├── .gitignore ├── data ├── Table1.1.RData ├── Table1.2.RData ├── DataSet3.1.RData ├── DataSet3.2.RData ├── DataSet3.3.RData ├── DataSet4.1.RData ├── DataSet5.1.RData ├── DataSet5.2.RData ├── DataSet7.1.RData ├── DataSet7.2.RData ├── DataSet7.3.RData ├── DataSet7.4.RData ├── DataSet7.6.RData ├── DataSet7.7.RData ├── DataSet8.1.RData ├── DataSet8.2.RData ├── DataSet8.3.RData ├── DataSet8.4.RData ├── DataSet9.1.RData ├── DataSet9.2.RData ├── DataSet9.4.RData ├── DataExam2.B.2.RData ├── DataExam2.B.3.RData ├── DataExam2.B.4.RData ├── DataExam2.B.7.RData └── DataSet7.4rsm.RData ├── docs ├── reference │ ├── Exam1.1-1.png │ ├── Exam1.1-2.png │ ├── Exam1.2-1.png │ ├── Exam7.1-1.png │ ├── Exam7.2-1.png │ ├── Exam7.3-1.png │ ├── Exam7.7-1.png │ ├── Exam8.2-1.png │ ├── Exam8.3-1.png │ ├── Exam8.3-2.png │ ├── Exam8.3-3.png │ ├── Exam7.6.2.1-1.png │ └── Exam7.6.2.1-2.png ├── deps │ ├── font-awesome-6.4.2 │ │ └── webfonts │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.woff2 │ │ │ ├── fa-v4compatibility.ttf │ │ │ └── fa-v4compatibility.woff2 │ ├── bootstrap-5.3.1 │ │ └── fonts │ │ │ ├── 4iCs6KVjbNBYlgoKfw72.woff2 │ │ │ ├── KFOmCnqEu92Fr1Mu4mxK.woff2 │ │ │ ├── S6u8w4BMUTPHjxsAXC-q.woff2 │ │ │ ├── S6uyw4BMUTPHjx4wXg.woff2 │ │ │ ├── S6uyw4BMUTPHjxAwXjeu.woff2 │ │ │ ├── XRXV3I6Li01BKofINeaB.woff2 │ │ │ ├── q5uGsou0JOdh94bfvQlt.woff2 │ │ │ ├── 1Ptug8zYS_SKggPNyC0ITw.woff2 │ │ │ ├── S6u9w4BMUTPHh6UVSwiPGQ.woff2 │ │ │ ├── S6u9w4BMUTPHh7USSwiPGQ.woff2 │ │ │ ├── 1Ptug8zYS_SKggPNyCAIT5lu.woff2 │ │ │ ├── 1Ptug8zYS_SKggPNyCIIT5lu.woff2 │ │ │ ├── 1Ptug8zYS_SKggPNyCMIT5lu.woff2 │ │ │ ├── 1Ptug8zYS_SKggPNyCkIT5lu.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKcQ72j00.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKcg72j00.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKcw72j00.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKew72j00.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKfA72j00.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjsGyN.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmEU9fBBc4.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmSU5fBBc4.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmWUlfBBc4.woff2 │ │ │ ├── KFOmCnqEu92Fr1Mu4WxKOzY.woff2 │ │ │ ├── KFOmCnqEu92Fr1Mu5mxKOzY.woff2 │ │ │ ├── KFOmCnqEu92Fr1Mu72xKOzY.woff2 │ │ │ ├── KFOmCnqEu92Fr1Mu7GxKOzY.woff2 │ │ │ ├── KFOmCnqEu92Fr1Mu7WxKOzY.woff2 │ │ │ ├── KFOmCnqEu92Fr1Mu7mxKOzY.woff2 │ │ │ ├── S6u8w4BMUTPHjxsAUi-qJCY.woff2 │ │ │ ├── S6u9w4BMUTPHh6UVSwaPGR_p.woff2 │ │ │ ├── S6u9w4BMUTPHh7USSwaPGR_p.woff2 │ │ │ ├── XRXV3I6Li01BKofIMeaBXso.woff2 │ │ │ ├── XRXV3I6Li01BKofIO-aBXso.woff2 │ │ │ ├── XRXV3I6Li01BKofIOOaBXso.woff2 │ │ │ ├── XRXV3I6Li01BKofIOuaBXso.woff2 │ │ │ ├── q5uGsou0JOdh94bfuQltOxU.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjs2yNL4U.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjtGyNL4U.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjvGyNL4U.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjvWyNL4U.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjvmyNL4U.woff2 │ │ │ ├── CSR64z1Qlv-GDxkbKVQ_fOAKTQ.woff2 │ │ │ ├── JTUSjIg1_i6t8kCHKm459Wlhyw.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmEU9fABc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmEU9fBxc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmEU9fCBc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmEU9fCRc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmEU9fChc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmEU9fCxc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmSU5fABc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmSU5fBxc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmSU5fCBc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmSU5fCRc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmSU5fChc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmSU5fCxc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmWUlfABc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmWUlfBxc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmWUlfCBc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmWUlfCRc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmWUlfChc4EsA.woff2 │ │ │ ├── KFOlCnqEu92Fr1MmWUlfCxc4EsA.woff2 │ │ │ ├── CSR54z1Qlv-GDxkbKVQ_dFsvWNReuQ.woff2 │ │ │ ├── CSR64z1Qlv-GDxkbKVQ_fO4KTet_.woff2 │ │ │ ├── JTUSjIg1_i6t8kCHKm459W1hyzbi.woff2 │ │ │ ├── JTUSjIg1_i6t8kCHKm459WRhyzbi.woff2 │ │ │ ├── JTUSjIg1_i6t8kCHKm459WZhyzbi.woff2 │ │ │ ├── JTUSjIg1_i6t8kCHKm459Wdhyzbi.woff2 │ │ │ ├── QGYpz_kZZAGCONcK2A4bGOj8mNhN.woff2 │ │ │ ├── 07d40e985ad7c747025dabb9f22142c4.woff2 │ │ │ ├── 1f5e011d6aae0d98fc0518e1a303e99a.woff2 │ │ │ ├── 626330658504e338ee86aec8e957426b.woff2 │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qOK7l.woff2 │ │ │ ├── CSR54z1Qlv-GDxkbKVQ_dFsvWNpeudwk.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlPevW.woff2 │ │ │ ├── c2f002b3a87d3f9bfeebb23d32cfd9f8.woff2 │ │ │ ├── ee91700cdbf7ce16c054c2bb8946c736.woff2 │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7nsDI.woff2 │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qN67lqDY.woff2 │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qNK7lqDY.woff2 │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qNa7lqDY.woff2 │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qNq7lqDY.woff2 │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qO67lqDY.woff2 │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qPK7lqDY.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvUlMI.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlM-vWjMY.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlMOvWjMY.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlMevWjMY.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlMuvWjMY.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlOevWjMY.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlPuvWjMY.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwlxdu.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdu.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlxdu.woff2 │ │ │ ├── UcC73FwrK3iLTeHuS_fvQtMwCp50KnMa1ZL7.woff2 │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7jsDJT9g.woff2 │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7ksDJT9g.woff2 │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7osDJT9g.woff2 │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7psDJT9g.woff2 │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7qsDJT9g.woff2 │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7rsDJT9g.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwkxduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwlBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmRduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmhduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmxduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwkxduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmRduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmhduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmxduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwkxduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmRduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmhduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmxduz8A.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvQlMIXxw.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvXlMIXxw.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvYlMIXxw.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvZlMIXxw.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvalMIXxw.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvblMIXxw.woff2 │ │ │ ├── UcC73FwrK3iLTeHuS_fvQtMwCp50KnMa0ZL7SUc.woff2 │ │ │ ├── UcC73FwrK3iLTeHuS_fvQtMwCp50KnMa1pL7SUc.woff2 │ │ │ ├── UcC73FwrK3iLTeHuS_fvQtMwCp50KnMa25L7SUc.woff2 │ │ │ ├── UcC73FwrK3iLTeHuS_fvQtMwCp50KnMa2JL7SUc.woff2 │ │ │ ├── UcC73FwrK3iLTeHuS_fvQtMwCp50KnMa2ZL7SUc.woff2 │ │ │ ├── UcC73FwrK3iLTeHuS_fvQtMwCp50KnMa2pL7SUc.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS-muw.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuU6F.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 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqW106F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWt06F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtE6F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtU6F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtk6F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWu06F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuk6F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWvU6F15M.woff2 │ │ │ └── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWxU6F15M.woff2 │ ├── headroom-0.11.0 │ │ └── jQuery.headroom.min.js │ ├── data-deps.txt │ └── bootstrap-toc-1.0.1 │ │ └── bootstrap-toc.min.js ├── pkgdown.yml ├── katex-auto.js ├── link.svg ├── jquery.sticky-kit.min.js └── lightswitch.js ├── CRAN-SUBMISSION ├── .Rbuildignore ├── NEWS.md ├── StroupGLMM.Rproj ├── inst └── CITATION ├── R ├── DataSet7.4.R ├── DataSet7.7.R ├── DataSet7.4rsm.R ├── DataSet7.1.R ├── DataSet7.2.R ├── DataSet7.3.R ├── DataSet7.6.R ├── DataSet9.1.R ├── DataSet9.4.R ├── DataSet8.1.R ├── DataSet9.2.R ├── DataExam2.B.3.R ├── Exam9.4.R ├── Table1.1.R ├── DataSet5.1.R ├── DataSet8.2.R ├── DataSet8.3.R ├── DataSet8.4.R ├── DataExam2.B.7.R ├── DataSet5.2.R ├── DataExam2.B.4.R ├── DataExam2.B.2.R ├── DataSet4.1.R ├── DataSet3.1.R ├── DataSet3.3.R ├── Table1.2.R ├── Exam8.1.R ├── Exam8.4.R ├── Exam1.2.R ├── Exam2.B.1.R ├── Exam2.B.2.R ├── DataSet3.2.R ├── Exam7.7.R ├── Exam2.B.6.R ├── Exam4.1.R ├── Exam2.B.3.R ├── Exam2.B.4.R ├── Exam8.2.R ├── Exam9.2.R ├── Exam5.3.R ├── Exam9.1.R ├── Exam7.3.R ├── Exam3.2.R ├── Exam3.5.R ├── Exam7.2.R ├── Exam2.B.5.R ├── Exam5.2.R └── Exam2.B.7.R ├── NAMESPACE ├── man ├── DataSet7.4.Rd ├── DataSet7.7.Rd ├── DataSet7.4rsm.Rd ├── DataSet7.1.Rd ├── DataSet7.2.Rd ├── DataSet7.3.Rd ├── DataSet7.6.Rd ├── DataSet9.1.Rd ├── Exam9.4.Rd ├── DataSet9.4.Rd ├── DataSet8.1.Rd ├── DataSet9.2.Rd ├── Table1.1.Rd ├── DataExam2.B.3.Rd ├── DataSet8.3.Rd ├── DataExam2.B.2.Rd ├── DataSet8.2.Rd ├── DataSet5.1.Rd ├── DataSet8.4.Rd ├── Exam8.1.Rd ├── DataSet5.2.Rd ├── DataExam2.B.7.Rd ├── DataExam2.B.4.Rd ├── DataSet4.1.Rd ├── Exam8.4.Rd ├── DataSet3.1.Rd ├── DataSet3.3.Rd ├── Table1.2.Rd ├── Exam1.2.Rd ├── Exam2.B.1.Rd ├── Exam2.B.2.Rd ├── Exam2.B.6.Rd ├── Exam7.7.Rd ├── Exam4.1.Rd ├── DataSet3.2.Rd ├── Exam2.B.3.Rd ├── Exam2.B.4.Rd ├── Exam8.2.Rd ├── Exam9.2.Rd ├── Exam5.3.Rd ├── Exam9.1.Rd ├── Exam7.3.Rd ├── Exam3.2.Rd ├── Exam3.5.Rd ├── Exam7.2.Rd ├── Exam2.B.5.Rd ├── Exam5.2.Rd └── Exam2.B.7.Rd └── DESCRIPTION /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | .Ruserdata 5 | packrat/lib*/ 6 | -------------------------------------------------------------------------------- /data/Table1.1.RData: 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-------------------------------------------------------------------------------- /docs/pkgdown.yml: -------------------------------------------------------------------------------- 1 | pandoc: '3.2' 2 | pkgdown: 2.1.1.9000 3 | pkgdown_sha: 0a18bc718640aee7160a0ebbcdef5ecaae2ac4a4 4 | articles: {} 5 | last_built: 2024-10-02T04:46Z 6 | urls: 7 | reference: https://myaseen208.com/StroupGLMM/reference 8 | article: https://myaseen208.com/StroupGLMM/articles 9 | -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- 1 | # Changes in StroupGLMM Version 0.3.0 2 | ## New Features 3 | 4 | * Added Chapters 8 and 9 5 | 6 | # Changes in StroupGLMM Version 0.2.0 7 | ## New Features 8 | 9 | * Revised the code and documentation 10 | * Updated the DESCRIPTION file to fulfill the requirements of CRAN 11 | 12 | # Changes in StroupGLMM Version 0.1.0 13 | ## New Features 14 | 15 | * First version of StroupGLMM 16 | -------------------------------------------------------------------------------- /StroupGLMM.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: knitr 13 | LaTeX: pdfLaTeX 14 | 15 | AutoAppendNewline: Yes 16 | StripTrailingWhitespace: Yes 17 | 18 | BuildType: Package 19 | PackageUseDevtools: Yes 20 | PackageInstallArgs: --no-multiarch --with-keep.source 21 | PackageRoxygenize: rd,collate,namespace,vignette 22 | -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- 1 | bibentry( 2 | "manual", 3 | header = "Please, support this project by citing it in your publications!", 4 | title = "StroupGLMM: R Codes and Datasets for Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup", 5 | author = c( 6 | person(c("Muhammad"), "Yaseen") 7 | , person(c("Adeela"), "Munawar") 8 | , person(c("Walter", "W."), "Stroup") 9 | , person(c("Kent", "M."), "Eskridge") 10 | ), 11 | year = 2016, 12 | journal = "The Comprehensive R Archive Network (CRAN)" 13 | ) 14 | -------------------------------------------------------------------------------- /docs/deps/headroom-0.11.0/jQuery.headroom.min.js: -------------------------------------------------------------------------------- 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); -------------------------------------------------------------------------------- /R/DataSet7.4.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 7.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet7.4 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet7.4) 6 | #' @author \enumerate{ 7 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 8 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 9 | #' } 10 | #' @references \enumerate{ 11 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 12 | #' CRC press. 13 | #' } 14 | #' 15 | #' @examples 16 | #' data(DataSet7.4) 17 | NULL 18 | -------------------------------------------------------------------------------- /R/DataSet7.7.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 7.7 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet7.7 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet7.7) 6 | #' @author \enumerate{ 7 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 8 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 9 | #' } 10 | #' @references \enumerate{ 11 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 12 | #' CRC press. 13 | #' } 14 | #' 15 | #' @examples 16 | #' data(DataSet7.7) 17 | NULL 18 | -------------------------------------------------------------------------------- /docs/katex-auto.js: -------------------------------------------------------------------------------- 1 | // https://github.com/jgm/pandoc/blob/29fa97ab96b8e2d62d48326e1b949a71dc41f47a/src/Text/Pandoc/Writers/HTML.hs#L332-L345 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 | -------------------------------------------------------------------------------- /R/DataSet7.4rsm.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 7.