A substantial part of my job has little to do with statistics; nevertheless, a large proportion of the statistical side of things relates to applications of linear mixed models. The bulk of my use of mixed models relates to the analysis of experiments that have a genetic structure.

## A brief history of time

At the beginning (1992-1995) I would use SAS (first `proc glm`

, later `proc mixed`

), but things started getting painfully slow and limiting if one wanted to move into animal model BLUP. At that time (1995-1996), I moved to DFREML (by Karen Meyer, now replaced by WOMBAT) and AIREML (by Dave Johnson, now defunct—the program I mean), which were designed for the analysis of animal breeding progeny trials, so it was a hassle to deal with experimental design features. At the end of 1996 (or was it the beginning of 1997?) I started playing with ASReml (programed by Arthur Gilmour mostly based on theoretical work by Robin Thompson and Brian Cullis). I was still using SAS for data preparation, but all my analyses went through ASReml (for which I wrote the cookbook), which was orders of magnitude faster than SAS (and could deal with much bigger problems). Around 1999, I started playing with R (prompted by a suggestion from Rod Ball), but I didn’t *really* use R/S+ often enough until 2003. At the end of 2005 I started using OS X and quickly realized that using a virtual machine or dual booting was not really worth it, so I dropped SAS and totally relied on R in 2009.

## Options

As for many other problems, there are several packages in R that let you deal with linear mixed models from a frequentist (REML) point of view. I will only mention nlme (Non-Linear Mixed Effects), lme4 (Linear Mixed Effects) and asreml (average spatial reml). There are also several options for Bayesian approaches, but that will be another post.

nlme is the most mature one and comes by default with any R installation. In addition to fitting hierarchical generalized linear mixed models it also allows fitting non-linear *mixed models following a Gaussian distribution* (my explanation wasn’t very clear, thanks to ucfagls below for pointing this out). Its main advantages are, in my humble opinion, the ability to fit fairly complex hierarchical models using linear or non-linear approaches, a good variety of variance and correlation structures, and access to several distributions and link functions for generalized models. In my opinion, its main drawbacks are i- fitting cross-classified random factors is a pain, ii- it can be slow and may struggle with lots of data, iii- it does not deal with pedigrees by default and iv- it does not deal with multivariate data.

lme4 is a project led by Douglas Bates (one of the co-authors of nlme), looking at modernizing the code and making room for trying new ideas. On the positive side, it seems to be a bit faster than nlme and it deals a lot better with cross-classified random factors. Drawbacks: similar to nlme’s, but dropping point i- and adding that it doesn’t deal with covariance and correlation structures yet. It is possible to fit pedigrees using the pedigreemm package, but I find the combination a bit flimsy.

ASReml-R is, unsurprisingly, an R package interface to ASReml. On the plus side it i- deals well with cross-classified random effects, ii- copes very well with pedigrees, iii- can work with fairly large datasets, iv-can run multivariate analyses and v- covers a large number of covariance and correlation structures. Main drawbacks are i- limited functionality for non-Gaussian responses, ii- it does not cover non-linear models and iii- it is non-free (as in beer and speech). The last drawback is *relative*; it is possible to freely use asreml for academic purposes (and there is also a version for developing countries). Besides researchers, the main users of ASReml/ASReml-R are breeding companies.

All these three packages are available for Windows, Linux and OS X.

## A (very) simple example

I will use a traditional dataset to show examples of the notation for the three packages: Yates’ variety and nitrogen split-plot experiment. We can get the dataset from the MASS package, after which it is a good idea to rename the variables using meaningful names. In addition, I will follow Bill Venables’s excellent advice and create additional variables for main plot and subplots, as it is confusing to use the same factor for two purposes (e.g. variety as treatment and main plot). Incidentally, if you haven’t read Bill’s post go and read it; it is one of the best explanations I have ever seen for a split-plot analysis.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
library(MASS) data(oats) names(oats) = c('block', 'variety', 'nitrogen', 'yield') oats$mainplot = oats$variety oats$subplot = oats$nitrogen summary(oats) block variety nitrogen yield mainplot I :12 Golden.rain:24 0.0cwt:18 Min. : 53.0 Golden.rain:24 II :12 Marvellous :24 0.2cwt:18 1st Qu.: 86.0 Marvellous :24 III:12 Victory :24 0.4cwt:18 Median :102.5 Victory :24 IV :12 0.6cwt:18 Mean :104.0 V :12 3rd Qu.:121.2 VI :12 Max. :174.0 subplot 0.0cwt:18 0.2cwt:18 0.4cwt:18 0.6cwt:18 |

