# Linear mixed models in R

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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—I mean the program), 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 ones. 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 mmpedigree 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 an 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 in 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.

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.

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.

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.

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.

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