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet7.4rsm 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet7.4rsm) 6 | #' @author \enumerate{ 7 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 8 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 9 | #' } 10 | #' @references \enumerate{ 11 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 12 | #' CRC press. 13 | #' } 14 | #' 15 | #' @examples 16 | #' data(DataSet7.4rsm) 17 | NULL 18 | -------------------------------------------------------------------------------- /R/DataSet7.1.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 7.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet7.1 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet7.1) 6 | #' @author \enumerate{ 7 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 8 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 9 | #' } 10 | #' @references \enumerate{ 11 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 12 | #' CRC press. 13 | #' } 14 | #' @seealso 15 | #' \code{\link{Exam7.1}} 16 | #' @examples 17 | #' data(DataSet7.1) 18 | NULL 19 | -------------------------------------------------------------------------------- /R/DataSet7.2.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 7.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet7.2 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet7.2) 6 | #' @author \enumerate{ 7 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 8 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 9 | #' } 10 | #' @references \enumerate{ 11 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 12 | #' CRC press. 13 | #' } 14 | #' @seealso 15 | #' \code{\link{Exam7.2}} 16 | #' @examples 17 | #' data(DataSet7.2) 18 | NULL 19 | -------------------------------------------------------------------------------- /R/DataSet7.3.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 7.3 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet7.3 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet7.3) 6 | #' @author \enumerate{ 7 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 8 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 9 | #' } 10 | #' @references \enumerate{ 11 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 12 | #' CRC press. 13 | #' } 14 | #' @seealso 15 | #' \code{\link{Exam7.3}} 16 | #' @examples 17 | #' data(DataSet7.3) 18 | NULL 19 | -------------------------------------------------------------------------------- /R/DataSet7.6.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 7.6 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet7.6 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet7.6) 6 | #' @author \enumerate{ 7 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 8 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 9 | #' } 10 | #' @references \enumerate{ 11 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 12 | #' CRC press. 13 | #' } 14 | #' @seealso 15 | #' \code{\link{Exam7.6.2.1}} 16 | #' @examples 17 | #' data(DataSet7.6) 18 | NULL 19 | -------------------------------------------------------------------------------- /docs/link.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 5 | 8 | 12 | 13 | -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- 1 | # Generated by roxygen2: do not edit by hand 2 | 3 | import(broom.mixed) 4 | import(dplyr) 5 | import(emmeans) 6 | import(ggplot2) 7 | import(lattice) 8 | import(lmerTest) 9 | import(magrittr) 10 | import(parameters) 11 | import(phia) 12 | import(scatterplot3d) 13 | import(splines) 14 | importFrom(MASS,glmmPQL) 15 | importFrom(aod,wald.test) 16 | importFrom(car,Anova) 17 | importFrom(car,linearHypothesis) 18 | importFrom(ggplot2,ggplot) 19 | importFrom(mutoss,sidak) 20 | importFrom(nlme,lme) 21 | importFrom(phia,testFactors) 22 | importFrom(phia,testInteractions) 23 | importFrom(stats,anova) 24 | importFrom(stats,coef) 25 | importFrom(stats,cor) 26 | importFrom(stats,glm) 27 | importFrom(stats,lm) 28 | importFrom(stats,lm.fit) 29 | importFrom(stats,model.matrix) 30 | importFrom(stats,summary.glm) 31 | importFrom(stats,summary.lm) 32 | importFrom(survey,svydesign) 33 | importFrom(survey,svyglm) 34 | -------------------------------------------------------------------------------- /man/DataSet7.4.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet7.4.R 3 | \docType{data} 4 | \name{DataSet7.4} 5 | \alias{DataSet7.4} 6 | \title{Data for Example 7.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \usage{ 8 | data(DataSet7.4) 9 | } 10 | \description{ 11 | Data for Example 7.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 12 | } 13 | \examples{ 14 | data(DataSet7.4) 15 | } 16 | \references{ 17 | \enumerate{ 18 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 19 | CRC press. 20 | } 21 | } 22 | \author{ 23 | \enumerate{ 24 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 25 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 26 | } 27 | } 28 | \keyword{datasets} 29 | -------------------------------------------------------------------------------- /man/DataSet7.7.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet7.7.R 3 | \docType{data} 4 | \name{DataSet7.7} 5 | \alias{DataSet7.7} 6 | \title{Data for Example 7.7 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \usage{ 8 | data(DataSet7.7) 9 | } 10 | \description{ 11 | Data for Example 7.7 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 12 | } 13 | \examples{ 14 | data(DataSet7.7) 15 | } 16 | \references{ 17 | \enumerate{ 18 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 19 | CRC press. 20 | } 21 | } 22 | \author{ 23 | \enumerate{ 24 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 25 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 26 | } 27 | } 28 | \keyword{datasets} 29 | -------------------------------------------------------------------------------- /docs/deps/data-deps.txt: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | -------------------------------------------------------------------------------- /man/DataSet7.4rsm.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet7.4rsm.R 3 | \docType{data} 4 | \name{DataSet7.4rsm} 5 | \alias{DataSet7.4rsm} 6 | \title{Data for Example 7.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \usage{ 8 | data(DataSet7.4rsm) 9 | } 10 | \description{ 11 | Data for Example 7.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 12 | } 13 | \examples{ 14 | data(DataSet7.4rsm) 15 | } 16 | \references{ 17 | \enumerate{ 18 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 19 | CRC press. 20 | } 21 | } 22 | \author{ 23 | \enumerate{ 24 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 25 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 26 | } 27 | } 28 | \keyword{datasets} 29 | -------------------------------------------------------------------------------- /R/DataSet9.1.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 9.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet9.1 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet9.1) 6 | #' @description DataSet9.1 is used for One-way random effects only model 7 | #' @format A \code{data.frame} with 24 rows and 2 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item a is a factor with 12 levels 11 | #' \item y is a Gaussian response variable 12 | #' } 13 | #' @author Muhammad Yaseen (\email{myaseen208@@gmail.com}) 14 | #' Adeela Munawar (\email{adeela.uaf@@gmail.com}) 15 | #' @references \enumerate{ 16 | #' \item Stroup, W. W. (2012).\emph{Generalized linear Mixed Models: Modern Concepts, Methods and Applications}. 17 | #' CRC press. 18 | #' } 19 | #' @seealso 20 | #' \code{\link{Exam9.1}} 21 | #' @examples 22 | #' data(DataSet9.1) 23 | NULL -------------------------------------------------------------------------------- /man/DataSet7.1.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet7.1.R 3 | \docType{data} 4 | \name{DataSet7.1} 5 | \alias{DataSet7.1} 6 | \title{Data for Example 7.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \usage{ 8 | data(DataSet7.1) 9 | } 10 | \description{ 11 | Data for Example 7.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 12 | } 13 | \examples{ 14 | data(DataSet7.1) 15 | } 16 | \references{ 17 | \enumerate{ 18 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 19 | CRC press. 20 | } 21 | } 22 | \seealso{ 23 | \code{\link{Exam7.1}} 24 | } 25 | \author{ 26 | \enumerate{ 27 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 28 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 29 | } 30 | } 31 | \keyword{datasets} 32 | -------------------------------------------------------------------------------- /man/DataSet7.2.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet7.2.R 3 | \docType{data} 4 | \name{DataSet7.2} 5 | \alias{DataSet7.2} 6 | \title{Data for Example 7.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \usage{ 8 | data(DataSet7.2) 9 | } 10 | \description{ 11 | Data for Example 7.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 12 | } 13 | \examples{ 14 | data(DataSet7.2) 15 | } 16 | \references{ 17 | \enumerate{ 18 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 19 | CRC press. 20 | } 21 | } 22 | \seealso{ 23 | \code{\link{Exam7.2}} 24 | } 25 | \author{ 26 | \enumerate{ 27 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 28 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 29 | } 30 | } 31 | \keyword{datasets} 32 | -------------------------------------------------------------------------------- /man/DataSet7.3.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet7.3.R 3 | \docType{data} 4 | \name{DataSet7.3} 5 | \alias{DataSet7.3} 6 | \title{Data for Example 7.3 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \usage{ 8 | data(DataSet7.3) 9 | } 10 | \description{ 11 | Data for Example 7.3 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 12 | } 13 | \examples{ 14 | data(DataSet7.3) 15 | } 16 | \references{ 17 | \enumerate{ 18 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 19 | CRC press. 20 | } 21 | } 22 | \seealso{ 23 | \code{\link{Exam7.3}} 24 | } 25 | \author{ 26 | \enumerate{ 27 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 28 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 29 | } 30 | } 31 | \keyword{datasets} 32 | -------------------------------------------------------------------------------- /man/DataSet7.6.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet7.6.R 3 | \docType{data} 4 | \name{DataSet7.6} 5 | \alias{DataSet7.6} 6 | \title{Data for Example 7.6 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \usage{ 8 | data(DataSet7.6) 9 | } 10 | \description{ 11 | Data for Example 7.6 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 12 | } 13 | \examples{ 14 | data(DataSet7.6) 15 | } 16 | \references{ 17 | \enumerate{ 18 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 19 | CRC press. 20 | } 21 | } 22 | \seealso{ 23 | \code{\link{Exam7.6.2.1}} 24 | } 25 | \author{ 26 | \enumerate{ 27 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 28 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 29 | } 30 | } 31 | \keyword{datasets} 32 | -------------------------------------------------------------------------------- /R/DataSet9.4.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 9.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet9.4 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet9.4) 6 | #' @description DataSet9.4 is used for Relationship between BLUP and Fixed Effect Estimators 7 | #' @format A \code{data.frame} with 32 rows and 3 variables 8 | #' @details 9 | #' \itemize{ 10 | #' \item a is a factor with 2 levels 11 | #' \item b is a factor with 8 levels 12 | #' \item y is a Gaussian response variable 13 | #' } 14 | #' @author Muhammad Yaseen (\email{myaseen208@@gmail.com}) 15 | #' Adeela Munawar (\email{adeela.uaf@@gmail.com}) 16 | #' @references \enumerate{ 17 | #' \item Stroup, W. W. (2012).\emph{Generalized linear Mixed Models: Modern Concepts, Methods and Applications}. 18 | #' CRC press. 19 | #' } 20 | #' @seealso 21 | #' \code{\link{Exam9.4}} 22 | #' @examples 23 | #' data(DataSet9.4) 24 | NULL -------------------------------------------------------------------------------- /R/DataSet8.1.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 8.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet8.1 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet8.1) 6 | #' @description DataSet8.1 is used for Nested factorial structure 7 | #' @format A \code{data.frame} with 30 rows and 4 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item block 10 blocks 11 | #' \item trt 6 treatments nested within sets 12 | #' \item set 2 sets 13 | #' \item y is a Gaussian response variable 14 | #' } 15 | #' @author Muhammad Yaseen (\email{myaseen208@@gmail.com}) 16 | #' Adeela Munawar (\email{adeela.uaf@@gmail.com}) 17 | #' @references \enumerate{ 18 | #' \item Stroup, W. W. (2012).\emph{Generalized linear Mixed Models: Modern Concepts, Methods and Applications}. 19 | #' CRC press. 20 | #' } 21 | #' @seealso 22 | #' \code{\link{Exam8.1}} 23 | #' @examples 24 | #' data(DataSet8.1) 25 | NULL -------------------------------------------------------------------------------- /R/DataSet9.2.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 9.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet9.2 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet9.2) 6 | #' @description DataSet9.2 is used for Two way random effects nested model 7 | #' @format A \code{data.frame} with 28 rows and 3 variables with levels of b nested within levels of. 8 | #' @details 9 | #' \itemize{ 10 | #' \item a is a factor with 7 levels 11 | #' \item b is a factor with 2 levels 12 | #' \item y is a Gaussian response variable 13 | #' } 14 | #' @author Muhammad Yaseen (\email{myaseen208@@gmail.com}) 15 | #' Adeela Munawar (\email{adeela.uaf@@gmail.com}) 16 | #' @references \enumerate{ 17 | #' \item Stroup, W. W. (2012).\emph{Generalized linear Mixed Models: Modern Concepts, Methods and Applications}. 18 | #' CRC press. 19 | #' } 20 | #' @seealso 21 | #' \code{\link{Exam9.2}} 22 | #' @examples 23 | #' data(DataSet9.2) 24 | NULL -------------------------------------------------------------------------------- /R/DataExam2.B.3.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 2.B.3 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-55) 2 | #' @name DataExam2.B.3 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataExam2.B.3) 6 | #' @description Exam2.B.3 is used to illustrate one way treatment design with Gaussian observations. 7 | #' @format A \code{data.frame} with 6 rows and 2 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item trt treatments as factor with number 1 to 3 11 | #' \item y response variable 12 | #' } 13 | #' @author \enumerate{ 14 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 15 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 16 | #' } 17 | #' @references \enumerate{ 18 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 19 | #' CRC press. 