The nlme code for this analysis is fairly simple: response on the left-hand side of the tilde, followed by the fixed effects (variety, nitrogen and their interaction). Then there is the specification of the random effects (which also uses a tilde) and the data set containing all the data. Notice that `1|block/mainplot`

is fitting block and mainplot within block. There is no reference to subplot as there is a single assessment for each subplot, which ends up being used at the residual level.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 |
library(nlme) m1.nlme = lme(yield ~ variety*nitrogen, random = ~ 1|block/mainplot, data = oats) summary(m1.nlme) Linear mixed-effects model fit by REML Data: oats AIC BIC logLik 559.0285 590.4437 -264.5143 Random effects: Formula: ~1 | block (Intercept) StdDev: 14.64496 Formula: ~1 | mainplot %in% block (Intercept) Residual StdDev: 10.29863 13.30727 Fixed effects: yield ~ variety * nitrogen Value Std.Error DF t-value p-value (Intercept) 80.00000 9.106958 45 8.784492 0.0000 varietyMarvellous 6.66667 9.715028 10 0.686222 0.5082 varietyVictory -8.50000 9.715028 10 -0.874933 0.4021 nitrogen0.2cwt 18.50000 7.682957 45 2.407927 0.0202 nitrogen0.4cwt 34.66667 7.682957 45 4.512152 0.0000 nitrogen0.6cwt 44.83333 7.682957 45 5.835427 0.0000 varietyMarvellous:nitrogen0.2cwt 3.33333 10.865342 45 0.306786 0.7604 varietyVictory:nitrogen0.2cwt -0.33333 10.865342 45 -0.030679 0.9757 varietyMarvellous:nitrogen0.4cwt -4.16667 10.865342 45 -0.383482 0.7032 varietyVictory:nitrogen0.4cwt 4.66667 10.865342 45 0.429500 0.6696 varietyMarvellous:nitrogen0.6cwt -4.66667 10.865342 45 -0.429500 0.6696 varietyVictory:nitrogen0.6cwt 2.16667 10.865342 45 0.199411 0.8428 anova(m1.nlme) numDF denDF F-value p-value (Intercept) 1 45 245.14299 <.0001 variety 2 10 1.48534 0.2724 nitrogen 3 45 37.68562 <.0001 variety:nitrogen 6 45 0.30282 0.9322 |

The syntax for lme4 is not that dissimilar, with random effects specified using a (1|something here) syntax. One difference between the two packages is that nlme reports standard deviations instead of variances for the random effects.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 |
library(lme4) m1.lme4 = lmer(yield ~ variety*nitrogen + (1|block/mainplot), data = oats) summary(m1.lme4) Linear mixed model fit by REML Formula: yield ~ variety * nitrogen + (1 | block/mainplot) Data: oats AIC BIC logLik deviance REMLdev 559 593.2 -264.5 595.9 529 Random effects: Groups Name Variance Std.Dev. mainplot:block (Intercept) 106.06 10.299 block (Intercept) 214.48 14.645 Residual 177.08 13.307 Number of obs: 72, groups: mainplot:block, 18; block, 6 Fixed effects: Estimate Std. Error t value (Intercept) 80.0000 9.1064 8.785 varietyMarvellous 6.6667 9.7150 0.686 varietyVictory -8.5000 9.7150 -0.875 nitrogen0.2cwt 18.5000 7.6830 2.408 nitrogen0.4cwt 34.6667 7.6830 4.512 nitrogen0.6cwt 44.8333 7.6830 5.835 varietyMarvellous:nitrogen0.2cwt 3.3333 10.8653 0.307 varietyVictory:nitrogen0.2cwt -0.3333 10.8653 -0.031 varietyMarvellous:nitrogen0.4cwt -4.1667 10.8653 -0.383 varietyVictory:nitrogen0.4cwt 4.6667 10.8653 0.430 varietyMarvellous:nitrogen0.6cwt -4.6667 10.8653 -0.430 varietyVictory:nitrogen0.6cwt 2.1667 10.8653 0.199 anova(m1.lme4) Analysis of Variance Table Df Sum Sq Mean Sq F value variety 2 526.1 263.0 1.4853 nitrogen 3 20020.5 6673.5 37.6856 variety:nitrogen 6 321.7 53.6 0.3028 |

For this type of problem, the notation for asreml is also very similar, particularly when compared to nlme.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 |
library(asreml) m1.asreml = asreml(yield ~ variety*nitrogen, random = ~ block/mainplot, data = oats) summary(m1.asreml)$varcomp gamma component std.error z.ratio constraint block!block.var 1.2111647 214.4771 168.83404 1.270343 Positive block:mainplot!block.var 0.5989373 106.0618 67.87553 1.562593 Positive R!variance 1.0000000 177.0833 37.33244 4.743416 Positive wald(m1.asreml, denDF = 'algebraic') $Wald Df denDF F.inc Pr (Intercept) 1 5 245.1000 1.931825e-05 variety 2 10 1.4850 2.723869e-01 nitrogen 3 45 37.6900 2.457710e-12 variety:nitrogen 6 45 0.3028 9.321988e-01 $stratumVariances df Variance block block:mainplot R!variance block 5 3175.0556 12 4 1 block:mainplot 10 601.3306 0 4 1 R!variance 45 177.0833 0 0 1 |

In this simple example one pretty much gets the same results, independently of the package used (which is certainly comforting). I will soon cover another simple model, but with much larger dataset, to highlight some performance differences between the packages.

