# Re: [R] lme and lmer syntax

From: Doran, Harold <HDoran_at_air.org>
Date: Wed 26 Oct 2005 - 03:24:44 EST

lmer(yield~irrigation*density*fertilizer+(1|fertilizer:density)+(1|density), data)

Which notes that fertilizer is nested in density.

Try this and then compare the results.

-----Original Message-----
From: r-help-bounces@stat.math.ethz.ch [mailto:r-help-bounces@stat.math.ethz.ch] On Behalf Of Ronaldo Reis-Jr. Sent: Tuesday, October 25, 2005 12:21 PM To: R-Help
Subject: Re: [R] lme and lmer syntax

Em Seg 24 Out 2005 18:08, Doran, Harold escreveu:
> Ronaldo
>
> See the article on lmer pasted below for syntax. It is the only
> current source documenting the code. In lmer(), the nesting structure
> for the ranmdom effects is handled in a slightly different way. If
> your observations are nested as you note, then you can use
>
> > lmer(y~x1 + x2 +(1|x1) + (1|x2), data)
>
> @Article{Rnews:Bates:2005,
> author = {Douglas Bates},
> title = {Fitting Linear Mixed Models in {R}},
> journal = {R News},
> year = 2005,
> volume = 5,
> number = 1,
> pages = {27--30},
> month = {May},
> url = {http://CRAN.R-project.org/doc/Rnews/},
> }
>

Hi,

I try this with a splitsplitplot example.

I make the correct model with aov, lme do compare with lmer.

But I cant make a correct model in lmer. Look that the aov and lme results are similars, but very different from lmer. In aov and lme is used the correct DF for each variable, in lmer it use a same DF for all? Denom=54.

What is my mistake?

Thanks
Ronaldo

• Begin of example ------

> summary(splitplot)

```     yield        block      irrigation   density   fertilizer
Min.   : 60.00   A:18   control  :36   high  :24   N :24
1st Qu.: 86.00   B:18   irrigated:36   low   :24   NP:24
Median : 95.00   C:18                  medium:24   P :24
Mean   : 99.72   D:18
3rd Qu.:114.00
Max.   :136.00
```

>
> attach(splitplot)
>
> m.aov <-
aov(yield~irrigation*density*fertilizer+Error(block/irrigation/density/fertilizer))
>
> summary(m.aov)

Error: block

```          Df  Sum Sq Mean Sq F value Pr(>F)
Residuals  3 194.444  64.815

Error: block:irrigation
Df Sum Sq Mean Sq F value  Pr(>F) irrigation  1 8277.6  8277.6  17.590 0.02473 *
Residuals   3 1411.8   470.6
```
```---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Error: block:irrigation:density
Df  Sum Sq Mean Sq F value  Pr(>F)
density             2 1758.36  879.18  3.7842 0.05318 .
irrigation:density  2 2747.03 1373.51  5.9119 0.01633 *
Residuals          12 2787.94  232.33
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Error: block:irrigation:density:fertilizer
Df  Sum Sq Mean Sq F value    Pr(>F)
fertilizer                     2 1977.44  988.72 11.4493 0.0001418 ***
irrigation:fertilizer          2  953.44  476.72  5.5204 0.0081078 **
density:fertilizer             4  304.89   76.22  0.8826 0.4840526
irrigation:density:fertilizer  4  234.72   58.68  0.6795 0.6106672
Residuals                     36 3108.83   86.36
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

>
> library(nlme)

>
> m.lme <- lme(yield~irrigation*density*fertilizer,random=~1|
block/irrigation/density/fertilizer)

>
> anova(m.lme)
numDF denDF   F-value p-value
(Intercept)                       1    36 2683.2245  <.0001
irrigation                        1     3   31.0269  0.0114
density                           2    12    3.7780  0.0534
fertilizer                        2    36   11.4490  0.0001
irrigation:density                2    12    5.9023  0.0164
irrigation:fertilizer             2    36    5.5203  0.0081
density:fertilizer                4    36    0.8826  0.4841
irrigation:density:fertilizer     4    36    0.6795  0.6107

>
> library(lme4)

>
> g1 <- block:irrigation

> g2 <- block:irrigation:density
> g3 <- block:irrigation:density:fertilizer
>
> m.lmer <-
> lmer(yield~irrigation*density*fertilizer+(1|g1)+(1|g2)+(1|g3))
>
> anova(m.lmer)
Analysis of Variance Table
Df Sum Sq Mean Sq  Denom F value    Pr(>F)
irrigation                     1 827.41  827.41  54.00 30.9203 8.546e-07 ***
density                        2 202.53  101.26  54.00  3.7842  0.028971 *
fertilizer                     2 612.76  306.38  54.00 11.4493 7.159e-05 ***
irrigation:density             2 316.40  158.20  54.00  5.9120  0.004767 **
irrigation:fertilizer          2 295.45  147.72  54.00  5.5204  0.006586 **
density:fertilizer             4  94.48   23.62  54.00  0.8826  0.480561
irrigation:density:fertilizer  4  72.73   18.18  54.00  0.6795  0.609157
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

----- End of example ------

--

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Received on Wed Oct 26 03:28:52 2005

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