20 | #' } 21 | #' @seealso 22 | #' \code{\link{Exam2.B.3}} 23 | #' @examples 24 | #' data(DataExam2.B.3) 25 | NULL 26 | -------------------------------------------------------------------------------- /man/DataSet9.1.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet9.1.R 3 | \docType{data} 4 | \name{DataSet9.1} 5 | \alias{DataSet9.1} 6 | \title{Data for Example 9.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \format{ 8 | A \code{data.frame} with 24 rows and 2 variables. 9 | } 10 | \usage{ 11 | data(DataSet9.1) 12 | } 13 | \description{ 14 | DataSet9.1 is used for One-way random effects only model 15 | } 16 | \details{ 17 | \itemize{ 18 | \item a is a factor with 12 levels 19 | \item y is a Gaussian response variable 20 | } 21 | } 22 | \examples{ 23 | data(DataSet9.1) 24 | } 25 | \references{ 26 | \enumerate{ 27 | \item Stroup, W. W. (2012).\emph{Generalized linear Mixed Models: Modern Concepts, Methods and Applications}. 28 | CRC press. 29 | } 30 | } 31 | \seealso{ 32 | \code{\link{Exam9.1}} 33 | } 34 | \author{ 35 | Muhammad Yaseen (\email{myaseen208@gmail.com}) 36 | Adeela Munawar (\email{adeela.uaf@gmail.com}) 37 | } 38 | \keyword{datasets} 39 | -------------------------------------------------------------------------------- /R/Exam9.4.R: -------------------------------------------------------------------------------- 1 | #' @title Example 9.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-288) 2 | #' @name Exam9.4 3 | #' @description Exam9.4 Relationship between BLUP and Fixed Effect Estimators 4 | #' @author \enumerate{ 5 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 6 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 7 | #' } 8 | #' @references \enumerate{ 9 | #' \item Stroup, W. W. (2012). 10 | #' \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 11 | #' CRC Press. 12 | #' } 13 | #' 14 | #' @seealso 15 | #' \code{\link{DataSet9.4}} 16 | #' 17 | #' @import emmeans lmerTest 18 | #' 19 | #' @examples 20 | #' data(DataSet9.4) 21 | #' DataSet9.4$a <- factor(x = DataSet9.4$a) 22 | #' DataSet9.4$b <- factor(x = DataSet9.4$b) 23 | #' 24 | #' library(lmerTest) 25 | #' Exam9.4lmer <- lmer(y ~ a + (1|b) + (1|a/b), data = DataSet9.4) 26 | #' summary(Exam9.4lmer) 27 | #' library(emmeans) 28 | #' emmeans(Exam9.4lmer, spec = ~a) 29 | #' 30 | NULL 31 | 32 | 33 | -------------------------------------------------------------------------------- /man/Exam9.4.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam9.4.R 3 | \name{Exam9.4} 4 | \alias{Exam9.4} 5 | \title{Example 9.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-288)} 6 | \description{ 7 | Exam9.4 Relationship between BLUP and Fixed Effect Estimators 8 | } 9 | \examples{ 10 | data(DataSet9.4) 11 | DataSet9.4$a <- factor(x = DataSet9.4$a) 12 | DataSet9.4$b <- factor(x = DataSet9.4$b) 13 | 14 | library(lmerTest) 15 | Exam9.4lmer <- lmer(y ~ a + (1|b) + (1|a/b), data = DataSet9.4) 16 | summary(Exam9.4lmer) 17 | library(emmeans) 18 | emmeans(Exam9.4lmer, spec = ~a) 19 | 20 | } 21 | \references{ 22 | \enumerate{ 23 | \item Stroup, W. W. (2012). 24 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 25 | CRC Press. 26 | } 27 | } 28 | \seealso{ 29 | \code{\link{DataSet9.4}} 30 | } 31 | \author{ 32 | \enumerate{ 33 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 34 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 35 | } 36 | } 37 | -------------------------------------------------------------------------------- /R/Table1.1.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Table1.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name Table1.1 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(Table1.1) 6 | #' @description \code{Table1.1} is used for inspecting probability distribution and to define a plausible process. 7 | #' @format A \code{data.frame} with 11 rows and 3 variables. 8 | #' 9 | #' @details 10 | #' \itemize{ 11 | #' \item x independent variable 12 | #' \item Nx bernouli trials (bernouli outcomes on each individual) 13 | #' \item y number of successes on each individual 14 | #' } 15 | #' 16 | #' @author 17 | #' \enumerate{ 18 | #' \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 19 | #' \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 20 | #' } 21 | #' 22 | #' @references 23 | #' \enumerate{ 24 | #' \item Stroup, W. W. (2012).Generalized linear mixed models: modern concepts, methods and applications. 25 | #' CRC press. 26 | #' } 27 | #' 28 | #' 29 | #' @examples 30 | #' library(StroupGLMM) 31 | #' data(Table1.1) 32 | NULL 33 | -------------------------------------------------------------------------------- /man/DataSet9.4.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet9.4.R 3 | \docType{data} 4 | \name{DataSet9.4} 5 | \alias{DataSet9.4} 6 | \title{Data for Example 9.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \format{ 8 | A \code{data.frame} with 32 rows and 3 variables 9 | } 10 | \usage{ 11 | data(DataSet9.4) 12 | } 13 | \description{ 14 | DataSet9.4 is used for Relationship between BLUP and Fixed Effect Estimators 15 | } 16 | \details{ 17 | \itemize{ 18 | \item a is a factor with 2 levels 19 | \item b is a factor with 8 levels 20 | \item y is a Gaussian response variable 21 | } 22 | } 23 | \examples{ 24 | data(DataSet9.4) 25 | } 26 | \references{ 27 | \enumerate{ 28 | \item Stroup, W. W. (2012).\emph{Generalized linear Mixed Models: Modern Concepts, Methods and Applications}. 29 | CRC press. 30 | } 31 | } 32 | \seealso{ 33 | \code{\link{Exam9.4}} 34 | } 35 | \author{ 36 | Muhammad Yaseen (\email{myaseen208@gmail.com}) 37 | Adeela Munawar (\email{adeela.uaf@gmail.com}) 38 | } 39 | \keyword{datasets} 40 | -------------------------------------------------------------------------------- /man/DataSet8.1.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet8.1.R 3 | \docType{data} 4 | \name{DataSet8.1} 5 | \alias{DataSet8.1} 6 | \title{Data for Example 8.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \format{ 8 | A \code{data.frame} with 30 rows and 4 variables. 9 | } 10 | \usage{ 11 | data(DataSet8.1) 12 | } 13 | \description{ 14 | DataSet8.1 is used for Nested factorial structure 15 | } 16 | \details{ 17 | \itemize{ 18 | \item block 10 blocks 19 | \item trt 6 treatments nested within sets 20 | \item set 2 sets 21 | \item y is a Gaussian response variable 22 | } 23 | } 24 | \examples{ 25 | data(DataSet8.1) 26 | } 27 | \references{ 28 | \enumerate{ 29 | \item Stroup, W. W. (2012).\emph{Generalized linear Mixed Models: Modern Concepts, Methods and Applications}. 30 | CRC press. 31 | } 32 | } 33 | \seealso{ 34 | \code{\link{Exam8.1}} 35 | } 36 | \author{ 37 | Muhammad Yaseen (\email{myaseen208@gmail.com}) 38 | Adeela Munawar (\email{adeela.uaf@gmail.com}) 39 | } 40 | \keyword{datasets} 41 | -------------------------------------------------------------------------------- /R/DataSet5.1.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 5.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet5.1 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet5.1) 6 | #' @description DataSet5.1 is used for polynomial multiple regression 7 | #' @format A \code{data.frame} with 14 rows and 3 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item X is predictor variable with level 0, 1, 2, 4, 8, 12, 16 11 | #' \item N is the number of independent bernoulli trials for a given observation 12 | #' \item F is the number of "successes"(N and F specify a binomial response) 13 | #' } 14 | #' @author \enumerate{ 15 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 16 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 17 | #' } 18 | #' @references \enumerate{ 19 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 20 | #' CRC press. 21 | #' } 22 | #' @seealso 23 | #' \code{\link{Exam5.1}} 24 | #' @examples 25 | #' data(DataSet5.1) 26 | NULL 27 | -------------------------------------------------------------------------------- /man/DataSet9.2.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet9.2.R 3 | \docType{data} 4 | \name{DataSet9.2} 5 | \alias{DataSet9.2} 6 | \title{Data for Example 9.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \format{ 8 | A \code{data.frame} with 28 rows and 3 variables with levels of b nested within levels of. 9 | } 10 | \usage{ 11 | data(DataSet9.2) 12 | } 13 | \description{ 14 | DataSet9.2 is used for Two way random effects nested model 15 | } 16 | \details{ 17 | \itemize{ 18 | \item a is a factor with 7 levels 19 | \item b is a factor with 2 levels 20 | \item y is a Gaussian response variable 21 | } 22 | } 23 | \examples{ 24 | data(DataSet9.2) 25 | } 26 | \references{ 27 | \enumerate{ 28 | \item Stroup, W. W. (2012).\emph{Generalized linear Mixed Models: Modern Concepts, Methods and Applications}. 29 | CRC press. 30 | } 31 | } 32 | \seealso{ 33 | \code{\link{Exam9.2}} 34 | } 35 | \author{ 36 | Muhammad Yaseen (\email{myaseen208@gmail.com}) 37 | Adeela Munawar (\email{adeela.uaf@gmail.com}) 38 | } 39 | \keyword{datasets} 40 | -------------------------------------------------------------------------------- /R/DataSet8.2.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 8.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet8.2 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet8.2) 6 | #' @description DataSet8.2 is used for Incomplete strip-plot ( 3 cross 3 factorial). 7 | #' @format A \code{data.frame} with 36 rows and 6 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item block 9 blocks each consisting of 2 rows and 2 coloumns 11 | #' \item a is a factor with 3 levels assigned at random to rows 12 | #' \item b is a factor with 3 levels assigned at random to columns 13 | #' \item y is a Gaussian response variable 14 | #' } 15 | #' @author Muhammad Yaseen (\email{myaseen208@@gmail.com}) 16 | #' Adeela Munawar (\email{adeela.uaf@@gmail.com}) 17 | #' @references \enumerate{ 18 | #' \item Stroup, W. W. (2012).\emph{Generalized linear Mixed Models: Modern Concepts, Methods and Applications}. 19 | #' CRC press. 20 | #' } 21 | #' @seealso 22 | #' \code{\link{Exam8.2}} 23 | #' @examples 24 | #' data(DataSet8.2) 25 | NULL -------------------------------------------------------------------------------- /R/DataSet8.3.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 8.3 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet8.3 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet8.3) 6 | #' @description DataSet8.3 is used for Response surface design with incomplete blocking 7 | #' @format A \code{data.frame} with 28 rows and 4 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item block with 7 blocks 11 | #' \item a is a factor with 3 levels 0,-1 and 1 12 | #' \item b is a factor with 3 levels 0,-1 and 1 13 | #' \item c is a factor with 3 levels 0,-1 and 1 14 | #' \item y is a Gaussian response variable 15 | #' } 16 | #' @author Muhammad Yaseen (\email{myaseen208@@gmail.com}) 17 | #' Adeela Munawar (\email{adeela.uaf@@gmail.com}) 18 | #' @references \enumerate{ 19 | #' \item Stroup, W. W. (2012).\emph{Generalized linear Mixed Models: Modern Concepts, Methods and Applications}. 20 | #' CRC press. 21 | #' } 22 | #' @seealso 23 | #' \code{\link{Exam8.3}} 24 | #' @examples 25 | #' data(DataSet8.3) 26 | NULL -------------------------------------------------------------------------------- /R/DataSet8.4.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 8.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet8.4 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet8.4) 6 | #' @description DataSet8.4 is used for Multifactor treatment and Multilevel design structures 7 | #' @format A \code{data.frame} with 36 rows and 6 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item block 9 blocks each consisting of 2 rows and 2 coloumns 11 | #' \item a is a factor with 3 levels assigned at random to rows 12 | #' \item b is a factor with 3 levels assigned at random to columns 13 | #' \item y is a Gaussian response variable 14 | #' } 15 | #' @author Muhammad Yaseen (\email{myaseen208@@gmail.com}) 16 | #' Adeela Munawar (\email{adeela.uaf@@gmail.com}) 17 | #' @references \enumerate{ 18 | #' \item Stroup, W. W. (2012).\emph{Generalized linear Mixed Models: Modern Concepts, Methods and Applications}. 19 | #' CRC press. 20 | #' } 21 | #' @seealso 22 | #' \code{\link{Exam8.4}} 23 | #' @examples 24 | #' data(DataSet8.4) 25 | NULL -------------------------------------------------------------------------------- /R/DataExam2.B.7.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 2.B.7 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-60) 2 | #' @name DataExam2.B.7 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataExam2.B.7) 6 | #' @description Exam2.B.7 is related to multi batch regression data assuming different forms of linear models with factorial experiment. 7 | #' @format A \code{data.frame} with 16 rows and 4 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item Rep number of replications 11 | #' \item a factor with two levels 1 and 2 12 | #' \item b factor with two levels 1 and 2 13 | #' \item y response variable 14 | #' } 15 | #' @author \enumerate{ 16 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 17 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 18 | #' } 19 | #' @references \enumerate{ 20 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 21 | #' CRC press. 22 | #' } 23 | #' @seealso 24 | #' \code{\link{Exam2.B.7}} 25 | #' @examples 26 | #' data(DataExam2.B.7) 27 | NULL 28 | -------------------------------------------------------------------------------- /R/DataSet5.2.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 5.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet5.2 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet5.2) 6 | #' @description DataSet5.2 is used for three factor orthogonal main effects only design with sequential fitting of predictors 7 | #' @format A \code{data.frame} with 9 rows and 4 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item a is predictor variable with level 0, 1 11 | #' \item b is predictor variable with level 0, 1 12 | #' \item c is predictor variable with level 0, 1 13 | #' \item y response variable 14 | #' } 15 | #' @author \enumerate{ 16 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 17 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 18 | #' } 19 | #' @references \enumerate{ 20 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 21 | #' CRC press. 22 | #' } 23 | #' @seealso 24 | #' \code{\link{Exam5.2}} 25 | #' @examples 26 | #' data(DataSet5.2) 27 | NULL 28 | -------------------------------------------------------------------------------- /man/Table1.1.