[R-sig-ME] [R] lme nesting/interaction advice

Mon May 12 15:31:43 CEST 2008

On 12 May 2008, at 13:39, toby909 at gmail.com wrote:

> this is not an easy and not a standard model.

I know it is not easy, but I would be able to calculate the model by  
hand, were it not for the fact that I would like to understand how to  
do it using R
>
> if your 3-way anova is fully factorial, with one factor being random,
> then you have a LOT of random effects. you have a random main effect,
> you will have a number of random 2-way interction terms, and also a
> random 3-way interaction effect, their covariance matrix most  
> likely to
> be nonpositive definite.
>
> The nested model is actually the simpler one, and I have the hint that
> the "basics" book does not present such a complicated model in its
> introductory chapter.
>
> also, you don't make it easy for people to help you. I could not  
> easily
> read in your data and I had to generate own data. :-(

I am sorry about this, it might be because I wrote the data to a text  
file with write.table() in OSX. The data was nothing more than a toy  
model
>
> Maybe you are looking for something similar to:
>
> set.seed(78987)
> a = rep(1:3,each=120)
> b = rep(1:3,3, each=40)
> c = rep(1:10,9,each=4)
> y = rnorm(360,0,10)
> x = cbind(a,b,c,y)
> colnames(x) = c("a", "b", "c", "y")
> x = as.data.frame(x)
>
> lme = lme(y ~ factor(a)*factor(b)*factor(c)-1, x, ~factor(c))
> anova(lme)

With the very same model you're using I get:

 > lme.mod = lme(y ~ selection * males * month-1, random = ~month,  
testdat)
Error in getGroups.data.frame(dataMix, groups) :
   Invalid formula for groups
 > lme.mod = lme(y ~ selection * males * (month-1), random = ~month,  
testdat)
Error in getGroups.data.frame(dataMix, groups) :
   Invalid formula for groups

I copy/paste the datset below, in case it makes things clearer.

