdown(pkg_name = "frombookdown", dir = ".")
8 | }
9 | \arguments{
10 | \item{pkg_name}{Name of package to be created.}
11 |
12 | \item{dir}{(Optional) Directory where .Rmd file should be created}
13 | }
14 | \description{
15 | This template shows how to make an R package from \code{bookdown}. It creates a directory called \verb{create-[pkg_name]} in \code{dir}. Rendering the file \code{index.Rmd}
16 | with \code{litr::render()} creates the bookdown and package.
17 | }
18 | \seealso{
19 | \code{\link{draft}} \code{\link{draft_data}} \code{\link{draft_rcpp}} \code{\link{draft_extras}} \code{\link{draft_armadillo}}
20 | }
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/litr/man/draft_data.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{draft_data}
4 | \alias{draft_data}
5 | \title{Create a new litr .Rmd document for creating an R package with a data set}
6 | \usage{
7 | draft_data(pkg_name = "rhasdata", dir = ".")
8 | }
9 | \arguments{
10 | \item{pkg_name}{Name of package to be created.}
11 |
12 | \item{dir}{(Optional) Directory where .Rmd file should be created}
13 | }
14 | \description{
15 | This creates \verb{create-[pkg_name].Rmd} that when knitted (i.e., when passed to
16 | \code{litr::render()}) will create an R package called \code{pkg_name}.
17 | This template shows how to make an R package with a data set in it.
18 | }
19 | \seealso{
20 | \code{\link{draft}} \code{\link{draft_bookdown}} \code{\link{draft_rcpp}} \code{\link{draft_extras}} \code{\link{draft_armadillo}}
21 | }
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/litr/man/draft_extras.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{draft_extras}
4 | \alias{draft_extras}
5 | \title{Create a new litr .Rmd document for creating an R package with extras}
6 | \usage{
7 | draft_extras(pkg_name = "withpkgdown", dir = ".")
8 | }
9 | \arguments{
10 | \item{pkg_name}{Name of package to be created.}
11 |
12 | \item{dir}{(Optional) Directory where .Rmd file should be created}
13 | }
14 | \description{
15 | This creates \verb{create-[pkg_name].Rmd} that when knitted (i.e., when passed to
16 | \code{litr::render()}) will create an R package called \code{pkg_name}.
17 | This template shows how to make an R package that has "extras" such as a
18 | README, vignette(s), a pkgdown site, and a hex sticker.
19 | }
20 | \seealso{
21 | \code{\link{draft}} \code{\link{draft_bookdown}} \code{\link{draft_data}} \code{\link{draft_rcpp}} \code{\link{draft_armadillo}}
22 | }
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/litr/man/draft_rcpp.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{draft_rcpp}
4 | \alias{draft_rcpp}
5 | \title{Create a new litr .Rmd document for creating an R package that uses \code{Rcpp}}
6 | \usage{
7 | draft_rcpp(pkg_name = "withrcpp", dir = ".")
8 | }
9 | \arguments{
10 | \item{pkg_name}{Name of package to be created.}
11 |
12 | \item{dir}{(Optional) Directory where .Rmd file should be created}
13 | }
14 | \description{
15 | This creates \verb{create-[pkg_name].Rmd} that when knitted (i.e., when passed to
16 | \code{litr::render()}) will create an R package called \code{pkg_name}.
17 | This template shows how to make an R package that uses \code{Rcpp}.
18 | }
19 | \seealso{
20 | \code{\link{draft}} \code{\link{draft_bookdown}} \code{\link{draft_data}} \code{\link{draft_extras}} \code{\link{draft_armadillo}}
21 | }
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/litr/man/find_labels.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in _main.Rmd.
3 | \name{find_labels}
4 | \alias{find_labels}
5 | \title{Find a .Rmd chunk label in a code chunk}
6 | \usage{
7 | find_labels(chunk_code)
8 | }
9 | \arguments{
10 | \item{chunk_code}{Character vector of code from a .Rmd code chunk. Each element is a line of the code chunk.}
11 | }
12 | \value{
13 | List where chunk_idx is a logical vector for each line of the chunk corresponding to whether a chunk label of the form \verb{<