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Table1.1.R 3 | \docType{data} 4 | \name{Table1.1} 5 | \alias{Table1.1} 6 | \title{Data for Table1.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \format{ 8 | A \code{data.frame} with 11 rows and 3 variables. 9 | } 10 | \usage{ 11 | data(Table1.1) 12 | } 13 | \description{ 14 | \code{Table1.1} is used for inspecting probability distribution and to define a plausible process. 15 | } 16 | \details{ 17 | \itemize{ 18 | \item x independent variable 19 | \item Nx bernouli trials (bernouli outcomes on each individual) 20 | \item y number of successes on each individual 21 | } 22 | } 23 | \examples{ 24 | library(StroupGLMM) 25 | data(Table1.1) 26 | } 27 | \references{ 28 | \enumerate{ 29 | \item Stroup, W. W. (2012).Generalized linear mixed models: modern concepts, methods and applications. 30 | CRC press. 31 | } 32 | } 33 | \author{ 34 | \enumerate{ 35 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 36 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 37 | } 38 | } 39 | \keyword{datasets} 40 | -------------------------------------------------------------------------------- /man/DataExam2.B.3.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataExam2.B.3.R 3 | \docType{data} 4 | \name{DataExam2.B.3} 5 | \alias{DataExam2.B.3} 6 | \title{Data for Example 2.B.3 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-55)} 7 | \format{ 8 | A \code{data.frame} with 6 rows and 2 variables. 9 | } 10 | \usage{ 11 | data(DataExam2.B.3) 12 | } 13 | \description{ 14 | Exam2.B.3 is used to illustrate one way treatment design with Gaussian observations. 15 | } 16 | \details{ 17 | \itemize{ 18 | \item trt treatments as factor with number 1 to 3 19 | \item y response variable 20 | } 21 | } 22 | \examples{ 23 | data(DataExam2.B.3) 24 | } 25 | \references{ 26 | \enumerate{ 27 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 28 | CRC press. 29 | } 30 | } 31 | \seealso{ 32 | \code{\link{Exam2.B.3}} 33 | } 34 | \author{ 35 | \enumerate{ 36 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 37 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 38 | } 39 | } 40 | \keyword{datasets} 41 | -------------------------------------------------------------------------------- /R/DataExam2.B.4.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 2.B.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-54) 2 | #' @name DataExam2.B.4 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataExam2.B.4) 6 | #' @description Exam2.B.4 is used to illustrate one way treatment design with Binomial observations. 7 | #' @format A \code{data.frame} with 6 rows and 4 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item obs number of observations 11 | #' \item trt three treatments with class factor 12 | #' \item Nij number of bernouli trials on each individual 13 | #' \item y number of successes on each individual 14 | #' } 15 | #' @author \enumerate{ 16 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 17 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 18 | #' } 19 | #' @references \enumerate{ 20 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 21 | #' CRC press. 22 | #' } 23 | #' @seealso 24 | #' \code{\link{Exam2.B.4}} 25 | #' @examples 26 | #' data(DataExam2.B.4) 27 | NULL 28 | -------------------------------------------------------------------------------- /R/DataExam2.B.2.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 2.B.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-54) 2 | #' @name DataExam2.B.2 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataExam2.B.2) 6 | #' @description Exam2.B.2 is used to visualize the effect of glm model statement with binomial data with logit and probit links. 7 | #' @format A \code{data.frame} with 11 rows and 3 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item x independent variable 11 | #' \item n bernouli trials (bernouli outcomes on each individual) 12 | #' \item y number of successes on each individual 13 | #' } 14 | #' 15 | #' @author 16 | #' \enumerate{ 17 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 18 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 19 | #' } 20 | #' 21 | #' @references 22 | #' \enumerate{ 23 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 24 | #' CRC press. 25 | #' } 26 | #' 27 | #' @seealso 28 | #' \link{Exam2.B.2} 29 | #' 30 | #' @examples 31 | #' data(DataExam2.B.2) 32 | NULL 33 | -------------------------------------------------------------------------------- /R/DataSet4.1.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 4.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet4.1 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet4.1) 6 | #' @description DataSet4.1 comes from Cochran and Cox (1957) Experimental Design 7 | #' @format A \code{data.frame} with 60 rows and 3 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item blocks 15 blocks in an incomplete block desgin 11 | #' \item trt treatments representing incomplete block desgin 12 | #' \item y is continuous & may be assumed Gaussian 13 | #' } 14 | #' @author \enumerate{ 15 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 16 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 17 | #' } 18 | #' @references \enumerate{ 19 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 20 | #' CRC press. 21 | #' \item Cochran, W. G., & Cox, G. M. (1957). \emph{Experimental designs}. 22 | #' } 23 | #' @seealso 24 | #' \code{\link{Exam4.1}} 25 | #' @examples 26 | #' data(DataSet4.1) 27 | NULL 28 | -------------------------------------------------------------------------------- /R/DataSet3.1.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example 3.1 and Example 3.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet3.1 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet3.1) 6 | #' @description DataSet3.1 is used for linear and generalized linear models 7 | #' @format A \code{data.frame} with 20 rows and 5 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item trt two treatment 0 and 1 11 | #' \item rep unit of observation or observation ID 12 | #' \item Y is continuous & may be assumed Gaussian 13 | #' \item N is the number of obs 14 | #' \item F is the number of "successes"(N and F specify a binomial response) 15 | #' } 16 | #' @author \enumerate{ 17 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 18 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 19 | #' } 20 | #' @references \enumerate{ 21 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 22 | #' CRC press. 23 | #' } 24 | #' @seealso 25 | #' \code{\link{Exam3.2}} 26 | #' @examples 27 | #' data(DataSet3.1) 28 | NULL 29 | -------------------------------------------------------------------------------- /R/DataSet3.3.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Example3.7 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet3.3 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet3.3) 6 | #' @description Exam1.2 is used to see types of model effects by plotting regression data 7 | #' @format A \code{data.frame} with 36 rows and 6 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item X Each batch observed at several times:0,3,6,12,24,36,48 months 11 | #' \item Y continuous variable observed at each level of X 12 | #' \item Fav number of successes 13 | #' \item N isndependent bernoulli trials 14 | #' \item Batch Batches as 1, 2, 3, 4 15 | #' \item Count binomial response variable 16 | #' } 17 | #' @author \enumerate{ 18 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 19 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 20 | #' } 21 | #' @references \enumerate{ 22 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 23 | #' CRC press. 24 | #' } 25 | #' @examples 26 | #' data(DataSet3.3) 27 | NULL 28 | -------------------------------------------------------------------------------- /R/Table1.2.R: -------------------------------------------------------------------------------- 1 | #' @title Data for Table1.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-10) 2 | #' @name Table1.2 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(Table1.2) 6 | #' @description Exam1.2 is used to see types of model effects by plotting regression data 7 | #' @format A \code{data.frame} with 36 rows and 5 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item X have 11 levels in varying intervals from 0 to 48 observed for multiple batches 11 | #' \item Y continuous variable observed at each level of X 12 | #' \item Fav number of successes 13 | #' \item N number of bernoulli trials 14 | #' \item Batch Batches as 1, 2, 3, 4 15 | #' } 16 | #' @author \enumerate{ 17 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 18 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 19 | #' } 20 | #' @references \enumerate{ 21 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 22 | #' CRC press. 23 | #' } 24 | #' @seealso 25 | #' \code{\link{Exam1.2}} 26 | #' @examples 27 | #' data(Table1.2) 28 | NULL 29 | -------------------------------------------------------------------------------- /R/Exam8.1.R: -------------------------------------------------------------------------------- 1 | #' @title Example 8.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-250) 2 | #' @name Exam8.1 3 | #' @description Exam8.1 Nested factorial structure 4 | #' @author \enumerate{ 5 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 6 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 7 | #' } 8 | #' @references \enumerate{ 9 | #' \item Stroup, W. W. (2012). 10 | #' \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 11 | #' CRC Press. 12 | #' } 13 | #' 14 | #' @seealso 15 | #' \code{\link{DataSet8.1}} 16 | #' 17 | #' @import emmeans lmerTest 18 | #' @examples 19 | #' 20 | #' data(DataSet8.1) 21 | #' DataSet8.1$block <- factor(x = DataSet8.1$block) 22 | #' DataSet8.1$set <- factor(x = DataSet8.1$set) 23 | #' DataSet8.1$trt <- factor(x = DataSet8.1$trt) 24 | #' 25 | #' library(lmerTest) 26 | #' Exam8.1Lmer <- lmer(y ~ set + trt %in% set + (1|set/block), DataSet8.1) 27 | #' summary(Exam8.1Lmer) 28 | #' anova(Exam8.1Lmer) 29 | #' 30 | #' library(emmeans) 31 | #' emmeans(object = Exam8.1Lmer, specs = ~trt|set) 32 | #' contrast(emmeans(object = Exam8.1Lmer, specs = ~trt|set), method = "pairwise", by = "set") 33 | #' 34 | NULL 35 | -------------------------------------------------------------------------------- /man/DataSet8.3.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet8.3.R 3 | \docType{data} 4 | \name{DataSet8.3} 5 | \alias{DataSet8.3} 6 | \title{Data for Example 8.3 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \format{ 8 | A \code{data.frame} with 28 rows and 4 variables. 9 | } 10 | \usage{ 11 | data(DataSet8.3) 12 | } 13 | \description{ 14 | DataSet8.3 is used for Response surface design with incomplete blocking 15 | } 16 | \details{ 17 | \itemize{ 18 | \item block with 7 blocks 19 | \item a is a factor with 3 levels 0,-1 and 1 20 | \item b is a factor with 3 levels 0,-1 and 1 21 | \item c is a factor with 3 levels 0,-1 and 1 22 | \item y is a Gaussian response variable 23 | } 24 | } 25 | \examples{ 26 | data(DataSet8.3) 27 | } 28 | \references{ 29 | \enumerate{ 30 | \item Stroup, W. W. (2012).\emph{Generalized linear Mixed Models: Modern Concepts, Methods and Applications}. 31 | CRC press. 32 | } 33 | } 34 | \seealso{ 35 | \code{\link{Exam8.3}} 36 | } 37 | \author{ 38 | Muhammad Yaseen (\email{myaseen208@gmail.com}) 39 | Adeela Munawar (\email{adeela.uaf@gmail.com}) 40 | } 41 | \keyword{datasets} 42 | -------------------------------------------------------------------------------- /man/DataExam2.B.2.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataExam2.B.2.R 3 | \docType{data} 4 | \name{DataExam2.B.2} 5 | \alias{DataExam2.B.2} 6 | \title{Data for Example 2.B.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-54)} 7 | \format{ 8 | A \code{data.frame} with 11 rows and 3 variables. 9 | } 10 | \usage{ 11 | data(DataExam2.B.2) 12 | } 13 | \description{ 14 | Exam2.B.2 is used to visualize the effect of glm model statement with binomial data with logit and probit links. 15 | } 16 | \details{ 17 | \itemize{ 18 | \item x independent variable 19 | \item n bernouli trials (bernouli outcomes on each individual) 20 | \item y number of successes on each individual 21 | } 22 | } 23 | \examples{ 24 | data(DataExam2.B.2) 25 | } 26 | \references{ 27 | \enumerate{ 28 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 29 | CRC press. 30 | } 31 | } 32 | \seealso{ 33 | \link{Exam2.B.2} 34 | } 35 | \author{ 36 | \enumerate{ 37 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 38 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 39 | } 40 | } 41 | \keyword{datasets} 42 | -------------------------------------------------------------------------------- /man/DataSet8.2.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet8.2.R 3 | \docType{data} 4 | \name{DataSet8.2} 5 | \alias{DataSet8.2} 6 | \title{Data for Example 8.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \format{ 8 | A \code{data.frame} with 36 rows and 6 variables. 9 | } 10 | \usage{ 11 | data(DataSet8.2) 12 | } 13 | \description{ 14 | DataSet8.2 is used for Incomplete strip-plot ( 3 cross 3 factorial). 15 | } 16 | \details{ 17 | \itemize{ 18 | \item block 9 blocks each consisting of 2 rows and 2 coloumns 19 | \item a is a factor with 3 levels assigned at random to rows 20 | \item b is a factor with 3 levels assigned at random to columns 21 | \item y is a Gaussian response variable 22 | } 23 | } 24 | \examples{ 25 | data(DataSet8.2) 26 | } 27 | \references{ 28 | \enumerate{ 29 | \item Stroup, W. W. (2012).\emph{Generalized linear Mixed Models: Modern Concepts, Methods and Applications}. 30 | CRC press. 31 | } 32 | } 33 | \seealso{ 34 | \code{\link{Exam8.2}} 35 | } 36 | \author{ 37 | Muhammad Yaseen (\email{myaseen208@gmail.com}) 38 | Adeela Munawar (\email{adeela.uaf@gmail.com}) 39 | } 40 | \keyword{datasets} 41 | -------------------------------------------------------------------------------- /man/DataSet5.1.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet5.1.R 3 | \docType{data} 4 | \name{DataSet5.1} 5 | \alias{DataSet5.1} 6 | \title{Data for Example 5.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \format{ 8 | A \code{data.frame} with 14 rows and 3 variables. 9 | } 10 | \usage{ 11 | data(DataSet5.1) 12 | } 13 | \description{ 14 | DataSet5.1 is used for polynomial multiple regression 15 | } 16 | \details{ 17 | \itemize{ 18 | \item X is predictor variable with level 0, 1, 2, 4, 8, 12, 16 19 | \item N is the number of independent bernoulli trials for a given observation 20 | \item F is the number of "successes"(N and F specify a binomial response) 21 | } 22 | } 23 | \examples{ 24 | data(DataSet5.1) 25 | } 26 | \references{ 27 | \enumerate{ 28 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 29 | CRC press. 