Thanks,

Federico

selection	line	males	month	block	y
L	L1	1	a	1	13.8156357121188
L	L1	1	a	1	12.5678496952169
L	L1	1	a	1	17.1313698710874
L	L1	1	a	1	3.87016302696429
L	L1	1	a	1	13.2627072110772
L	L2	1	a	1	17.835768135963
L	L2	1	a	1	19.3615794742946
L	L2	1	a	1	1.73416316602379
L	L2	1	a	1	12.9440758333076
L	L2	1	a	1	2.09191741654649
S	S1	1	a	1	1.56137526640669
S	S1	1	a	1	17.6580698778853
S	S1	1	a	1	18.1417595115490
S	S1	1	a	1	15.5621050691698
S	S1	1	a	1	17.0240987658035
S	S2	1	a	1	12.4378062419128
S	S2	1	a	1	6.63962595071644
S	S2	1	a	1	16.6060689473525
S	S2	1	a	1	7.1222553497646
S	S2	1	a	1	18.0590278783347
L	L1	2	a	1	1.24710303940810
L	L1	2	a	1	4.62720696791075
L	L1	2	a	1	16.0327167815994
L	L1	2	a	1	6.12926463945769
L	L1	2	a	1	7.65810538828373
L	L2	2	a	1	7.44077128893696
L	L2	2	a	1	14.9197938004509
L	L2	2	a	1	13.4244954204187
L	L2	2	a	1	11.5361888066400
L	L2	2	a	1	2.60056478204206
S	S1	2	a	1	14.8965472229756
S	S1	2	a	1	18.777876078384
S	S1	2	a	1	6.80722737265751
S	S1	2	a	1	13.1697203880176
S	S1	2	a	1	3.74557441123761
S	S2	2	a	1	5.41025308240205
S	S2	2	a	1	19.8277674221899
S	S2	2	a	1	4.76206006342545
S	S2	2	a	1	3.08200096315704
S	S2	2	a	1	11.7220768791158
L	L1	1	a	2	17.8684629611671
L	L1	1	a	2	18.5609889889602
L	L1	1	a	2	1.33335256157443
L	L1	1	a	2	12.2590920312796
L	L1	1	a	2	10.3133576815017
L	L2	1	a	2	9.08117202203721
L	L2	1	a	2	11.8387454338372
L	L2	1	a	2	2.17258459446020
L	L2	1	a	2	7.64467771397904
L	L2	1	a	2	10.1472946784925
S	S1	1	a	2	6.33078282815404
S	S1	1	a	2	14.2109518861398
S	S1	1	a	2	2.86901426501572
S	S1	1	a	2	1.33705932833254
S	S1	1	a	2	3.62769498769194
S	S2	1	a	2	10.6116549053695
S	S2	1	a	2	19.2579759012442
S	S2	1	a	2	4.93543729488738
S	S2	1	a	2	14.0185110287275
S	S2	1	a	2	13.0477287801914
L	L1	2	a	2	7.81632485729642
L	L1	2	a	2	15.8365131700411
L	L1	2	a	2	13.6505087725818
L	L1	2	a	2	4.30545190884732
L	L1	2	a	2	5.62008981755935
L	L2	2	a	2	11.6415019945707
L	L2	2	a	2	17.4424436504487
L	L2	2	a	2	5.51907726703212
L	L2	2	a	2	3.24006642703898
L	L2	2	a	2	2.96195078082383
S	S1	2	a	2	16.2962908495683
S	S1	2	a	2	11.919979267288
S	S1	2	a	2	2.93063819734380
S	S1	2	a	2	15.6936508698855
S	S1	2	a	2	2.295168728102
S	S2	2	a	2	11.7390888168011
S	S2	2	a	2	10.4391786744818
S	S2	2	a	2	11.1727120177820
S	S2	2	a	2	11.4406719871331
S	S2	2	a	2	5.20650001661852
L	L1	1	b	3	9.53833453846164
L	L1	1	b	3	1.95979442284442
L	L1	1	b	3	8.31046994985081
L	L1	1	b	3	4.39192276610993
L	L1	1	b	3	16.0887561799027
L	L2	1	b	3	5.20481191016734
L	L2	1	b	3	8.32888073613867
L	L2	1	b	3	3.47083900799043
L	L2	1	b	3	12.2260039008688
L	L2	1	b	3	12.2011876017787
S	S1	1	b	3	10.6229240614921
S	S1	1	b	3	9.49411644623615
S	S1	1	b	3	18.4179708964657
S	S1	1	b	3	4.12228938611224
S	S1	1	b	3	5.55325478035957
S	S2	1	b	3	10.4130052563269
S	S2	1	b	3	12.6257456133608
S	S2	1	b	3	19.8305484240409
S	S2	1	b	3	2.6487210446503
S	S2	1	b	3	15.9869729799684
L	L1	2	b	3	14.6902481422294
L	L1	2	b	3	16.9090498948935
L	L1	2	b	3	3.90413530776277
L	L1	2	b	3	1.89122105599381
L	L1	2	b	3	14.2131580882706
L	L2	2	b	3	16.1121652075090
L	L2	2	b	3	16.8070402105805
L	L2	2	b	3	2.19568496150896
L	L2	2	b	3	2.96183063089848
L	L2	2	b	3	12.6824307644274
S	S1	2	b	3	12.8504637307487
S	S1	2	b	3	6.1809710978996
S	S1	2	b	3	7.47571811126545
S	S1	2	b	3	8.81466605700552
S	S1	2	b	3	12.3395618333016
S	S2	2	b	3	19.9728567516431
S	S2	2	b	3	11.3028548071161
S	S2	2	b	3	6.50141697842628
S	S2	2	b	3	13.0698232366703
S	S2	2	b	3	11.474319845438
L	L1	1	b	4	1.03187379334122
