MMFAIR sources

Links & References

Packages

Mixed Model

lme4

• Reference manual
• Vignettes
  • lmer Performance Tips
  • Fitting Linear Mixed-Effects Models using lme4
  • PLS vs GLS for LMMs
  • Computational Methods

glmmTMB

• Reference manual
• Vignettes
  • random effect structures
  • post-hoc MCMC
  • miscellaneous examples
  • parallel optimization
  • simulate
  • troubleshooting
  • basic examples of glmmTMB usage
  • model evaluation

nlme

• Reference manual
• Vignettes: none

sommer

• Reference manual
• Vignettes
  • FAQ for the sommer package
  • Quantitative genetics using the sommer package
  • Moving to newer versions of sommer
  • Quick start for the sommer package

Helper Packages

AICcmodavg

• Reference manual
• Vignettes: none

broom.mixed

• Reference manual
• Vignettes
  • introduction to broom.mixed

mixedup

• github repositroy
• Vignettes
  • For more details and examples see here

Data/Examples

agridat

• Reference manual
• Vignettes
  • Additional agricultural data
  • Graphical Gems in the agridat Package
  • Using Papadakis covariates for nearest neighbor analysis

agritutorial

• Reference manual
• Vignettes
  • Tutorial Analysis of Some Agricultural Experiments

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.

Piepho, H. P. (2009). Data transformation in statistical analysis of field trials with changing treatment variance. Agronomy Journal, 101(4), 865-869.

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.

Websites

“GLMM FAQ” by Ben Bolker and others

“Mixed Models with R” by Michael Clark

Contributions

Proofreader

• Muhammad Afzal
• Harimurti Buntaran

Session Info

## 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

 

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schmidtpaul1989@outlook.com