30 | } 31 | } 32 | \seealso{ 33 | \code{\link{Exam5.1}} 34 | } 35 | \author{ 36 | \enumerate{ 37 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 38 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 39 | } 40 | } 41 | \keyword{datasets} 42 | -------------------------------------------------------------------------------- /man/DataSet8.4.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet8.4.R 3 | \docType{data} 4 | \name{DataSet8.4} 5 | \alias{DataSet8.4} 6 | \title{Data for Example 8.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \format{ 8 | A \code{data.frame} with 36 rows and 6 variables. 9 | } 10 | \usage{ 11 | data(DataSet8.4) 12 | } 13 | \description{ 14 | DataSet8.4 is used for Multifactor treatment and Multilevel design structures 15 | } 16 | \details{ 17 | \itemize{ 18 | \item block 9 blocks each consisting of 2 rows and 2 coloumns 19 | \item a is a factor with 3 levels assigned at random to rows 20 | \item b is a factor with 3 levels assigned at random to columns 21 | \item y is a Gaussian response variable 22 | } 23 | } 24 | \examples{ 25 | data(DataSet8.4) 26 | } 27 | \references{ 28 | \enumerate{ 29 | \item Stroup, W. W. (2012).\emph{Generalized linear Mixed Models: Modern Concepts, Methods and Applications}. 30 | CRC press. 31 | } 32 | } 33 | \seealso{ 34 | \code{\link{Exam8.4}} 35 | } 36 | \author{ 37 | Muhammad Yaseen (\email{myaseen208@gmail.com}) 38 | Adeela Munawar (\email{adeela.uaf@gmail.com}) 39 | } 40 | \keyword{datasets} 41 | -------------------------------------------------------------------------------- /man/Exam8.1.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam8.1.R 3 | \name{Exam8.1} 4 | \alias{Exam8.1} 5 | \title{Example 8.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-250)} 6 | \description{ 7 | Exam8.1 Nested factorial structure 8 | } 9 | \examples{ 10 | 11 | data(DataSet8.1) 12 | DataSet8.1$block <- factor(x = DataSet8.1$block) 13 | DataSet8.1$set <- factor(x = DataSet8.1$set) 14 | DataSet8.1$trt <- factor(x = DataSet8.1$trt) 15 | 16 | library(lmerTest) 17 | Exam8.1Lmer <- lmer(y ~ set + trt \%in\% set + (1|set/block), DataSet8.1) 18 | summary(Exam8.1Lmer) 19 | anova(Exam8.1Lmer) 20 | 21 | library(emmeans) 22 | emmeans(object = Exam8.1Lmer, specs = ~trt|set) 23 | contrast(emmeans(object = Exam8.1Lmer, specs = ~trt|set), method = "pairwise", by = "set") 24 | 25 | } 26 | \references{ 27 | \enumerate{ 28 | \item Stroup, W. W. (2012). 29 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 30 | CRC Press. 31 | } 32 | } 33 | \seealso{ 34 | \code{\link{DataSet8.1}} 35 | } 36 | \author{ 37 | \enumerate{ 38 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 39 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 40 | } 41 | } 42 | -------------------------------------------------------------------------------- /man/DataSet5.2.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet5.2.R 3 | \docType{data} 4 | \name{DataSet5.2} 5 | \alias{DataSet5.2} 6 | \title{Data for Example 5.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \format{ 8 | A \code{data.frame} with 9 rows and 4 variables. 9 | } 10 | \usage{ 11 | data(DataSet5.2) 12 | } 13 | \description{ 14 | DataSet5.2 is used for three factor orthogonal main effects only design with sequential fitting of predictors 15 | } 16 | \details{ 17 | \itemize{ 18 | \item a is predictor variable with level 0, 1 19 | \item b is predictor variable with level 0, 1 20 | \item c is predictor variable with level 0, 1 21 | \item y response variable 22 | } 23 | } 24 | \examples{ 25 | data(DataSet5.2) 26 | } 27 | \references{ 28 | \enumerate{ 29 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 30 | CRC press. 31 | } 32 | } 33 | \seealso{ 34 | \code{\link{Exam5.2}} 35 | } 36 | \author{ 37 | \enumerate{ 38 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 39 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 40 | } 41 | } 42 | \keyword{datasets} 43 | -------------------------------------------------------------------------------- /man/DataExam2.B.7.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataExam2.B.7.R 3 | \docType{data} 4 | \name{DataExam2.B.7} 5 | \alias{DataExam2.B.7} 6 | \title{Data for Example 2.B.7 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-60)} 7 | \format{ 8 | A \code{data.frame} with 16 rows and 4 variables. 9 | } 10 | \usage{ 11 | data(DataExam2.B.7) 12 | } 13 | \description{ 14 | Exam2.B.7 is related to multi batch regression data assuming different forms of linear models with factorial experiment. 15 | } 16 | \details{ 17 | \itemize{ 18 | \item Rep number of replications 19 | \item a factor with two levels 1 and 2 20 | \item b factor with two levels 1 and 2 21 | \item y response variable 22 | } 23 | } 24 | \examples{ 25 | data(DataExam2.B.7) 26 | } 27 | \references{ 28 | \enumerate{ 29 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 30 | CRC press. 31 | } 32 | } 33 | \seealso{ 34 | \code{\link{Exam2.B.7}} 35 | } 36 | \author{ 37 | \enumerate{ 38 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 39 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 40 | } 41 | } 42 | \keyword{datasets} 43 | -------------------------------------------------------------------------------- /man/DataExam2.B.4.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataExam2.B.4.R 3 | \docType{data} 4 | \name{DataExam2.B.4} 5 | \alias{DataExam2.B.4} 6 | \title{Data for Example 2.B.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-54)} 7 | \format{ 8 | A \code{data.frame} with 6 rows and 4 variables. 9 | } 10 | \usage{ 11 | data(DataExam2.B.4) 12 | } 13 | \description{ 14 | Exam2.B.4 is used to illustrate one way treatment design with Binomial observations. 15 | } 16 | \details{ 17 | \itemize{ 18 | \item obs number of observations 19 | \item trt three treatments with class factor 20 | \item Nij number of bernouli trials on each individual 21 | \item y number of successes on each individual 22 | } 23 | } 24 | \examples{ 25 | data(DataExam2.B.4) 26 | } 27 | \references{ 28 | \enumerate{ 29 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 30 | CRC press. 31 | } 32 | } 33 | \seealso{ 34 | \code{\link{Exam2.B.4}} 35 | } 36 | \author{ 37 | \enumerate{ 38 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 39 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 40 | } 41 | } 42 | \keyword{datasets} 43 | -------------------------------------------------------------------------------- /R/Exam8.4.R: -------------------------------------------------------------------------------- 1 | #' @title Example 8.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-259) 2 | #' @name Exam8.4 3 | #' @description Exam8.4 Multifactor treatment and Multilevel design structures 4 | #' @author \enumerate{ 5 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 6 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 7 | #' } 8 | #' @references \enumerate{ 9 | #' \item Stroup, W. W. (2012). 10 | #' \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 11 | #' CRC Press. 12 | #' } 13 | #' 14 | #' @seealso 15 | #' \code{\link{DataSet8.4}} 16 | #' 17 | #' @import emmeans lmerTest 18 | #' 19 | #' @examples 20 | #' 21 | #' data(DataSet8.4) 22 | #' DataSet8.4$block <- factor(x = DataSet8.4$block) 23 | #' DataSet8.4$a <- factor(x = DataSet8.4$a) 24 | #' DataSet8.4$b <- factor(x = DataSet8.4$b) 25 | #' 26 | #' library(lmerTest) 27 | #' Exam8.4lmer <- 28 | #' lmer( 29 | #' y ~ a + b %in% a + 30 | #' (1|block) + (1|block:a) + (1|block:b) 31 | #' , data = DataSet8.4 32 | #' ) 33 | #' anova(Exam8.4lmer, ddf = "Kenward-Roger") 34 | #' 35 | #' library(emmeans) 36 | #' emmeans(object = Exam8.4lmer, specs = ~a|b) 37 | NULL 38 | -------------------------------------------------------------------------------- /man/DataSet4.1.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet4.1.R 3 | \docType{data} 4 | \name{DataSet4.1} 5 | \alias{DataSet4.1} 6 | \title{Data for Example 4.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \format{ 8 | A \code{data.frame} with 60 rows and 3 variables. 9 | } 10 | \usage{ 11 | data(DataSet4.1) 12 | } 13 | \description{ 14 | DataSet4.1 comes from Cochran and Cox (1957) Experimental Design 15 | } 16 | \details{ 17 | \itemize{ 18 | \item blocks 15 blocks in an incomplete block desgin 19 | \item trt treatments representing incomplete block desgin 20 | \item y is continuous & may be assumed Gaussian 21 | } 22 | } 23 | \examples{ 24 | data(DataSet4.1) 25 | } 26 | \references{ 27 | \enumerate{ 28 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 29 | CRC press. 30 | \item Cochran, W. G., & Cox, G. M. (1957). \emph{Experimental designs}. 31 | } 32 | } 33 | \seealso{ 34 | \code{\link{Exam4.1}} 35 | } 36 | \author{ 37 | \enumerate{ 38 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 39 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 40 | } 41 | } 42 | \keyword{datasets} 43 | -------------------------------------------------------------------------------- /man/Exam8.4.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam8.4.R 3 | \name{Exam8.4} 4 | \alias{Exam8.4} 5 | \title{Example 8.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-259)} 6 | \description{ 7 | Exam8.4 Multifactor treatment and Multilevel design structures 8 | } 9 | \examples{ 10 | 11 | data(DataSet8.4) 12 | DataSet8.4$block <- factor(x = DataSet8.4$block) 13 | DataSet8.4$a <- factor(x = DataSet8.4$a) 14 | DataSet8.4$b <- factor(x = DataSet8.4$b) 15 | 16 | library(lmerTest) 17 | Exam8.4lmer <- 18 | lmer( 19 | y ~ a + b \%in\% a + 20 | (1|block) + (1|block:a) + (1|block:b) 21 | , data = DataSet8.4 22 | ) 23 | anova(Exam8.4lmer, ddf = "Kenward-Roger") 24 | 25 | library(emmeans) 26 | emmeans(object = Exam8.4lmer, specs = ~a|b) 27 | } 28 | \references{ 29 | \enumerate{ 30 | \item Stroup, W. W. (2012). 31 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 32 | CRC Press. 33 | } 34 | } 35 | \seealso{ 36 | \code{\link{DataSet8.4}} 37 | } 38 | \author{ 39 | \enumerate{ 40 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 41 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 42 | } 43 | } 44 | -------------------------------------------------------------------------------- /man/DataSet3.1.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet3.1.R 3 | \docType{data} 4 | \name{DataSet3.1} 5 | \alias{DataSet3.1} 6 | \title{Data for Example 3.1 and Example 3.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \format{ 8 | A \code{data.frame} with 20 rows and 5 variables. 9 | } 10 | \usage{ 11 | data(DataSet3.1) 12 | } 13 | \description{ 14 | DataSet3.1 is used for linear and generalized linear models 15 | } 16 | \details{ 17 | \itemize{ 18 | \item trt two treatment 0 and 1 19 | \item rep unit of observation or observation ID 20 | \item Y is continuous & may be assumed Gaussian 21 | \item N is the number of obs 22 | \item F is the number of "successes"(N and F specify a binomial response) 23 | } 24 | } 25 | \examples{ 26 | data(DataSet3.1) 27 | } 28 | \references{ 29 | \enumerate{ 30 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 31 | CRC press. 32 | } 33 | } 34 | \seealso{ 35 | \code{\link{Exam3.2}} 36 | } 37 | \author{ 38 | \enumerate{ 39 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 40 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 41 | } 42 | } 43 | \keyword{datasets} 44 | -------------------------------------------------------------------------------- /man/DataSet3.3.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet3.3.R 3 | \docType{data} 4 | \name{DataSet3.3} 5 | \alias{DataSet3.3} 6 | \title{Data for Example3.7 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \format{ 8 | A \code{data.frame} with 36 rows and 6 variables. 9 | } 10 | \usage{ 11 | data(DataSet3.3) 12 | } 13 | \description{ 14 | Exam1.2 is used to see types of model effects by plotting regression data 15 | } 16 | \details{ 17 | \itemize{ 18 | \item X Each batch observed at several times:0,3,6,12,24,36,48 months 19 | \item Y continuous variable observed at each level of X 20 | \item Fav number of successes 21 | \item N isndependent bernoulli trials 22 | \item Batch Batches as 1, 2, 3, 4 23 | \item Count binomial response variable 24 | } 25 | } 26 | \examples{ 27 | data(DataSet3.3) 28 | } 29 | \references{ 30 | \enumerate{ 31 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 32 | CRC press. 33 | } 34 | } 35 | \author{ 36 | \enumerate{ 37 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 38 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 39 | } 40 | } 41 | \keyword{datasets} 42 | -------------------------------------------------------------------------------- /man/Table1.2.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Table1.2.R 3 | \docType{data} 4 | \name{Table1.2} 5 | \alias{Table1.2} 6 | \title{Data for Table1.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-10)} 7 | \format{ 8 | A \code{data.frame} with 36 rows and 5 variables. 9 | } 10 | \usage{ 11 | data(Table1.2) 12 | } 13 | \description{ 14 | Exam1.2 is used to see types of model effects by plotting regression data 15 | } 16 | \details{ 17 | \itemize{ 18 | \item X have 11 levels in varying intervals from 0 to 48 observed for multiple batches 19 | \item Y continuous variable observed at each level of X 20 | \item Fav number of successes 21 | \item N number of bernoulli trials 22 | \item Batch Batches as 1, 2, 3, 4 23 | } 24 | } 25 | \examples{ 26 | data(Table1.2) 27 | } 28 | \references{ 29 | \enumerate{ 30 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 31 | CRC press. 32 | } 33 | } 34 | \seealso{ 35 | \code{\link{Exam1.2}} 36 | } 37 | \author{ 38 | \enumerate{ 39 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 40 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 41 | } 42 | } 43 | \keyword{datasets} 44 | -------------------------------------------------------------------------------- /R/Exam1.2.R: -------------------------------------------------------------------------------- 1 | #' @title Example1.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-9) 2 | #' @name Exam1.2 3 | #' @description Exam1.2 is used to see types of model effects by plotting regression data 4 | #' @author \enumerate{ 5 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 6 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 7 | #' } 8 | #' @references \enumerate{ 9 | #' \item Stroup, W. W. (2012). 10 | #' \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 11 | #' CRC Press. 