2011/10/17 at 9:41 am

Hi there, this looks like to become a very interesting blog! Looking forward to it!

cheers

2011/10/17 at 10:37 am

Thanks and I hope you are right!

2011/10/17 at 10:03 am

A small clarification: nlme doesn't fit generalized LMMs just linear ones. It is lme4 that implements generalized linear and non-linear MMs (as well as linear ones).

2011/10/17 at 10:40 am

Thanks for the clarification. nlme deals only with Gaussian non-linear mixed models; I'll update the post.

2011/10/17 at 2:01 pm

I was going to make the same comment as ucfagls. Nice post, though, looking forward to future posts.

2011/10/17 at 7:25 pm

MCMCglmm, it may be another choice. It is a Bayesian animal modeler. You may need to turn to it. And, R-INLR package, is also attractive. All these two R packages are free.

2011/10/17 at 8:50 pm

Hi Jianfeng, You are right, and I will cover them with more detail in future posts. I used MCMCglmm for a multivariate animal model when working in this paper and am submitting soon another paper using INLA. Both packages are really good, but I am still getting my head around some of their notation.

2011/10/18 at 2:33 am

An alternative to the packages already mentioned is the hglm package on CRAN (developed by me and collaborators). There it is possible to give arbitrary design matrices (both for fixed and random effects) as inputs to the hglm-function, which allows modelling of correlated random effects. In our R Journal publication (The R Journal 2:20-28) we have an example of a an animal model being fitted (see Example 4 in the paper). Note that arbitrary correlation structures can be fitted, allowing for eg modelling of IBD-matrices in QTL analysis and genomic relationship matrices as well.

2011/10/18 at 7:59 am

Hi Lars, Thanks for the pointer to hglm and its publication in the R-Journal (PDF). I hope to check it when we finish our semester (I'm trying to keep my head above the water at the moment).

By the way, it is hard to beat the name for your PhD topic; my childhood dream come true! I visited SLU in Uppsala in Dec 2009, cool place.

2011/10/21 at 2:18 am

Well Luis, I'm pretty proud of being one of very few who has been doing research on animal breeding in reindeer. Northern Sweden can be a pretty cool place. Even cooler than Uppsala.

Another package, recently available on CRAN, is dhglm developed by Noh & Lee. There you can fit GLMs having random effects both in the mean and the dispersion part, which has some interesting applications in genetics (see for instance my recent papers in this field http://www.gsejournal.org/content/pdf/1297-9686-4… and http://www.genetics.org/content/188/2/435.full ) . In the dhglm package you can also fit arbitrary correlation structures.

2011/11/29 at 11:30 am

I am very very late to this post but I have a question, if somewhat off topic: how did you collect the output of several lme objects in an useful format for model comparison and, later, for latex table? I've been struggling with that recently. Best, Antonio.

2011/11/30 at 12:19 am

You can create a list in R and assign the results of the analyses as one more element of the list (I normally save only the variance components and log-likelihood). Something like this:

results = list()

…

loop iterating i here

… results[i] = list(summary(den.uni)$varcomp) # in the case of asreml

end loop

You can even pre-allocate the list of whatever size to save some time, but in my experience when running this type of analyses the time to growth the list is minimal compared to the time to run a single analysis.

Concerning Latex tables, I haven't done that in R.

2015/01/26 at 3:08 am

could any one forward syntax for A matrix generation (Y=xB +Zu +e) A is pedgree information

2015/01/26 at 2:25 pm

Search for pedigree in the search box and you’ll see examples on how to specify the pedigree for different packages that can be used for genetic analysis.

2016/01/15 at 9:45 am

Thanks Luis, a very suitable post for a beginner. However,the link to “Bill Venables’s post on linear mixed model” is broken. Would you mind update it?

2016/01/15 at 9:52 pm

Thanks for pointing out the broken link. It referred to a 16 year old email in the s-plus email list, which is not active anymore. Fortunately there are still a couple of copies circulating in internet, so I have updated the link to one of the surviving copies.