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Chapters
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Summaries
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<a href="variance_structures.html">Variance Structures</a>
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<a href="model_selection.html">Model Selection</a>
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<li>
<a href="glmmtmbdispformula0.html">Error varcov struct with glmmTMB</a>
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<h1 class="title toc-ignore">MMFAIR sources</h1>
</div>
<div id="links-references" class="section level1 tabset tabset-fade tabset-pills">
<h1>Links & References</h1>
<div id="packages" class="section level2">
<h2>Packages</h2>
<div id="mixed-model" class="section level3">
<h3>Mixed Model</h3>
<div id="lme4" class="section level4">
<h4>lme4</h4>
<ul>
<li><a href="https://cran.r-project.org/web/packages/lme4/lme4.pdf" target="_blank">Reference manual</a></li>
<li>Vignettes
<ul>
<li><a href="https://cran.r-project.org/web/packages/lme4/vignettes/lmerperf.html" target="_blank">lmer Performance Tips</a></li>
<li><a href="https://cran.r-project.org/web/packages/lme4/vignettes/lmer.pdf" target="_blank">Fitting Linear Mixed-Effects Models using lme4</a></li>
<li><a href="https://cran.r-project.org/web/packages/lme4/vignettes/PLSvGLS.pdf" target="_blank">PLS vs GLS for LMMs</a></li>
<li><a href="https://cran.r-project.org/web/packages/lme4/vignettes/Theory.pdf" target="_blank">Computational Methods</a></li>
</ul></li>
</ul>
</div>
<div id="glmmtmb" class="section level4">
<h4>glmmTMB</h4>
<ul>
<li><a href="https://cran.r-project.org/web/packages/glmmTMB/glmmTMB.pdf" target="_blank">Reference manual</a></li>
<li>Vignettes
<ul>
<li><a href="https://cran.r-project.org/web/packages/glmmTMB/vignettes/covstruct.html" target="_blank">random effect structures</a></li>
<li><a href="https://cran.r-project.org/web/packages/glmmTMB/vignettes/mcmc.html" target="_blank">post-hoc MCMC</a></li>
<li><a href="https://cran.r-project.org/web/packages/glmmTMB/vignettes/miscEx.html" target="_blank">miscellaneous examples</a></li>
<li><a href="https://cran.r-project.org/web/packages/glmmTMB/vignettes/parallel.html" target="_blank">parallel optimization</a></li>
<li><a href="https://cran.r-project.org/web/packages/glmmTMB/vignettes/sim.html" target="_blank">simulate</a></li>
<li><a href="https://cran.r-project.org/web/packages/glmmTMB/vignettes/troubleshooting.html" target="_blank">troubleshooting</a></li>
<li><a href="https://cran.r-project.org/web/packages/glmmTMB/vignettes/glmmTMB.pdf" target="_blank">basic examples of glmmTMB usage</a></li>
<li><a href="https://cran.r-project.org/web/packages/glmmTMB/vignettes/model_evaluation.pdf" target="_blank">model evaluation</a></li>
</ul></li>
</ul>
</div>
<div id="nlme" class="section level4">
<h4>nlme</h4>
<ul>
<li><a href="https://cran.r-project.org/web/packages/nlme/nlme.pdf" target="_blank">Reference manual</a></li>
<li>Vignettes: none</li>
</ul>
</div>
<div id="sommer" class="section level4">
<h4>sommer</h4>
<ul>
<li><a href="https://cran.r-project.org/web/packages/sommer/sommer.pdf" target="_blank">Reference manual</a></li>
<li>Vignettes
<ul>
<li><a href="https://cran.r-project.org/web/packages/sommer/vignettes/sommer.FAQ.pdf" target="_blank">FAQ for the sommer package</a></li>