L	L1	1	b	4	9.6801089819055
L	L1	1	b	4	4.00592510355636
L	L1	1	b	4	4.63362230593339
L	L1	1	b	4	15.4505966042634
L	L2	1	b	4	14.9346919001546
L	L2	1	b	4	18.3153922208585
L	L2	1	b	4	8.57050257665105
L	L2	1	b	4	1.31918784533627
L	L2	1	b	4	19.5731912786141
S	S1	1	b	4	4.34415089036338
S	S1	1	b	4	9.66746214497834
S	S1	1	b	4	12.4202494181227
S	S1	1	b	4	17.0269973296672
S	S1	1	b	4	15.1591323411558
S	S2	1	b	4	7.3169305799529
S	S2	1	b	4	14.9331590640359
S	S2	1	b	4	13.4191052850801
S	S2	1	b	4	3.8695620871149
S	S2	1	b	4	14.8654785933904
L	L1	2	b	4	18.5652933202218
L	L1	2	b	4	1.33474090369418
L	L1	2	b	4	12.9836367180105
L	L1	2	b	4	8.14379613753408
L	L1	2	b	4	17.5245339989197
L	L2	2	b	4	19.4962712256238
L	L2	2	b	4	8.36269160197116
L	L2	2	b	4	16.4331527492031
L	L2	2	b	4	19.9028004400898
L	L2	2	b	4	8.9440936667379
S	S1	2	b	4	5.1467830883339
S	S1	2	b	4	13.0068403361365
S	S1	2	b	4	17.9727395507507
S	S1	2	b	4	7.75389035535045
S	S1	2	b	4	13.1991689843126
S	S2	2	b	4	1.86596546205692
S	S2	2	b	4	13.6726454407908
S	S2	2	b	4	5.46787238144316
S	S2	2	b	4	14.9116268747021
S	S2	2	b	4	17.4470446316991
L	L1	1	c	5	6.0449733575806
L	L1	1	c	5	9.23758197389543
L	L1	1	c	5	11.8805425714236
L	L1	1	c	5	11.097381018335
L	L1	1	c	5	6.2186355558224
L	L2	1	c	5	15.4524628254585
L	L2	1	c	5	10.8791305767372
L	L2	1	c	5	8.53259862400591
L	L2	1	c	5	17.7329147965647
L	L2	1	c	5	7.95771266217344
S	S1	1	c	5	14.2891584723257
S	S1	1	c	5	18.7194010075182
S	S1	1	c	5	5.8396331758704
S	S1	1	c	5	12.2250114120543
S	S1	1	c	5	19.9965940725524
S	S2	1	c	5	8.086333316518
S	S2	1	c	5	1.02154314704239
S	S2	1	c	5	2.71978635899723
S	S2	1	c	5	11.7734509080183
S	S2	1	c	5	10.7842262475751
L	L1	2	c	5	15.3013315075077
L	L1	2	c	5	6.12277858285233
L	L1	2	c	5	6.58965252665803
L	L1	2	c	5	13.0980647155084
L	L1	2	c	5	11.3858233471401
L	L2	2	c	5	13.8056075817440
L	L2	2	c	5	11.4665438272059
L	L2	2	c	5	6.37498314119875
L	L2	2	c	5	3.85318743507378
L	L2	2	c	5	7.959969348507
S	S1	2	c	5	13.8249646106269
S	S1	2	c	5	13.3112728327978
S	S1	2	c	5	9.67586784437299
S	S1	2	c	5	17.8595201659482
S	S1	2	c	5	3.14554875413887
S	S2	2	c	5	10.4300375301391
S	S2	2	c	5	15.4386686717626
S	S2	2	c	5	7.93477151589468
S	S2	2	c	5	3.66100515658036
S	S2	2	c	5	13.5765222932678
L	L1	1	c	6	11.3484169594012
L	L1	1	c	6	12.7286028855015
L	L1	1	c	6	17.2616694702301
L	L1	1	c	6	19.8529832861386
L	L1	1	c	6	13.6375724875834
L	L2	1	c	6	1.47241126280278
L	L2	1	c	6	1.95706973574124
L	L2	1	c	6	5.88739864598028
L	L2	1	c	6	8.16921139019541
L	L2	1	c	6	15.4799758975860
S	S1	1	c	6	2.47244948730804
S	S1	1	c	6	4.87303283042274
S	S1	1	c	6	6.15663269115612
S	S1	1	c	6	1.31718108500354
S	S1	1	c	6	16.4325702653732
S	S2	1	c	6	8.77171974466182
S	S2	1	c	6	13.4219867731445
S	S2	1	c	6	15.79551491444
S	S2	1	c	6	8.52955200499855
S	S2	1	c	6	14.4046092615463
L	L1	2	c	6	17.4255252447911
L	L1	2	c	6	5.80786765902303
L	L1	2	c	6	3.27889802469872
L	L1	2	c	6	7.55257236934267
L	L1	2	c	6	10.3537469459698
L	L2	2	c	6	10.1472219382413
L	L2	2	c	6	15.3184245729353
L	L2	2	c	6	12.6165662519634
L	L2	2	c	6	11.2075877587777
L	L2	2	c	6	17.0927850408480
S	S1	2	c	6	19.5778706537094
S	S1	2	c	6	5.56091665173881
S	S1	2	c	6	6.32830694783479
S	S1	2	c	6	7.46368952002376
S	S1	2	c	6	14.5648785342928
S	S2	2	c	6	14.7789344959892
S	S2	2	c	6	3.21725518512540
S	S2	2	c	6	2.26359746395610
S	S2	2	c	6	9.14707987429574
S	S2	2	c	6	8.6291270784568

--
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602   Fax +44 (0)20 75943193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com