12 | #' } 13 | #' @seealso 14 | #' \code{\link{Table1.2}} 15 | 16 | #' @importFrom ggplot2 ggplot 17 | #' 18 | #' @examples 19 | #' 20 | #' #------------------------------------------------------------- 21 | #' ## Plot of multi-batch regression data discussed in Article 1.3 22 | #' #------------------------------------------------------------- 23 | #' data(Table1.1) 24 | #' 25 | #' Table1.2$Batch <- factor(x = Table1.2$Batch) 26 | #' 27 | #' library(ggplot2) 28 | #' Plot <- 29 | #' ggplot(data = Table1.2, mapping = aes(y = Y, x = X, colour = Batch, shape = Batch)) + 30 | #' geom_point() + 31 | #' geom_smooth(method = "lm", fill = NA) + 32 | #' labs(title = "Plot of Multi Batch Regression data") + 33 | #' theme_bw() 34 | #' Plot 35 | NULL 36 | -------------------------------------------------------------------------------- /man/Exam1.2.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam1.2.R 3 | \name{Exam1.2} 4 | \alias{Exam1.2} 5 | \title{Example1.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-9)} 6 | \description{ 7 | Exam1.2 is used to see types of model effects by plotting regression data 8 | } 9 | \examples{ 10 | 11 | #------------------------------------------------------------- 12 | ## Plot of multi-batch regression data discussed in Article 1.3 13 | #------------------------------------------------------------- 14 | data(Table1.1) 15 | 16 | Table1.2$Batch <- factor(x = Table1.2$Batch) 17 | 18 | library(ggplot2) 19 | Plot <- 20 | ggplot(data = Table1.2, mapping = aes(y = Y, x = X, colour = Batch, shape = Batch)) + 21 | geom_point() + 22 | geom_smooth(method = "lm", fill = NA) + 23 | labs(title = "Plot of Multi Batch Regression data") + 24 | theme_bw() 25 | Plot 26 | } 27 | \references{ 28 | \enumerate{ 29 | \item Stroup, W. W. (2012). 30 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 31 | CRC Press. 32 | } 33 | } 34 | \seealso{ 35 | \code{\link{Table1.2}} 36 | } 37 | \author{ 38 | \enumerate{ 39 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 40 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 41 | } 42 | } 43 | -------------------------------------------------------------------------------- /R/Exam2.B.1.R: -------------------------------------------------------------------------------- 1 | #' @title Example 2.B.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-53) 2 | #' @name Exam2.B.1 3 | #' @description Exam2.B.1 is used to visualize the effect of lm model statement with Gaussian data and their design matrix 4 | #' @author \enumerate{ 5 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 6 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 7 | #' } 8 | #' @references \enumerate{ 9 | #' \item Stroup, W. W. (2012). 10 | #' \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 11 | #' CRC Press. 12 | #' } 13 | #' @seealso 14 | #' \code{\link{Table1.1}} 15 | #' 16 | #' @import parameters 17 | #' @importFrom stats lm summary.lm 18 | #' 19 | #' @examples 20 | #' #----------------------------------------------------------------------------------- 21 | #' ## Linear Model discussed in Example 2.B.1 using simple regression data of Table1.1 22 | #' #----------------------------------------------------------------------------------- 23 | #' 24 | #' data(Table1.1) 25 | #' 26 | #' Exam2.B.1.lm1 <- lm(formula = y~x, data = Table1.1) 27 | #' summary(Exam2.B.1.lm1) 28 | #' library(parameters) 29 | #' model_parameters(Exam2.B.1.lm1) 30 | #' 31 | #' DesignMatrix.lm1 <- model.matrix (object = Exam2.B.1.lm1) 32 | #' DesignMatrix.lm1 33 | #' 34 | NULL 35 | -------------------------------------------------------------------------------- /man/Exam2.B.1.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam2.B.1.R 3 | \name{Exam2.B.1} 4 | \alias{Exam2.B.1} 5 | \title{Example 2.B.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-53)} 6 | \description{ 7 | Exam2.B.1 is used to visualize the effect of lm model statement with Gaussian data and their design matrix 8 | } 9 | \examples{ 10 | #----------------------------------------------------------------------------------- 11 | ## Linear Model discussed in Example 2.B.1 using simple regression data of Table1.1 12 | #----------------------------------------------------------------------------------- 13 | 14 | data(Table1.1) 15 | 16 | Exam2.B.1.lm1 <- lm(formula = y~x, data = Table1.1) 17 | summary(Exam2.B.1.lm1) 18 | library(parameters) 19 | model_parameters(Exam2.B.1.lm1) 20 | 21 | DesignMatrix.lm1 <- model.matrix (object = Exam2.B.1.lm1) 22 | DesignMatrix.lm1 23 | 24 | } 25 | \references{ 26 | \enumerate{ 27 | \item Stroup, W. W. (2012). 28 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 29 | CRC Press. 30 | } 31 | } 32 | \seealso{ 33 | \code{\link{Table1.1}} 34 | } 35 | \author{ 36 | \enumerate{ 37 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 38 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 39 | } 40 | } 41 | -------------------------------------------------------------------------------- /R/Exam2.B.2.R: -------------------------------------------------------------------------------- 1 | #' @title Example 2.B.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-54) 2 | #' @name Exam2.B.2 3 | #' @description Exam2.B.2 is used to visualize the effect of glm model statement with binomial data with logit and probit links. 4 | #' @author \enumerate{ 5 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 6 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 7 | #' } 8 | #' @references \enumerate{ 9 | #' \item Stroup, W. W. (2012). 10 | #' \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 11 | #' CRC Press. 12 | #' } 13 | #' @seealso 14 | #' \code{\link{DataExam2.B.2}} 15 | #' 16 | #' @import parameters 17 | #' @importFrom stats glm summary.glm 18 | #' 19 | #' @examples 20 | #' #----------------------------------------------------------------------------------- 21 | #' ## probitit Model discussed in Example 2.B.2 using DataExam2.B.2 22 | #' ## Default link is logit 23 | #' ## using fmaily = binomial gives warning message of no-integer successes 24 | #' #----------------------------------------------------------------------------------- 25 | #' data(DataExam2.B.2) 26 | #' Exam2.B.2glm <- glm(formula = y/n~x, family = quasibinomial(link = "probit"), data = DataExam2.B.2) 27 | #' summary(Exam2.B.2glm) 28 | #' library(parameters) 29 | #' model_parameters(Exam2.B.2glm) 30 | NULL 31 | -------------------------------------------------------------------------------- /man/Exam2.B.2.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam2.B.2.R 3 | \name{Exam2.B.2} 4 | \alias{Exam2.B.2} 5 | \title{Example 2.B.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-54)} 6 | \description{ 7 | Exam2.B.2 is used to visualize the effect of glm model statement with binomial data with logit and probit links. 8 | } 9 | \examples{ 10 | #----------------------------------------------------------------------------------- 11 | ## probitit Model discussed in Example 2.B.2 using DataExam2.B.2 12 | ## Default link is logit 13 | ## using fmaily = binomial gives warning message of no-integer successes 14 | #----------------------------------------------------------------------------------- 15 | data(DataExam2.B.2) 16 | Exam2.B.2glm <- glm(formula = y/n~x, family = quasibinomial(link = "probit"), data = DataExam2.B.2) 17 | summary(Exam2.B.2glm) 18 | library(parameters) 19 | model_parameters(Exam2.B.2glm) 20 | } 21 | \references{ 22 | \enumerate{ 23 | \item Stroup, W. W. (2012). 24 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 25 | CRC Press. 26 | } 27 | } 28 | \seealso{ 29 | \code{\link{DataExam2.B.2}} 30 | } 31 | \author{ 32 | \enumerate{ 33 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 34 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 35 | } 36 | } 37 | -------------------------------------------------------------------------------- /man/Exam2.B.6.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam2.B.6.R 3 | \name{Exam2.B.6} 4 | \alias{Exam2.B.6} 5 | \title{Example 2.B.6 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-58)} 6 | \description{ 7 | Exam2.B.6 is related to multi batch regression data assuming different forms of linear models keeping batch effect random. 8 | } 9 | \examples{ 10 | #----------------------------------------------------------------------------------- 11 | ## Nested Model with no intercept 12 | #----------------------------------------------------------------------------------- 13 | 14 | data(Table1.2) 15 | Table1.2$Batch <- factor(x = Table1.2$Batch) 16 | library(nlme) 17 | Exam2.B.6fm1 <- lme( 18 | fixed = Y ~ X 19 | , data = Table1.2 20 | , random = list(Batch = pdDiag(~1), X = pdDiag(~1)) 21 | , method = c("REML", "ML")[1] 22 | ) 23 | Exam2.B.6fm1 24 | library(broom.mixed) 25 | tidy(Exam2.B.6fm1) 26 | } 27 | \references{ 28 | \enumerate{ 29 | \item Stroup, W. W. (2012). 30 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 31 | CRC Press. 32 | } 33 | } 34 | \seealso{ 35 | \code{\link{Table1.2}} 36 | } 37 | \author{ 38 | \enumerate{ 39 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 40 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 41 | } 42 | } 43 | -------------------------------------------------------------------------------- /R/DataSet3.2.R: -------------------------------------------------------------------------------- 1 | #' @title DataSt3.2 for Example 3.3, Example 3.4, Example3.6, Example3.8 and Example 3.9 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 2 | #' @name DataSet3.2 3 | #' @docType data 4 | #' @keywords datasets 5 | #' @usage data(DataSet3.2) 6 | #' @description DataSet3.2 Multi-Location, 4 Treatment Randomized Block 7 | #' @format A \code{data.frame} with 32 rows and 10 variables. 8 | #' @details 9 | #' \itemize{ 10 | #' \item trt two treatment 0 and 1 11 | #' \item loc four locations used as blocks 12 | #' \item Y is Gaussian response variable 13 | #' \item Nbin subjects at each Loc x Trt for binomial response 14 | #' \item S1 and S2 are two binomial response variables 15 | #' \item count1 and count 2 used later 16 | #' \item A and B are factors with level 0 and 1 17 | #' } 18 | #' @author \enumerate{ 19 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 20 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 21 | #' } 22 | #' @references \enumerate{ 23 | #' \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 24 | #' CRC press. 25 | #' } 26 | #' @seealso 27 | #' \code{\link{Exam3.3}} 28 | #' \code{\link{Exam3.9}} 29 | #' @examples 30 | #' data(DataSet3.2) 31 | NULL 32 | -------------------------------------------------------------------------------- /R/Exam7.7.R: -------------------------------------------------------------------------------- 1 | #' @title Example 7.7 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-235) 2 | #' @name Exam7.7 3 | #' @description Exam7.7 is an explaination of segmented regression 4 | #' @author \enumerate{ 5 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 6 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 7 | #' } 8 | #' @references \enumerate{ 9 | #' \item Stroup, W. W. (2012). 10 | #' \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 11 | #' CRC Press. 12 | #' } 13 | #' @seealso 14 | #' \code{\link{DataSet7.7}} 15 | #' @import splines ggplot2 16 | #' @examples 17 | #' 18 | #' library(splines) 19 | #' library(ggplot2) 20 | #' 21 | #' DataSet7.7$a <- factor(x = DataSet7.7$a) 22 | #' knots <- c(0, 0, 0, 0, 10, 10, 20, 30, 40, 40, 40, 45, 45, 45, 50, 50, 50) 23 | #' 24 | #' bx <- splineDesign(knots = knots, x = DataSet7.7$x, outer.ok = TRUE) 25 | #' 26 | #' Exam7.7fm <- lm(formula = y ~ a*bx, data = DataSet7.7) 27 | #' anova(Exam7.7fm) 28 | #' 29 | #' Data <- data.frame(DataSet7.7, fit = Exam7.7fm$fit) 30 | #' ##---Estimated response surface by using segmented regression 31 | #' Plot <- 32 | #' ggplot(data = Data , mapping = aes(x = x, y = y, colour = a)) + 33 | #' geom_point() + 34 | #' geom_line(linewidth = 1) + 35 | #' ggtitle("Response surface by using segmented regression") 36 | #' 37 | #' print(Plot) 38 | NULL 39 | -------------------------------------------------------------------------------- /R/Exam2.B.6.R: -------------------------------------------------------------------------------- 1 | #' @title Example 2.B.6 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-58) 2 | #' @name Exam2.B.6 3 | #' @description Exam2.B.6 is related to multi batch regression data assuming different forms of linear models keeping batch effect random. 4 | #' @author \enumerate{ 5 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 6 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 7 | #' } 8 | #' @references \enumerate{ 9 | #' \item Stroup, W. W. (2012). 10 | #' \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 11 | #' CRC Press. 12 | #' } 13 | #' @seealso 14 | #' \code{\link{Table1.2}} 15 | #' 16 | #' @import parameters 17 | #' @import broom.mixed 18 | #' @importFrom nlme lme 19 | #' 20 | #' @examples 21 | #' #----------------------------------------------------------------------------------- 22 | #' ## Nested Model with no intercept 23 | #' #----------------------------------------------------------------------------------- 24 | #' 25 | #' data(Table1.2) 26 | #' Table1.2$Batch <- factor(x = Table1.2$Batch) 27 | #' library(nlme) 28 | #' Exam2.B.6fm1 <- lme( 29 | #' fixed = Y ~ X 30 | #' , data = Table1.2 31 | #' , random = list(Batch = pdDiag(~1), X = pdDiag(~1)) 32 | #' , method = c("REML", "ML")[1] 33 | #' ) 34 | #' Exam2.B.6fm1 35 | #' library(broom.mixed) 36 | #' tidy(Exam2.B.6fm1) 37 | NULL 38 | 39 | 40 | -------------------------------------------------------------------------------- /man/Exam7.7.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam7.7.R 3 | \name{Exam7.7} 4 | \alias{Exam7.7} 5 | \title{Example 7.7 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-235)} 6 | \description{ 7 | Exam7.7 is an explaination of segmented regression 8 | } 9 | \examples{ 10 | 11 | library(splines) 12 | library(ggplot2) 13 | 14 | DataSet7.7$a <- factor(x = DataSet7.7$a) 15 | knots <- c(0, 0, 0, 0, 10, 10, 20, 30, 40, 40, 40, 45, 45, 45, 50, 50, 50) 16 | 17 | bx <- splineDesign(knots = knots, x = DataSet7.7$x, outer.ok = TRUE) 18 | 19 | Exam7.7fm <- lm(formula = y ~ a*bx, data = DataSet7.7) 20 | anova(Exam7.7fm) 21 | 22 | Data <- data.frame(DataSet7.7, fit = Exam7.7fm$fit) 23 | ##---Estimated response surface by using segmented regression 24 | Plot <- 25 | ggplot(data = Data , mapping = aes(x = x, y = y, colour = a)) + 26 | geom_point() + 27 | geom_line(linewidth = 1) + 28 | ggtitle("Response surface by using segmented regression") 29 | 30 | print(Plot) 31 | } 32 | \references{ 33 | \enumerate{ 34 | \item Stroup, W. W. (2012). 35 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 36 | CRC Press. 