<li><a href="https://cran.r-project.org/web/packages/sommer/vignettes/sommer.pdf" target="_blank">Quantitative genetics using the sommer package</a></li>
<li><a href="https://cran.r-project.org/web/packages/sommer/vignettes/sommer.changes.pdf" target="_blank">Moving to newer versions of sommer</a></li>
<li><a href="https://cran.r-project.org/web/packages/sommer/vignettes/sommer.start.pdf" target="_blank">Quick start for the sommer package</a></li>
</ul></li>
</ul>
</div>
</div>
<div id="helper-packages" class="section level3">
<h3>Helper Packages</h3>
<div id="aiccmodavg" class="section level4">
<h4>AICcmodavg</h4>
<ul>
<li><a href="https://cran.r-project.org/web/packages/AICcmodavg/AICcmodavg.pdf" target="_blank">Reference manual</a></li>
<li>Vignettes: none</li>
</ul>
</div>
<div id="broom.mixed" class="section level4">
<h4>broom.mixed</h4>
<ul>
<li><a href="https://cran.r-project.org/web/packages/broom.mixed/broom.mixed.pdf" target="_blank">Reference manual</a></li>
<li>Vignettes
<ul>
<li><a href="https://cran.r-project.org/web/packages/broom.mixed/vignettes/broom_mixed_intro.html" target="_blank">introduction to broom.mixed</a></li>
</ul></li>
</ul>
</div>
<div id="mixedup" class="section level4">
<h4>mixedup</h4>
<ul>
<li><a href="https://github.com/m-clark/mixedup" target="_blank">github repositroy</a></li>
<li>Vignettes
<ul>
<li><a href="https://m-clark.github.io/mixedup/" target="_blank">For more details and examples see here</a></li>
</ul></li>
</ul>
</div>
</div>
<div id="dataexamples" class="section level3">
<h3>Data/Examples</h3>
<div id="agridat" class="section level4">
<h4>agridat</h4>
<ul>
<li><a href="https://cran.r-project.org/web/packages/agridat/agridat.pdf" target="_blank">Reference manual</a></li>
<li>Vignettes
<ul>
<li><a href="https://cran.r-project.org/web/packages/agridat/vignettes/agridat_data.html" target="_blank">Additional agricultural data</a></li>
<li><a href="https://cran.r-project.org/web/packages/agridat/vignettes/agridat_examples.html" target="_blank">Graphical Gems in the agridat Package</a></li>
<li><a href="https://cran.r-project.org/web/packages/agridat/vignettes/agridat_papadakis.html" target="_blank">Using Papadakis covariates for nearest neighbor analysis</a></li>
</ul></li>
</ul>
</div>
<div id="agritutorial" class="section level4">
<h4>agritutorial</h4>
<ul>
<li><a href="https://cran.r-project.org/web/packages/agriTutorial/agriTutorial.pdf" target="_blank">Reference manual</a></li>
<li>Vignettes
<ul>
<li><a href="https://cran.r-project.org/web/packages/agriTutorial/vignettes/agriTutorialVignette.pdf" target="_blank">Tutorial Analysis of Some Agricultural Experiments</a></li>
</ul></li>
</ul>
</div>
</div>
</div>
<div id="publications" class="section level2">
<h2>Publications</h2>
<p><a href="https://acsess.onlinelibrary.wiley.com/doi/full/10.1002/csc2.20177" target="_blank">Buntaran, Harimurti, et al. (2020). Cross‐validation of stage‐wise mixed‐model analysis of Swedish variety trials with winter wheat and spring barley. Crop Science.</a></p>
<p><a href="https://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/agronj2008.0226x" target="_blank">Piepho, H. P. (2009). Data transformation in statistical analysis of field trials with changing treatment variance. Agronomy Journal, 101(4), 865-869.</a></p>
