Hi there!

This is a project under construction. Our aim is to provide a cookbook with mixed model analyses of typical examples in life sciences (focus on agriculture/biology) and compare the possibilities or rather limitations of the R-packages

to each other, but also to SAS’ PROC MIXED.

Find chapters by navigating the menu at the top of the page. Each chapter focuses on a certain aspect of mixed modelling. Within each chapter, switch between tabs with codes from the different packages via these buttons:

nlme

lme4

glmmTMB

sommer

SAS

Chapters

		Possible in
Topic	Chapter	nlme	lme4	glmmTMB	sommer	SAS
R-side	Heterogeneous err. var.	yes	no	kind of	yes	yes
	First-order autoregressive	yes	no	kind of	not really	yes
	Fixed scalar (Smith’s weights)	in progress	in progress	in progress	in progress	yes
	Fixed matrix (fully efficient weighting)	in progress	in progress	in progress	in progress	yes
G-side	Fixed matrix (kinship/pedigree)	in progress	in progress	in progress	in progress	in progress
	Unstructured	in progress	in progress	in progress	in progress	in progress
	First-order factor analytic	in progress	in progress	in progress	in progress	in progress
ModelFit	log-likelihood, AIC, BIC	in progress	in progress	in progress	in progress	in progress
ANOVA	with DF adjustments	in progress	in progress	in progress	in progress	in progress
BLUPs	raw/conditional predicted()	in progress	in progress	in progress	in progress	in progress
BLUEs	raw/conditional emmeans()	in progress	in progress	in progress	in progress	in progress
Extract	estimated R-side matrix	in progress	in progress	in progress	in progress	in progress
	estimated G-side matrix	in progress	in progress	in progress	in progress	in progress
	MMEq solutions	in progress	in progress	in progress	in progress	in progress

Approach

In addition to the chapters, there are summaries for certain topics where we felt additional info may be beneficial, but should not bloat the chapters themselves. Just like chapters, summaries can be found by navigating the menu at the top of the page.

Where possible, we try to use example data/analyses for our chapters that have been published in peer-reviewed journals.

In terms of R syntax, we generally try to follow the approach presented on the “R for Data Science” website, making use of:

Mixed Models for Agriculture in R