The topic of Mixed Models is an old-friend of this blog, but I want to focus today on the R code for these models.

Amongst all the packages that deal with linear mixed models in R (see lmm, ASReml, MCMCglmm, glmmADMB,…), lme4 by Bates, Maechler and Bolker, and nlme by Pinheiro and Bates are probably the most commonly used -in the frequentist arena-, with their respective main functions *lmer* and *lme*.

I am still unsure as to which one I would choose - if I had to -, but I am sharing here a summary of some of their capabilities, in case it can be of help:

*Model specification*

I will be using for all of the following examples the balanced dataset *Orthodont* from the package *nlme*, which reflects the change in an orthodontic measurement over time for a sample of 27 children (see *Fig. 1*).

*Fig. 1. Spaghetti plots. Distance vs age by gender – dataset Orthodont*

For simplicity´s sake, I will consider the following initial models with a simple random factor (please see ref. [3] for centering and further analysis):

model_lmer<-lmer(distance~age+Sex+(1|Subject),data=Orthodont) model_lme<-lme(distance~age+Sex, random=~1|Subject,data=Orthodont)

*Tests*

*lmer*

The results for t-tests and F-tests based on Restricted Maximum Lilkelihood (REML) can be found by using the following lines of code (you can add *REML=FALSE* to change this default setting):

summary(model_lmer)

…

Fixed effects:

Estimate Std. Error t value

(Intercept) 17.70671 0.83391 21.233

age 0.66019 0.06161 10.716

SexFemale -2.32102 0.76139 -3.048

…

(Please notice that the reference category in Sex can be changed by using *relevel*).

anova(model_lmer)

Analysis of Variance Table

Df Sum Sq Mean Sq F value

age 1 235.356 235.356 114.8383

Sex 1 19.034 19.034 9.2875

*lme*

Conditional t-tests and F-tests are used for assessing the significance of terms in the fixed effects in *lme*.

Both F and t conditional tests results are based on REML conditional estimate of the variance. This option will be the default, but we can specify *method=”ML”* for Maximum Likelihood estimates.

For the results from the conditional t-test testing the marginal significance of each fixed effect coefficient with the other fixed effects in the model, we can use:

summary(model_lme)

…

Fixed effects: distance ~ age + Sex

Value Std.Error DF t-value p-value

(Intercept) 17.706713 0.8339225 80 21.233044 0.0000

age 0.660185 0.0616059 80 10.716263 0.0000

SexFemale -2.321023 0.7614168 25 -3.048294 0.0054

…

For the results from the conditional F-test testing the significance of terms in the fixed effects model (sequentially by default), we can use:

anova(model_lme)

numDF denDF F-value p-value

(Intercept) 1 80 4123.156 <.0001

age 1 80 114.838 <.0001

Sex 1 25 9.292 0.0054

(The argument *type *would also allow us to specify *marginal *F-tests).

These conditional tests for fixed-effects terms require denominator degrees of freedom, which will be the focus of the next section.

*Degrees of freedom*

*lme*

The denominator degrees of freedom correspond to “the classical decomposition of degrees of freedom in balanced, multilevel ANOVA designs” [3]. It is worth noticing that the values for these degrees of freedom do not match those provided by other software procedures such as SAS PROC MIXED (see discussions on the topic here and here).

Additionally to the denominator degrees of freedom aforementioned, conditional F-tests also require numerator degrees of freedom defined by the term (see output from previous section).

- A good explanation regarding the reporting of degrees of freedom in
*lmer*is given by the author of the package in this article (page 28).

*p-values*

*lme*reports p-values (see previous output), whereas*lmer*doesn’t but this has been justified by Bates.

*Random effects*

*lme*allows for nested random effects in a very straightforward way (*random=~1|a/b*, where factor*b*is nested in*a*). Crossed random effects on the other hand, can be dealt with through “a combination of*pdBlocked*and*pdldent*objects” [3].- Nested random effects can again be easily modelled in
*lmer*(*+(1|a/b)*). Crossed random effects are handled in an easier way than in*lme*(*+(1|a)+(1|b)*). You can find further explanations in [2].

*Random effects plots*

Two different approaches to the plotting of the random effects can be obtained through the following lines of code:

*lme*

plot(ranef(model_lme))

*lmer*

qqmath(ranef(model_lmer))

*Fig. 2. Random effects plots for model_lme and model_lmer. *

*Residuals plots*

*lme*allows to plot the residuals in the following ways:

res_lme=residuals(model_lme) plot(res_lme) qqnorm(res_lme) qqline(res_lme) plot(model_lme)

*Fig. 3. Residual plots for model_lme. *

- We can also plot the first two graphs in
*lmer,*but the last line of code does not seem to work with this function.