<p><a href="https://onlinelibrary.wiley.com/doi/full/10.1111/jac.12267" target="_blank">Piepho, H. P. & Edmondson, R. N. (2018). A tutorial on the statistical analysis of factorial experiments with qualitative and quantitative treatment factor levels. Journal of Agronomy and Crop Science 204(5): 429-455.</a></p>
</div>
<div id="websites" class="section level2">
<h2>Websites</h2>
<p><a href="http://bbolker.github.io/mixedmodels-misc/glmmFAQ.html" target="_blank">“GLMM FAQ”</a> by Ben Bolker and others</p>
<p><a href="https://m-clark.github.io/mixed-models-with-R/introduction.html" target="_blank">“Mixed Models with R”</a> by Michael Clark</p>
</div>
<div id="contributions" class="section level2">
<h2>Contributions</h2>
<p><strong>Proofreader</strong></p>
<ul>
<li><a href="https://www.linkedin.com/in/mafzal2/" target="_blank">Muhammad Afzal</a></li>
<li><a href="https://www.linkedin.com/in/harimurti-buntaran/" target="_blank">Harimurti Buntaran</a></li>
</ul>
</div>
<div id="session-info" class="section level2">
<h2>Session Info</h2>
<pre><code>## R version 4.0.3 (2020-10-10)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 18363)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252
## [4] LC_NUMERIC=C LC_TIME=German_Germany.1252
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] mixedup_0.3.7 viridis_0.5.1 viridisLite_0.3.0 gifski_0.8.6 gganimate_1.0.7
## [6] htmltools_0.5.0 formattable_0.2.0.1 kableExtra_1.3.1 rmarkdown_2.6 AICcmodavg_2.3-1
## [11] sommer_4.1.1 crayon_1.3.4 lattice_0.20-41 MASS_7.3-53 lme4_1.1-26
## [16] Matrix_1.2-18 flair_0.0.2 emo_0.0.0.9000 broom.mixed_0.2.6 glmmTMB_1.0.2.1
## [21] nlme_3.1-149 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.2 purrr_0.3.4
## [26] readr_1.4.0 tidyr_1.1.2 tibble_3.0.4 ggplot2_3.3.2 tidyverse_1.3.0
## [31] conflicted_1.0.4
##
## loaded via a namespace (and not attached):
## [1] TH.data_1.0-10 VGAM_1.1-4 minqa_1.2.4 colorspace_2.0-0 selectr_0.4-2
## [6] ellipsis_0.3.1 rsconnect_0.8.16 estimability_1.3 fs_1.5.0 rstudioapi_0.13
## [11] farver_2.0.3 fansi_0.4.1 mvtnorm_1.1-1 lubridate_1.7.9.2 xml2_1.3.2
## [16] codetools_0.2-16 splines_4.0.3 knitr_1.30 jsonlite_1.7.2 nloptr_1.2.2.2
## [21] pbkrtest_0.5-0.1 packrat_0.5.0 broom_0.7.3 dbplyr_2.0.0 compiler_4.0.3
## [26] httr_1.4.2 emmeans_1.5.3 backports_1.2.1 assertthat_0.2.1 cli_2.2.0
## [31] tweenr_1.0.1 prettyunits_1.1.1 tools_4.0.3 lmerTest_3.1-3 coda_0.19-4
## [36] gtable_0.3.0 glue_1.4.2 reshape2_1.4.4 Rcpp_1.0.5 cellranger_1.1.0
## [41] raster_3.4-5 vctrs_0.3.6 xfun_0.19 rvest_0.3.6 lifecycle_0.2.0
## [46] pacman_0.5.1 statmod_1.4.35 zoo_1.8-8 scales_1.1.1 hms_0.5.3
## [51] parallel_4.0.3 sandwich_3.0-0 TMB_1.7.18 yaml_2.2.1 gridExtra_2.3
## [56] memoise_1.1.0 stringi_1.5.3 highr_0.8 agriTutorial_0.1.5 boot_1.3-25
## [61] rlang_0.4.9 pkgconfig_2.0.3 evaluate_0.14 labeling_0.4.2 htmlwidgets_1.5.3
## [66] tidyselect_1.1.0 plyr_1.8.6 magrittr_2.0.1 R6_2.5.0 generics_0.1.0
## [71] multcomp_1.4-15 DBI_1.1.0 pillar_1.4.7 haven_2.3.1 withr_2.3.0
## [76] survival_3.2-7 sp_1.4-4 modelr_0.1.8 progress_1.2.2 agridat_1.17
## [81] grid_4.0.3 readxl_1.3.1 reprex_0.3.0 digest_0.6.27 webshot_0.5.2
## [86] xtable_1.8-4 numDeriv_2016.8-1.1 stats4_4.0.3 munsell_0.5.0 unmarked_1.0.1</code></pre>
</div>
</div>
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<p style="text-align: center;">Please feel free to contact us about any of this! </p>
<p style="text-align: center;"><span style="color: #003f75ff;"><em>schmidtpaul1989@outlook.com</em></span></p>
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