[R] nlme predict with se?
Dr. Emilio A. Laca
ealaca at ucdavis.edu
Fri Mar 17 22:54:57 CET 2006
I am trying to make predictions with se's using a nlme (kew11.nlme
below). I get an error indicating levels for a factor are not allowed.
I have searched and read Rnews, MEMSS, MASS, R-Help, and other lists
in Spanish where I found questions similar to mine but not solution.
I do not really care about the method used. Any suggestions to obtain
predictions with se's from an nlme would be appreciated.
eal
R Version 2.2.1 (2005-12-20 r36812)
mac osx 10.4.5 on G5 DP
> predict(kew11.nlme,x.for.lw.pred, se=T)
Error in predict.nlme(kew11.nlme, x.for.lw.pred, se = T) :
Levels 1. Fall-Winter,2. Spring,3. Summer,4. Fall not allowed for
Season
> x.for.lw.pred[1:10,]
Season ecoreg MBreed ageyr2 sheep farm
1 1. Fall-Winter desert Meat 0.60 1 AksToKa
2 2. Spring desert Meat 1.00 1 AksToKa
3 3. Summer desert Meat 1.25 1 AksToKa
4 4. Fall desert Meat 1.50 1 AksToKa
5 1. Fall-Winter foothills Half 0.60 1 AksToKa
6 2. Spring foothills Half 1.00 1 AksToKa
7 3. Summer foothills Half 1.25 1 AksToKa
8 4. Fall foothills Half 1.50 1 AksToKa
9 1. Fall-Winter foothills Meat 0.60 1 AksToKa
10 2. Spring foothills Meat 1.00 1 AksToKa
> kew11.nlme$call
nlme.formula(model = lw ~ SSasympOff(ageyr2, mw, lgr, age0),
data = kew, fixed = list(mw + lgr + age0 ~ Season * MBreed +
ecoreg + ecoreg:Season), random = list(farm = list(mw ~
1, lgr ~ 1), sheep = list(mw ~ 1)), start = c(fixef
(kew8.nlme)[1:15],
0, 0, 0, 0, 0, 0, 0, 0, 0, fixef(kew8.nlme)[16:30], 0,
0, 0, 0, 0, 0, 0, 0, 0, fixef(kew8.nlme)[31:45], 0, 0,
0, 0, 0, 0, 0, 0, 0), correlation = corSymm())
> levels(kew$Season)==levels(x.for.lw.pred$Season)
[1] TRUE TRUE TRUE TRUE
> kew[1:10,]
Grouped Data: lw ~ ageyr2 | farm
X sheep doe ageyr2 MBreEco Season ecoreg
farm village Breed MBreed date doy lw ebw
1 1 1 1 2.500000 Meatsemidesert 1. Fall-Winter semidesert
AksToKa Aksenger KZP Meat 11/23/02 327 63.8 55.63211
2 2 1 139 2.883333 Meatsemidesert 2. Spring semidesert
AksToKa Aksenger KZP Meat 4/10/03 100 51.7 44.53119
3 3 1 250 3.191667 Meatsemidesert 3. Summer semidesert
AksToKa Aksenger KZP Meat 7/30/03 211 58.3 50.58624
4 4 1 330 3.413889 Meatsemidesert 4. Fall semidesert
AksToKa Aksenger KZP Meat 10/18/03 291 59.9 52.05413
5 5 2 1 6.000000 Meatsemidesert 1. Fall-Winter semidesert
AksToKa Aksenger KZP Meat 11/23/02 327 58.0 50.31101
6 6 2 139 6.383333 Meatsemidesert 2. Spring semidesert
AksToKa Aksenger KZP Meat 4/10/03 100 41.2 34.89817
7 7 2 250 6.691667 Meatsemidesert 3. Summer semidesert
AksToKa Aksenger KZP Meat 7/30/03 211 53.3 45.99908
8 8 2 330 6.913889 Meatsemidesert 4. Fall semidesert
AksToKa Aksenger KZP Meat 10/18/03 291 63.7 55.54037
9 9 3 1 4.000000 Meatsemidesert 1. Fall-Winter semidesert
AksToKa Aksenger KZP Meat 11/23/02 327 62.3 54.25596
10 10 3 139 4.383333 Meatsemidesert 2. Spring semidesert
AksToKa Aksenger KZP Meat 4/10/03 100 47.3 40.49450
bcs prcfat cageyrs
1 2.75 26.533 -0.46162659
2 2.00 20.192 -0.07829326
3 2.50 24.478 0.23004008
4 2.50 24.414 0.45226230
5 2.50 24.490 3.03837341
6 1.75 18.337 3.42170674
7 2.25 22.403 3.73004008
8 3.25 31.087 3.95226230
9 2.50 24.318 1.03837341
10 2.00 20.368 1.42170675
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