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sources.Rmd
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---
title: "MMFAIR sources"
output:
html_document:
includes:
in_header: header.html
after_body: footer.html
params:
hilang:
- sas
---
# Links & References {.tabset .tabset-fade .tabset-pills}
## Packages
### Mixed Model
#### lme4
* [Reference manual](https://cran.r-project.org/web/packages/lme4/lme4.pdf){target="_blank"}
* Vignettes
+ [lmer Performance Tips](https://cran.r-project.org/web/packages/lme4/vignettes/lmerperf.html){target="_blank"}
+ [Fitting Linear Mixed-Effects Models using lme4](https://cran.r-project.org/web/packages/lme4/vignettes/lmer.pdf){target="_blank"}
+ [PLS vs GLS for LMMs](https://cran.r-project.org/web/packages/lme4/vignettes/PLSvGLS.pdf){target="_blank"}
+ [Computational Methods](https://cran.r-project.org/web/packages/lme4/vignettes/Theory.pdf){target="_blank"}
#### glmmTMB
* [Reference manual](https://cran.r-project.org/web/packages/glmmTMB/glmmTMB.pdf){target="_blank"}
* Vignettes
+ [random effect structures](https://cran.r-project.org/web/packages/glmmTMB/vignettes/covstruct.html){target="_blank"}
+ [post-hoc MCMC](https://cran.r-project.org/web/packages/glmmTMB/vignettes/mcmc.html){target="_blank"}
+ [miscellaneous examples](https://cran.r-project.org/web/packages/glmmTMB/vignettes/miscEx.html){target="_blank"}
+ [parallel optimization](https://cran.r-project.org/web/packages/glmmTMB/vignettes/parallel.html){target="_blank"}
+ [simulate](https://cran.r-project.org/web/packages/glmmTMB/vignettes/sim.html){target="_blank"}
+ [troubleshooting](https://cran.r-project.org/web/packages/glmmTMB/vignettes/troubleshooting.html){target="_blank"}
+ [basic examples of glmmTMB usage](https://cran.r-project.org/web/packages/glmmTMB/vignettes/glmmTMB.pdf){target="_blank"}
+ [model evaluation](https://cran.r-project.org/web/packages/glmmTMB/vignettes/model_evaluation.pdf){target="_blank"}
#### nlme
* [Reference manual](https://cran.r-project.org/web/packages/nlme/nlme.pdf){target="_blank"}
* Vignettes: none
#### sommer
* [Reference manual](https://cran.r-project.org/web/packages/sommer/sommer.pdf){target="_blank"}
* Vignettes
+ [FAQ for the sommer package](https://cran.r-project.org/web/packages/sommer/vignettes/sommer.FAQ.pdf){target="_blank"}
+ [Quantitative genetics using the sommer package](https://cran.r-project.org/web/packages/sommer/vignettes/sommer.pdf){target="_blank"}
+ [Moving to newer versions of sommer](https://cran.r-project.org/web/packages/sommer/vignettes/sommer.changes.pdf){target="_blank"}
+ [Quick start for the sommer package](https://cran.r-project.org/web/packages/sommer/vignettes/sommer.start.pdf){target="_blank"}
### Helper Packages
#### AICcmodavg
* [Reference manual](https://cran.r-project.org/web/packages/AICcmodavg/AICcmodavg.pdf){target="_blank"}
* Vignettes: none
#### broom.mixed
* [Reference manual](https://cran.r-project.org/web/packages/broom.mixed/broom.mixed.pdf){target="_blank"}
* Vignettes
+ [introduction to broom.mixed](https://cran.r-project.org/web/packages/broom.mixed/vignettes/broom_mixed_intro.html){target="_blank"}
#### mixedup
* [github repositroy](https://github.com/m-clark/mixedup){target="_blank"}
* Vignettes
+ [For more details and examples see here](https://m-clark.github.io/mixedup/){target="_blank"}
### Data/Examples
#### agridat
* [Reference manual](https://cran.r-project.org/web/packages/agridat/agridat.pdf){target="_blank"}
* Vignettes
+ [Additional agricultural data](https://cran.r-project.org/web/packages/agridat/vignettes/agridat_data.html){target="_blank"}
+ [Graphical Gems in the agridat Package](https://cran.r-project.org/web/packages/agridat/vignettes/agridat_examples.html){target="_blank"}
+ [Using Papadakis covariates for nearest neighbor analysis](https://cran.r-project.org/web/packages/agridat/vignettes/agridat_papadakis.html){target="_blank"}
#### agritutorial
* [Reference manual](https://cran.r-project.org/web/packages/agriTutorial/agriTutorial.pdf){target="_blank"}
* Vignettes
+ [Tutorial Analysis of Some Agricultural Experiments](https://cran.r-project.org/web/packages/agriTutorial/vignettes/agriTutorialVignette.pdf){target="_blank"}
## Publications
[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.](https://acsess.onlinelibrary.wiley.com/doi/full/10.1002/csc2.20177){target="_blank"}
[Piepho, H. P. (2009). Data transformation in statistical analysis of field trials with changing treatment variance. Agronomy Journal, 101(4), 865-869.](https://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/agronj2008.0226x){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.](https://onlinelibrary.wiley.com/doi/full/10.1111/jac.12267){target="_blank"}
## Websites
["GLMM FAQ"](http://bbolker.github.io/mixedmodels-misc/glmmFAQ.html){target="_blank"} by Ben Bolker and others
["Mixed Models with R"](https://m-clark.github.io/mixed-models-with-R/introduction.html){target="_blank"} by Michael Clark
## Contributions
**Proofreader**
* [Muhammad Afzal](https://www.linkedin.com/in/mafzal2/){target="_blank"}
* [Harimurti Buntaran](https://www.linkedin.com/in/harimurti-buntaran/){target="_blank"}
## Session Info
```{r, echo=FALSE}
sessionInfo()
```