37 | } 38 | } 39 | \seealso{ 40 | \code{\link{DataSet7.7}} 41 | } 42 | \author{ 43 | \enumerate{ 44 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 45 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 46 | } 47 | } 48 | -------------------------------------------------------------------------------- /R/Exam4.1.R: -------------------------------------------------------------------------------- 1 | #' @title Example 4.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-138) 2 | #' @name Exam4.1 3 | #' @description Exam4.1 REML vs ML criterion is used keeping block effects random 4 | #' @author \enumerate{ 5 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 6 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 7 | #' } 8 | #' @references \enumerate{ 9 | #' \item Stroup, W. W. (2012). 10 | #' \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 11 | #' CRC Press. 12 | #' } 13 | #' @seealso 14 | #' \code{\link{DataSet4.1}} 15 | #' 16 | #' @import parameters 17 | #' @import lmerTest 18 | #' 19 | #' @examples 20 | #' 21 | #' DataSet4.1$trt <- factor(x = DataSet4.1$trt) 22 | #' DataSet4.1$block <- factor(x = DataSet4.1$block) 23 | #' 24 | #' #---REML estimates on page 138(article 4.4.3.3) 25 | #' library(lmerTest) 26 | #' 27 | #' Exam4.1REML <- lmer(formula = y~ trt +( 1|block ), data = DataSet4.1) 28 | #' library(parameters) 29 | #' model_parameters(Exam4.1REML) 30 | #' print(VarCorr(x = Exam4.1REML), comp = c("Variance")) 31 | #' 32 | #' ##---ML estimates on page 138(article 4.4.3.3) 33 | #' Exam4.1ML <- lmer(formula = y ~ trt + (1|block), data = DataSet4.1, REML = FALSE) 34 | #' model_parameters(Exam4.1ML) 35 | #' print(VarCorr(x = Exam4.1ML), comp = c("Variance")) 36 | #' 37 | #' Exam4.1.lm <- lm(formula = y~ trt + block, data = DataSet4.1) 38 | #' anova(object = Exam4.1.lm) 39 | NULL 40 | -------------------------------------------------------------------------------- /man/Exam4.1.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam4.1.R 3 | \name{Exam4.1} 4 | \alias{Exam4.1} 5 | \title{Example 4.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-138)} 6 | \description{ 7 | Exam4.1 REML vs ML criterion is used keeping block effects random 8 | } 9 | \examples{ 10 | 11 | DataSet4.1$trt <- factor(x = DataSet4.1$trt) 12 | DataSet4.1$block <- factor(x = DataSet4.1$block) 13 | 14 | #---REML estimates on page 138(article 4.4.3.3) 15 | library(lmerTest) 16 | 17 | Exam4.1REML <- lmer(formula = y~ trt +( 1|block ), data = DataSet4.1) 18 | library(parameters) 19 | model_parameters(Exam4.1REML) 20 | print(VarCorr(x = Exam4.1REML), comp = c("Variance")) 21 | 22 | ##---ML estimates on page 138(article 4.4.3.3) 23 | Exam4.1ML <- lmer(formula = y ~ trt + (1|block), data = DataSet4.1, REML = FALSE) 24 | model_parameters(Exam4.1ML) 25 | print(VarCorr(x = Exam4.1ML), comp = c("Variance")) 26 | 27 | Exam4.1.lm <- lm(formula = y~ trt + block, data = DataSet4.1) 28 | anova(object = Exam4.1.lm) 29 | } 30 | \references{ 31 | \enumerate{ 32 | \item Stroup, W. W. (2012). 33 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 34 | CRC Press. 35 | } 36 | } 37 | \seealso{ 38 | \code{\link{DataSet4.1}} 39 | } 40 | \author{ 41 | \enumerate{ 42 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 43 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 44 | } 45 | } 46 | -------------------------------------------------------------------------------- /man/DataSet3.2.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/DataSet3.2.R 3 | \docType{data} 4 | \name{DataSet3.2} 5 | \alias{DataSet3.2} 6 | \title{DataSt3.2 for Example 3.3, Example 3.4, Example3.6, Example3.8 and Example 3.9 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup} 7 | \format{ 8 | A \code{data.frame} with 32 rows and 10 variables. 9 | } 10 | \usage{ 11 | data(DataSet3.2) 12 | } 13 | \description{ 14 | DataSet3.2 Multi-Location, 4 Treatment Randomized Block 15 | } 16 | \details{ 17 | \itemize{ 18 | \item trt two treatment 0 and 1 19 | \item loc four locations used as blocks 20 | \item Y is Gaussian response variable 21 | \item Nbin subjects at each Loc x Trt for binomial response 22 | \item S1 and S2 are two binomial response variables 23 | \item count1 and count 2 used later 24 | \item A and B are factors with level 0 and 1 25 | } 26 | } 27 | \examples{ 28 | data(DataSet3.2) 29 | } 30 | \references{ 31 | \enumerate{ 32 | \item Stroup, W. W. (2012).\emph{Generalized linear mixed models: modern concepts, methods and applications}. 33 | CRC press. 34 | } 35 | } 36 | \seealso{ 37 | \code{\link{Exam3.3}} 38 | \code{\link{Exam3.9}} 39 | } 40 | \author{ 41 | \enumerate{ 42 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 43 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 44 | } 45 | } 46 | \keyword{datasets} 47 | -------------------------------------------------------------------------------- /R/Exam2.B.3.R: -------------------------------------------------------------------------------- 1 | #' @title Example 2.B.3 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-55) 2 | #' @name Exam2.B.3 3 | #' @description Exam2.B.3 is used to illustrate one way treatment design with Gaussian observations. 4 | #' @author \enumerate{ 5 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 6 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 7 | #' } 8 | #' @references \enumerate{ 9 | #' \item Stroup, W. W. (2012). 10 | #' \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 11 | #' CRC Press. 12 | #' } 13 | #' @seealso 14 | #' \code{\link{DataExam2.B.3}} 15 | #' 16 | #' @import parameters 17 | #' @importFrom stats lm summary.lm 18 | #' 19 | #' @examples 20 | #' #----------------------------------------------------------------------------------- 21 | #' ## Means Model discussed in Example 2.B.3 using DataExam2.B.3 22 | #' #----------------------------------------------------------------------------------- 23 | #' Exam2.B.3.lm1 <- lm(formula = y ~ trt, data = DataExam2.B.3) 24 | #' summary(Exam2.B.3.lm1) 25 | #' 26 | #' #----------------------------------------------------------------------------------- 27 | #' ## Effectss Model discussed in Example 2.B.3 using DataExam2.B.3 28 | #' #----------------------------------------------------------------------------------- 29 | #' Exam2.B.3.lm2 <- lm(formula = y ~ 0 + trt, data = DataExam2.B.3) 30 | #' summary(Exam2.B.3.lm2) 31 | #' library(parameters) 32 | #' model_parameters(Exam2.B.3.lm2) 33 | NULL 34 | -------------------------------------------------------------------------------- /man/Exam2.B.3.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam2.B.3.R 3 | \name{Exam2.B.3} 4 | \alias{Exam2.B.3} 5 | \title{Example 2.B.3 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-55)} 6 | \description{ 7 | Exam2.B.3 is used to illustrate one way treatment design with Gaussian observations. 8 | } 9 | \examples{ 10 | #----------------------------------------------------------------------------------- 11 | ## Means Model discussed in Example 2.B.3 using DataExam2.B.3 12 | #----------------------------------------------------------------------------------- 13 | Exam2.B.3.lm1 <- lm(formula = y ~ trt, data = DataExam2.B.3) 14 | summary(Exam2.B.3.lm1) 15 | 16 | #----------------------------------------------------------------------------------- 17 | ## Effectss Model discussed in Example 2.B.3 using DataExam2.B.3 18 | #----------------------------------------------------------------------------------- 19 | Exam2.B.3.lm2 <- lm(formula = y ~ 0 + trt, data = DataExam2.B.3) 20 | summary(Exam2.B.3.lm2) 21 | library(parameters) 22 | model_parameters(Exam2.B.3.lm2) 23 | } 24 | \references{ 25 | \enumerate{ 26 | \item Stroup, W. W. (2012). 27 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 28 | CRC Press. 29 | } 30 | } 31 | \seealso{ 32 | \code{\link{DataExam2.B.3}} 33 | } 34 | \author{ 35 | \enumerate{ 36 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 37 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 38 | } 39 | } 40 | -------------------------------------------------------------------------------- /man/Exam2.B.4.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam2.B.4.R 3 | \name{Exam2.B.4} 4 | \alias{Exam2.B.4} 5 | \title{Example 2.B.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-56)} 6 | \description{ 7 | Exam2.B.4 is used to illustrate one way treatment design with Binomial observations. 8 | } 9 | \examples{ 10 | #----------------------------------------------------------------------------------- 11 | ## logit Model discussed in Example 2.B.2 using DataExam2.B.4 12 | ## Default link is logit 13 | ## using fmaily=binomial gives warning message of no-integer successes 14 | #----------------------------------------------------------------------------------- 15 | data(DataExam2.B.4) 16 | DataExam2.B.4$trt <- factor(x = DataExam2.B.4$trt) 17 | Exam2.B.4glm <- 18 | glm( 19 | formula = Yij/Nij ~ trt 20 | , family = quasibinomial(link = "probit") 21 | , data = DataExam2.B.4 22 | ) 23 | summary(Exam2.B.4glm) 24 | library(parameters) 25 | model_parameters(Exam2.B.4glm) 26 | } 27 | \references{ 28 | \enumerate{ 29 | \item Stroup, W. W. (2012). 30 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 31 | CRC Press. 32 | } 33 | } 34 | \seealso{ 35 | \code{\link{DataExam2.B.4}} 36 | } 37 | \author{ 38 | \enumerate{ 39 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 40 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 41 | } 42 | } 43 | -------------------------------------------------------------------------------- /R/Exam2.B.4.R: -------------------------------------------------------------------------------- 1 | #' @title Example 2.B.4 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-56) 2 | #' @name Exam2.B.4 3 | #' @description Exam2.B.4 is used to illustrate one way treatment design with Binomial observations. 4 | #' @author \enumerate{ 5 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 6 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 7 | #' } 8 | #' @references \enumerate{ 9 | #' \item Stroup, W. W. (2012). 10 | #' \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 11 | #' CRC Press. 12 | #' } 13 | #' @seealso 14 | #' \code{\link{DataExam2.B.4}} 15 | #' 16 | #' @import parameters 17 | #' @importFrom stats glm summary.glm 18 | #' 19 | #' @examples 20 | #' #----------------------------------------------------------------------------------- 21 | #' ## logit Model discussed in Example 2.B.2 using DataExam2.B.4 22 | #' ## Default link is logit 23 | #' ## using fmaily=binomial gives warning message of no-integer successes 24 | #' #----------------------------------------------------------------------------------- 25 | #' data(DataExam2.B.4) 26 | #' DataExam2.B.4$trt <- factor(x = DataExam2.B.4$trt) 27 | #' Exam2.B.4glm <- 28 | #' glm( 29 | #' formula = Yij/Nij ~ trt 30 | #' , family = quasibinomial(link = "probit") 31 | #' , data = DataExam2.B.4 32 | #' ) 33 | #' summary(Exam2.B.4glm) 34 | #' library(parameters) 35 | #' model_parameters(Exam2.B.4glm) 36 | NULL 37 | -------------------------------------------------------------------------------- /man/Exam8.2.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam8.2.R 3 | \name{Exam8.2} 4 | \alias{Exam8.2} 5 | \title{Example 8.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-252)} 6 | \description{ 7 | Exam8.2 Incomplete strip-plot 8 | } 9 | \examples{ 10 | 11 | data(DataSet8.2) 12 | DataSet8.2$block <- factor(x = DataSet8.2$block) 13 | DataSet8.2$a <- factor(x = DataSet8.2$a) 14 | DataSet8.2$b <- factor(x = DataSet8.2$b) 15 | 16 | library(lmerTest) 17 | 18 | Exam8.2lmer <- 19 | lmer( 20 | formula = y ~ a*b + (1|block) + (1|block:a) + (1|block:b) 21 | , data = DataSet8.2 22 | ) 23 | anova(Exam8.2lmer,ddf="Kenward-Roger") 24 | 25 | library(emmeans) 26 | emmeans(object = Exam8.2lmer, specs = ~a|b) 27 | emmip( 28 | object = emmeans(object = Exam8.2lmer, specs = ~a|b) 29 | , formula = a~b 30 | , ylab = "y Lsmeans" 31 | , main = "Lsmeans for a*b" 32 | ) 33 | 34 | ##---Simple effect comparisons of a*b Least Squares Means by a ( page # 254) 35 | emmeans(Exam8.2lmer, pairwise ~ b|a) 36 | 37 | 38 | } 39 | \references{ 40 | \enumerate{ 41 | \item Stroup, W. W. (2012). 42 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 43 | CRC Press. 44 | } 45 | } 46 | \seealso{ 47 | \code{\link{DataSet8.2}} 48 | } 49 | \author{ 50 | \enumerate{ 51 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 52 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 53 | } 54 | } 55 | -------------------------------------------------------------------------------- /R/Exam8.2.R: -------------------------------------------------------------------------------- 1 | #' @title Example 8.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-252) 2 | #' @name Exam8.2 3 | #' @description Exam8.2 Incomplete strip-plot 4 | #' @author \enumerate{ 5 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 6 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 7 | #' } 8 | #' @references \enumerate{ 9 | #' \item Stroup, W. W. (2012). 10 | #' \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 11 | #' CRC Press. 12 | #' } 13 | #' 14 | #' @seealso 15 | #' \code{\link{DataSet8.2}} 16 | #' 17 | #' @import emmeans lmerTest 18 | #' @examples 19 | #' 20 | #' data(DataSet8.2) 21 | #' DataSet8.2$block <- factor(x = DataSet8.2$block) 22 | #' DataSet8.2$a <- factor(x = DataSet8.2$a) 23 | #' DataSet8.2$b <- factor(x = DataSet8.2$b) 24 | #' 25 | #' library(lmerTest) 26 | #' 27 | #' Exam8.2lmer <- 28 | #' lmer( 29 | #' formula = y ~ a*b + (1|block) + (1|block:a) + (1|block:b) 30 | #' , data = DataSet8.2 31 | #' ) 32 | #' anova(Exam8.2lmer,ddf="Kenward-Roger") 33 | #' 34 | #' library(emmeans) 35 | #' emmeans(object = Exam8.2lmer, specs = ~a|b) 36 | #' emmip( 37 | #' object = emmeans(object = Exam8.2lmer, specs = ~a|b) 38 | #' , formula = a~b 39 | #' , ylab = "y Lsmeans" 40 | #' , main = "Lsmeans for a*b" 41 | #' ) 42 | #' 43 | #' ##---Simple effect comparisons of a*b Least Squares Means by a ( page # 254) 44 | #' emmeans(Exam8.2lmer, pairwise ~ b|a) 45 | #' 46 | #' 47 | NULL 48 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: StroupGLMM 2 | Type: Package 3 | Title: R Codes and Datasets for Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup 4 | Version: 0.3.0 5 | Authors@R: c( 6 | person(c("Muhammad"), "Yaseen", email = "myaseen208@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-5923-1714")) 7 | , person(c("Adeela"), "Munawar", email = "adeela.uaf@gmail.com", role = c("aut", "ctb")) 8 | , person(c("Walter", "W."), "Stroup", email = "wstroup@unl.edu", role = c("aut", "ctb")) 9 | , person(c("Kent", "M."), "Eskridge", email = "keskridge1@unl.edu ", role = c("aut", "ctb")) 10 | ) 11 | Maintainer: Muhammad Yaseen 12 | Description: R Codes and Datasets for Stroup, W. W. (2012). Generalized Linear Mixed Models Modern Concepts, Methods and Applications, CRC Press. 