Simple repository of links to tools for plant breeding and genetics, with some annotation. This is for information purposes only.
A section on mixed-models. See my other repository on examples of mixed-model applications for plant breeding experiments.
- CRAN task view for mixed-models
- lme4
- Can be forced to fit compound symmetry, unstructured, and diagonal covariance structures
- glmmTMB
- Allows for some cool covariance structures, including Toeplitz, AR1, spatial exponential; see here
- blme
- Extends lme4 and allows for prior distributions; it also allows for the residual variance to be fixed (useful for two-stage analysis)
- rrBLUP
- Very nice for a single random effect; the go-to for genomewide selection
- sommer
- Great for mixed models with multiple random effects and with kinship
- lme4GS
- lme4 language with flexibility for kinship; in theory the more complex covariance structures of lme4 (us, cs, diag) could be deployed
- asreml
- The gold standard for quickly fitting models with complex covariance sturctures, but you need a license
- mmrm
- Mixed-models for repeated measures; allows for time-dependent covariance structures like AR1, ante, toep, and exp
- The Biometris group has several useful R packages:
- statgenGWAS
- single-trait GWAS
- statgenQTLxT
- multi-trait, multi-environment GWAS
- statgenIBD
- Calculate identity-by-decent probabilities in two-, three-, and four-way crosses
- statgenGWAS
- statgenGxE
- Mega-environment analysis, stability, FW-regression, AMMI and GGE, etc. all the fun stuff
- statgenSTA
- Mixed-model analysis of field trials with or without spatial trends