*Correlation structure*

- We can easily incorporate correlation structures in
*lme*. Mostly used for temporal correlation structures are*corAR1*,*corCAR1*(autoregressive and continuous autoregressive correlation structures of order 1), and*corCompSymm*(compound symmetry).

model_lme<-lme(distance ~ age + factor(Sex),random = ~ 1 | Subject, cor=corAR1(0.6,form=~1|Subject),data = Orthodont)

…

Correlation Structure: AR(1)

Formula: ~1 | Subject

Parameter estimate(s):

Phi

0.05849311

…

Further structures available can be found in the help for *corClasses**.*

- There is not an argument in
*lmer*for doing this, but guidance on how to incorporate the structures can be found here.

*Heteroscedasticity*

*lme*allows you to model heteroscedasticity using the*varFunc*object, but- it is not covered by
*lmer*.

Although some other differences could be mentioned, future posts will cover those other matters.

The following books have been found extremely useful:

[1] Badiella, L., Sánchez, J.A. “Modelos mixtos con R versión 0.3” ( from the course “Modelos Mixtos utilizando R”)

[2] Bates, D. (2010). *lme4: Mixed-effects modelling with R*. Springer

[3] Pinheiro, J.C. and Bates, D.M. (2000). *Mixed-Effects Models in S and S-Plus*. Springer

[4] Zuur, A.F. et al. (2009). *Mixed effects models and extensions in ecology with R*. Springer

*I will be more than happy to read your comments and tips! :-)*

Great post Altea!!! Nowadays, if you only want to fit a linear o no linear mixed model (LMM, LNMM) I think it’s more appropriate to use the nlme package of Pinheiro (J. C. Pinheiro and D. M. Bates. Mixed-Effects Models in S and S-PLUS. Springer, 2000), but if you want to fit a Generalized linear mixed model (GLMM) it’s better the lme4 package. In spite of that, we have to take into account that the lme4 is in development and the lme4 developers will announce a scheduled release of lme4 version 1.0 soon. The new version will tend to have fewer problems with false convergence and more flexibility for exploring and fixing convergence problems. Latsly, if somebody is interested in the introduction of mixed models, I would like to recommend the course of Badiella, L., Sánchez (reference number one). Thanks for you post!!!!

Thanks very much, Martí, for your kind and very helpful comment!!

I completely agree with your suggestions.

Also, great news about the new version of lme4, thank you for sharing, so much looking forward to that!

The course was indeed of great help for me too, I strongly recommend it!

[2] Bates, D. (2010). lme4: Mixed-effects modelling with R. Springer

This book is still vaporware.

Thank you very much, Dieter, for your comment.

We have indeed accessed the electronic version available on the lme4 repository:

http://lme4.r-forge.r-project.org/lMMwR/lrgprt.pdf

Any other references will be very welcome!

This code has an error

“model_lme<-lme(distance~age+Sex, random=~Subject,data=Orthodont)"

It should be "model_lme<-lme(distance~age+Sex, random=~1|Subject,data=Orthodont)"

Indeed, many thanks nitro for pointing out the typo! Fixed now :)

Thanks very much for sharing to us on mixed models using R. I am though learning it. So far I do not understand how to obtain covariance estimates. In addition, I use lsmeans(sorry am SAS user) or doBy to obtain mean estimates? can you comment on these?

Thanks so much for your comment, Abraham, and sorry for my late reply.

I am afraid I am not a SAS user so I can´t be of much help. In R, you could use extract.lme.cov (find more info in the following link: http://stuff.mit.edu/afs/sipb/project/r-project/arch/sun4x_59/lib/R/library/mgcv/html/extract.lme.cov.html)

Will investigate further and let you know if I find some SAS tips regarding this!

The absence of ls means is by design:

http://r-project.markmail.org/thread/quectj4sslht6fft

Douglas Bates: I am having difficulty grasping how you obtain a prediction from a model involving a factor ‘d’ without assigning a value to that factor. I suppose that someone who understands the deep magic of quantities like SAS’s LS-means may be able to tell you what you want to know but I can’t.

Thank you s much for that, Dieter!

Hi Altea. I have a lme model, with 2 fixed and 1 random factor, no significant interaction.

m3 <- lme(LengthT10 ~ Temp+pH, random=~1|Tank)

My question is, can I do

anova(m3)

and report F and DF from there? Is this reliable information from lme?

Thank you

Hi Fatima, thank you for your comment. You can, for a further insight you can find the details on how lme calculates the df on pages 91 and 92 of Pinheiro and Bates (2000):

http://books.google.co.uk/books?id=N3WeyHFbHLQC&printsec=frontcover&dq=pinheiro+bates&ei=GKUxSqujF4WKygSSnrCUBg&redir_esc=y#v=onepage&q=pinheiro%20bates&f=false

I hope this helps!

Thank you Altea. It helped.