Dear Thierry, Thanks for the quick answer. I'm moving this to r-sig-mixed-models (but also posting on r-help to notify).
I reserved "Mixed-effects models in S and S-PLUS" by Pinheiro and Bates, New York : Springer, 2000. Do you know any other good references? Cheers, Mikkel. 2010/9/2 ONKELINX, Thierry <thierry.onkel...@inbo.be>: > Dear Mikkel, > > You need to do some reading on terminology. > > In your model the fixed effects are channel 1, 2 and 3. samplenumber is > a random effect and the error term is an error term > > The model you described has the notation below. You do not need to > create the grouped data structure. > > lme(channel0 ~ pos + samplenumber + channel1 + channel2 + channel3, > random = ~ 1 | samplenumber, > correlation = corAR1(value = 0.5, form = ~ pos | samplenumber), > data = channel.matrix) > > HTH, > > Thierry > > PS There is a dedicated mailing list for mixed models: > R-sig-mixed-models > > ------------------------------------------------------------------------ > ---- > ir. Thierry Onkelinx > Instituut voor natuur- en bosonderzoek > team Biometrie & Kwaliteitszorg > Gaverstraat 4 > 9500 Geraardsbergen > Belgium > > Research Institute for Nature and Forest > team Biometrics & Quality Assurance > Gaverstraat 4 > 9500 Geraardsbergen > Belgium > > tel. + 32 54/436 185 > thierry.onkel...@inbo.be > www.inbo.be > > To call in the statistician after the experiment is done may be no more > than asking him to perform a post-mortem examination: he may be able to > say what the experiment died of. > ~ Sir Ronald Aylmer Fisher > > The plural of anecdote is not data. > ~ Roger Brinner > > The combination of some data and an aching desire for an answer does not > ensure that a reasonable answer can be extracted from a given body of > data. > ~ John Tukey > > >> -----Oorspronkelijk bericht----- >> Van: r-help-boun...@r-project.org >> [mailto:r-help-boun...@r-project.org] Namens Mikkel Meyer Andersen >> Verzonden: donderdag 2 september 2010 13:30 >> Aan: r-help@r-project.org >> Onderwerp: [R] nlme formula from model specification >> >> Dear R-community, >> >> I'm analysing some noise using the nlme-package. I'm writing >> in order to get my usage of lme verified. >> >> In practise, a number of samples have been processed by a >> machine measuring the same signal at four different channels. >> I want to model the noise. I have taken the noise (the signal >> is from position 1 to 3500, and after that there is only noise). >> >> My data looks like this: >> channel.matrix: >> pos channel0 channel1 channel2 channel3 samplenumber >> 1 3501 8 3 12 1 1 >> 2 3502 3 7 0 14 1 >> 3 3503 9 1 13 3 1 >> 4 3504 3 7 3 14 1 >> 5 3505 6 5 4 5 1 >> 6 3506 7 0 16 0 1 >> ... >> 495 3995 5 2 9 9 1 >> 496 3996 2 4 6 10 1 >> 497 3997 3 2 7 7 1 >> 498 3998 2 4 3 9 1 >> 499 3999 3 1 6 11 1 >> 500 4000 0 3 6 7 1 >> 2301 3501 1 4 3 9 2 >> 2302 3502 3 3 4 13 2 >> 2303 3503 4 1 8 5 2 >> 2304 3504 3 1 10 2 2 >> 2305 3505 2 3 5 8 2 >> 2306 3506 0 5 8 2 2 >> ... >> >> The model is >> channel0 ~ alpha_i + eps_{i, j} + channel1 + channel2 + >> channel3 where i is sample number, j is position, and: >> alpha_i: fixed effect for each samplenumber >> eps_{i, j}: random effect, here with correlation >> structure as AR(1) >> channel1, ..., channel3: fixed effect for each channel not >> depending on >> samplenumber nor position >> >> (And then afterwards I would model channel1 ~ ... + channel2 >> + channel3 etc.) >> >> I then use this function call: >> channel.matrix.grouped <- groupedData(channel0 ~ pos | samplenumber, >> data = channel.matrix) >> >> fit <- lme(channel0 ~ pos + samplenumber + channel1 + >> channel2 + channel3, >> random = ~ pos | samplenumber, >> correlation = corAR1(value = 0.5, form = ~ pos | samplenumber), >> data = channel.matrix.grouped) >> >> Is that the right way to express the model in (n)lme-notation? >> >> Cheers, Mikkel. >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > > Druk dit bericht a.u.b. niet onnodig af. > Please do not print this message unnecessarily. > > Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer > en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd > is > door een geldig ondertekend document. The views expressed in this message > and any annex are purely those of the writer and may not be regarded as > stating > an official position of INBO, as long as the message is not confirmed by a > duly > signed document. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.