13 | URL: https://myaseen208.com/StroupGLMM/ 14 | https://CRAN.R-project.org/package=StroupGLMM 15 | BugReports: https://github.com/myaseen208/StroupGLMM/issues 16 | Depends: R (>= 3.1) 17 | Imports: 18 | aod, 19 | broom.mixed, 20 | car, 21 | dplyr, 22 | emmeans, 23 | ggplot2, 24 | lattice, 25 | lmerTest, 26 | magrittr, 27 | MASS, 28 | mutoss, 29 | nlme, 30 | parameters, 31 | phia, 32 | scatterplot3d, 33 | splines, 34 | stats, 35 | survey 36 | License: GPL-3 37 | LazyData: true 38 | RoxygenNote: 7.3.2 39 | Encoding: UTF-8 40 | Note: 1. School of Mathematical & Statistical Sciences, Clemson University, Clemson, South Carolina, USA 41 | 2. Department of Mathematics and Statistics, University of Agriculture Faisalabad, Faisalabad, Pakistan 42 | -------------------------------------------------------------------------------- /man/Exam9.2.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam9.2.R 3 | \name{Exam9.2} 4 | \alias{Exam9.2} 5 | \title{Example 9.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-276)} 6 | \description{ 7 | Exam9.2 Two way random effects nested model 8 | } 9 | \examples{ 10 | 11 | data(DataSet9.2) 12 | DataSet9.2$a <- factor(x = DataSet9.2$a) 13 | DataSet9.2$b <- factor(x = DataSet9.2$b) 14 | 15 | library(lmerTest) 16 | Exam9.2lmer <- lmer(y ~ (1|b/a), data = DataSet9.2) 17 | summary(Exam9.2lmer) 18 | 19 | Exam9.2lmer2 <- lm(y ~ a + b \%in\% a, data = DataSet9.2) 20 | summary(Exam9.2lmer2) 21 | 22 | ##--- Over all mean 23 | library(phia) 24 | list9.2 <- list(a = c("1" = 1/7,"2" = 1/7 25 | , "3" = 1/7,"4" = 1/7 26 | , "5" = 1/7,"6" = 1/7 27 | , "7" = 1/7 28 | )) 29 | phia::testFactors(model = Exam9.2lmer2, levels = list9.2) 30 | 31 | #---BLUP Estimates 32 | coef <- unlist(ranef(Exam9.2lmer)$a) 33 | BLUPa <- NULL 34 | for(i in 1:length(coef)){ 35 | BLUPa[i] <- (mean(DataSet9.2$y) + coef[i]) 36 | } 37 | print(BLUPa) 38 | 39 | #---BLUP Estimates Narrow 40 | BLUPaNar <- NULL 41 | for( i in 1:length(coef)) { 42 | BLUPaNar[i] <- (mean(DataSet9.2$y) + coef[i]) 43 | } 44 | 45 | BLUPaNar 46 | 47 | } 48 | \references{ 49 | \enumerate{ 50 | \item Stroup, W. W. (2012). 51 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 52 | CRC Press. 53 | } 54 | } 55 | \seealso{ 56 | \code{\link{DataSet9.2}} 57 | } 58 | \author{ 59 | \enumerate{ 60 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 61 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 62 | } 63 | } 64 | -------------------------------------------------------------------------------- /R/Exam9.2.R: -------------------------------------------------------------------------------- 1 | #' @title Example 9.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-276) 2 | #' @name Exam9.2 3 | #' @description Exam9.2 Two way random effects nested model 4 | #' @author \enumerate{ 5 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 6 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 7 | #' } 8 | #' @references \enumerate{ 9 | #' \item Stroup, W. W. (2012). 10 | #' \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 11 | #' CRC Press. 12 | #' } 13 | #' 14 | #' @seealso 15 | #' \code{\link{DataSet9.2}} 16 | #' 17 | #' @import lmerTest phia 18 | #' @examples 19 | #' 20 | #' data(DataSet9.2) 21 | #' DataSet9.2$a <- factor(x = DataSet9.2$a) 22 | #' DataSet9.2$b <- factor(x = DataSet9.2$b) 23 | #' 24 | #' library(lmerTest) 25 | #' Exam9.2lmer <- lmer(y ~ (1|b/a), data = DataSet9.2) 26 | #' summary(Exam9.2lmer) 27 | #' 28 | #' Exam9.2lmer2 <- lm(y ~ a + b %in% a, data = DataSet9.2) 29 | #' summary(Exam9.2lmer2) 30 | #' 31 | #' ##--- Over all mean 32 | #' library(phia) 33 | #' list9.2 <- list(a = c("1" = 1/7,"2" = 1/7 34 | #' , "3" = 1/7,"4" = 1/7 35 | #' , "5" = 1/7,"6" = 1/7 36 | #' , "7" = 1/7 37 | #' )) 38 | #' phia::testFactors(model = Exam9.2lmer2, levels = list9.2) 39 | #' 40 | #' #---BLUP Estimates 41 | #' coef <- unlist(ranef(Exam9.2lmer)$a) 42 | #' BLUPa <- NULL 43 | #' for(i in 1:length(coef)){ 44 | #' BLUPa[i] <- (mean(DataSet9.2$y) + coef[i]) 45 | #' } 46 | #' print(BLUPa) 47 | #' 48 | #' #---BLUP Estimates Narrow 49 | #' BLUPaNar <- NULL 50 | #' for( i in 1:length(coef)) { 51 | #' BLUPaNar[i] <- (mean(DataSet9.2$y) + coef[i]) 52 | #' } 53 | #' 54 | #' BLUPaNar 55 | #' 56 | NULL 57 | -------------------------------------------------------------------------------- /man/Exam5.3.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam5.3.R 3 | \name{Exam5.3} 4 | \alias{Exam5.3} 5 | \title{Example 5.3 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-172)} 6 | \description{ 7 | Exam5.3 Inference using empirical standard error with different Bias connection 8 | } 9 | \examples{ 10 | 11 | data(DataSet4.1) 12 | DataSet4.1$trt <- factor(x = DataSet4.1$trt) 13 | DataSet4.1$block <- factor( x = DataSet4.1$block) 14 | 15 | ##---REML estimates on page 172 16 | library(lmerTest) 17 | Exam5.3REML <- lmerTest::lmer(formula = y ~ trt + (1|block), data = DataSet4.1, REML = TRUE) 18 | Exam5.3REML 19 | library(parameters) 20 | model_parameters(Exam5.3REML) 21 | ##---Standard Error Type "Model Based" with no Bias Connection 22 | anova(object = Exam5.3REML) 23 | anova(object = Exam5.3REML, ddf = "Satterthwaite") 24 | 25 | 26 | ##---Standard Error Type "Model Based" with "Kenward-Roger approximation" Bias Connection 27 | anova(object = Exam5.3REML, ddf = "Kenward-Roger") 28 | 29 | ##---ML estimates on page 172 30 | Exam5.3ML <- lmerTest::lmer(formula = y ~ trt + ( 1|block ), data = DataSet4.1, REML = FALSE) 31 | Exam5.3ML 32 | library(parameters) 33 | model_parameters(Exam5.3ML) 34 | 35 | ##---Standard Error Type "Model Based" with no Bias Connection 36 | anova(object = Exam5.3ML ) 37 | anova(object = Exam5.3ML, ddf = "Satterthwaite") 38 | 39 | } 40 | \references{ 41 | \enumerate{ 42 | \item Stroup, W. W. (2012). 43 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 44 | CRC Press. 45 | } 46 | } 47 | \seealso{ 48 | \code{\link{DataSet4.1}} 49 | } 50 | \author{ 51 | \enumerate{ 52 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 53 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 54 | } 55 | } 56 | -------------------------------------------------------------------------------- /R/Exam5.3.R: -------------------------------------------------------------------------------- 1 | #' @title Example 5.3 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-172) 2 | #' @name Exam5.3 3 | #' @description Exam5.3 Inference using empirical standard error with different Bias connection 4 | #' @author \enumerate{ 5 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 6 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 7 | #' } 8 | #' @references \enumerate{ 9 | #' \item Stroup, W. W. (2012). 10 | #' \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 11 | #' CRC Press. 12 | #' } 13 | #' @seealso 14 | #' \code{\link{DataSet4.1}} 15 | #' 16 | #' @import parameters lmerTest 17 | #' 18 | #' 19 | #' @examples 20 | #' 21 | #' data(DataSet4.1) 22 | #' DataSet4.1$trt <- factor(x = DataSet4.1$trt) 23 | #' DataSet4.1$block <- factor( x = DataSet4.1$block) 24 | #' 25 | #' ##---REML estimates on page 172 26 | #' library(lmerTest) 27 | #' Exam5.3REML <- lmerTest::lmer(formula = y ~ trt + (1|block), data = DataSet4.1, REML = TRUE) 28 | #' Exam5.3REML 29 | #' library(parameters) 30 | #' model_parameters(Exam5.3REML) 31 | #' ##---Standard Error Type "Model Based" with no Bias Connection 32 | #' anova(object = Exam5.3REML) 33 | #' anova(object = Exam5.3REML, ddf = "Satterthwaite") 34 | #' 35 | #' 36 | #' ##---Standard Error Type "Model Based" with "Kenward-Roger approximation" Bias Connection 37 | #' anova(object = Exam5.3REML, ddf = "Kenward-Roger") 38 | #' 39 | #' ##---ML estimates on page 172 40 | #' Exam5.3ML <- lmerTest::lmer(formula = y ~ trt + ( 1|block ), data = DataSet4.1, REML = FALSE) 41 | #' Exam5.3ML 42 | #' library(parameters) 43 | #' model_parameters(Exam5.3ML) 44 | #' 45 | #' ##---Standard Error Type "Model Based" with no Bias Connection 46 | #' anova(object = Exam5.3ML ) 47 | #' anova(object = Exam5.3ML, ddf = "Satterthwaite") 48 | #' 49 | NULL 50 | -------------------------------------------------------------------------------- /man/Exam9.1.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam9.1.R 3 | \name{Exam9.1} 4 | \alias{Exam9.1} 5 | \title{Example 9.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-273)} 6 | \description{ 7 | Exam9.1 One-way random effects only model 8 | } 9 | \examples{ 10 | 11 | data(DataSet9.1) 12 | DataSet9.1$a <- factor(x = DataSet9.1$a) 13 | 14 | ##---Random effects model 15 | library(lmerTest) 16 | Exam9.1lmer <- lmer( y ~ 1 + (1|a), data = DataSet9.1) 17 | summary(Exam9.1lmer) 18 | 19 | ##---fixed effects model 20 | Exam9.1lmer2 <- lm(y ~ a, data = DataSet9.1) 21 | summary(Exam9.1lmer2) 22 | 23 | #--------------------------------------------------- 24 | ## Over all mean narrow( page # 274) 25 | #--------------------------------------------------- 26 | library(emmeans) 27 | library(phia) 28 | list9.1 <- list(a = c( "1" = 1/12,"2" = 1/12 29 | , "3" = 1/12,"4" = 1/12 30 | , "5" = 1/12,"6" = 1/12 31 | , "7" = 1/12,"8" = 1/12 32 | , "9" = 1/12,"10" = 1/12 33 | , "11" = 1/12,"12" = 1/12 34 | )) 35 | phia::testFactors(model = Exam9.1lmer2, levels = list9.1) 36 | 37 | 38 | #---BLUP Estimates (Table 9.1) 39 | coef <- unlist(ranef(Exam9.1lmer)) 40 | BLUPa <- NULL 41 | for( i in 1:length(coef)) { 42 | BLUPa[i] <- (mean(DataSet9.1$y)+coef[i]) 43 | } 44 | print(BLUPa) 45 | 46 | } 47 | \references{ 48 | \enumerate{ 49 | \item Stroup, W. W. (2012). 50 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 51 | CRC Press. 52 | } 53 | } 54 | \seealso{ 55 | \code{\link{DataSet9.1}} 56 | } 57 | \author{ 58 | \enumerate{ 59 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 60 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 61 | } 62 | } 63 | -------------------------------------------------------------------------------- /R/Exam9.1.R: -------------------------------------------------------------------------------- 1 | #' @title Example 9.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-273) 2 | #' @name Exam9.1 3 | #' @description Exam9.1 One-way random effects only model 4 | #' @author \enumerate{ 5 | #' \item Muhammad Yaseen (\email{myaseen208@@gmail.com}) 6 | #' \item Adeela Munawar (\email{adeela.uaf@@gmail.com}) 7 | #' } 8 | #' @references \enumerate{ 9 | #' \item Stroup, W. W. (2012). 10 | #' \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 11 | #' CRC Press. 12 | #' } 13 | #' @seealso 14 | #' \code{\link{DataSet9.1}} 15 | #' @import emmeans lmerTest phia 16 | #' @examples 17 | #' 18 | #' data(DataSet9.1) 19 | #' DataSet9.1$a <- factor(x = DataSet9.1$a) 20 | #' 21 | #' ##---Random effects model 22 | #' library(lmerTest) 23 | #' Exam9.1lmer <- lmer( y ~ 1 + (1|a), data = DataSet9.1) 24 | #' summary(Exam9.1lmer) 25 | #' 26 | #' ##---fixed effects model 27 | #' Exam9.1lmer2 <- lm(y ~ a, data = DataSet9.1) 28 | #' summary(Exam9.1lmer2) 29 | #' 30 | #' #--------------------------------------------------- 31 | #' ## Over all mean narrow( page # 274) 32 | #' #--------------------------------------------------- 33 | #' library(emmeans) 34 | #' library(phia) 35 | #' list9.1 <- list(a = c( "1" = 1/12,"2" = 1/12 36 | #' , "3" = 1/12,"4" = 1/12 37 | #' , "5" = 1/12,"6" = 1/12 38 | #' , "7" = 1/12,"8" = 1/12 39 | #' , "9" = 1/12,"10" = 1/12 40 | #' , "11" = 1/12,"12" = 1/12 41 | #' )) 42 | #' phia::testFactors(model = Exam9.1lmer2, levels = list9.1) 43 | #' 44 | #' 45 | #' #---BLUP Estimates (Table 9.1) 46 | #' coef <- unlist(ranef(Exam9.1lmer)) 47 | #' BLUPa <- NULL 48 | #' for( i in 1:length(coef)) { 49 | #' BLUPa[i] <- (mean(DataSet9.1$y)+coef[i]) 50 | #' } 51 | #' print(BLUPa) 52 | #' 53 | NULL 54 | -------------------------------------------------------------------------------- /man/Exam7.3.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Exam7.3.R 3 | \name{Exam7.3} 4 | \alias{Exam7.3} 5 | \title{Example 7.3 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-223)} 6 | \description{ 7 | Exam7.3 explains multifactor models with some factors qualitative and some quantitative(Unequal slopes ANCOVA) 8 | } 9 | \examples{ 10 | 11 | library(car) 12 | library(ggplot2) 13 | library(emmeans) 14 | data(DataSet7.3) 15 | 16 | DataSet7.3$trt <- factor(x = DataSet7.3$trt ) 17 | 18 | ##----ANCOVA(Unequal slope Model) 19 | Exam7.3fm1 <- aov(formula = y ~ trt*x, data = DataSet7.3) 20 | car::Anova( mod = Exam7.3fm1 , type = "III") 21 | 22 | Plot <- 23 | ggplot( 24 | data = DataSet7.3 25 | , mapping = aes(x = factor(trt), y = x) 26 | ) + 27 | geom_boxplot(width = 0.5) + 28 | coord_flip() + 29 | geom_point() + 30 | stat_summary( 31 | fun = "mean" 32 | , geom = "point" 33 | , shape = 23 34 | , size = 2 35 | , fill = "red" 36 | ) + 37 | theme_bw() + 38 | ggtitle("Covariate by treatment Box Plot") + 39 | xlab("Treatment") 40 | print(Plot) 41 | 42 | ##----ANCOVA(Unequal slope Model without intercept at page 224) 43 | Exam7.3fm2 <- lm(formula = y ~ 0 + trt/x, data = DataSet7.3) 44 | summary(Exam7.3fm2) 45 | library(parameters) 46 | model_parameters(Exam7.3fm2) 47 | 48 | ##--Lsmeans treatment at x=7 & 12 at page 225 49 | emmeans(object = Exam7.3fm2, specs = ~trt|x, at = list(x = c(7, 12))) 50 | 51 | } 52 | \references{ 53 | \enumerate{ 54 | \item Stroup, W. W. (2012). 55 | \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}. 56 | CRC Press. 57 | } 58 | 59 | 60 | @seealso 61 | \code{\link{DataSet7.3}} 62 | } 63 | \author{ 64 | \enumerate{ 65 | \item Muhammad Yaseen (\email{myaseen208@gmail.com}) 66 | \item Adeela Munawar (\email{adeela.uaf@gmail.com}) 67 | } 68 | } 69 | -------------------------------------------------------------------------------- /docs/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js: -------------------------------------------------------------------------------- 1 | /*! 2 | * Bootstrap Table of Contents v1.0.1 (http://afeld.github.io/bootstrap-toc/) 3 | * Copyright 2015 Aidan Feldman 4 | * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ 5 | !function(a){"use strict";window.Toc={helpers:{findOrFilter:function(e,t){var n=e.find(t);return e.filter(t).add(n).filter(":not([data-toc-skip])")},generateUniqueIdBase:function(e){return a(e).text().trim().replace(/\'/gi,"").replace(/[& +$,:;=?@"#{}|^~[`%!'<>\]\.\/\(\)\*\\\n\t\b\v]/g,"-").replace(/-{2,}/g,"-").substring(0,64).replace(/^-+|-+$/gm,"").toLowerCase()||e.tagName.toLowerCase()},generateUniqueId:function(e){for(var t=this.generateUniqueIdBase(e),n=0;;n++){var r=t;if(0')},createChildNavList:function(e){var t=this.createNavList();return e.append(t),t},generateNavEl:function(e,t){var n=a('');n.attr("href","#"+e),n.text(t);var r=a("
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