[R-sig-ME] NLME model syntax

[nrm2010]

Dear Thierry,

That solved the problem.  Thank you very much for your help.
I had read ?nlme but found it somewhat confusing.

Toby




---- On Mon, 28 Feb 2011 07:56:50 -0700  Thierry ONKELINX  wrote ---- 

>Dear Toby, 
> 
>Now I see what the problem is. You need to specify which parameter will be used in the random effects. See also the example in ?nlme 
> 
>Suppose that you only want b0 to vary per chamber 
> 
>test  0) 
> 
>Best regards, 
> 
>Thierry 
> 
>---------------------------------------------------------------------------- 
>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.Onkelinx at 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: nrm2010 [mailto:nrm2010 at zoho.com] 
>> Verzonden: vrijdag 25 februari 2011 18:52 
>> Aan: ONKELINX, Thierry 
>> CC: r-sig-mixed-models at r-project.org 
>> Onderwerp: RE: [R-sig-ME] NLME model syntax 
>> 
>> 
>> Yes, I did try that and I had the same problem. 
>> I also tried it without the "list", as in "fixed = list...", 
>> based on previous bug reports, and that doesn't run either. 
>> But if I linearize it and use lme instead of nlme, it runs perfectly. 
>> 
>> Also, since I failed to mention this in the original message, 
>> it's nlme v. 3.1-98, R v. 2.11.1 with TINN-R interface on Windows OS. 
>> 
>> Thank you. 
>> 
>> Toby 
>> 
>> 
>> 
>> ---- On Fri, 25 Feb 2011 02:29:37 -0700 Thierry ONKELINX wrote ---- 
>> 
>> >Have you tried to use a regular data.frame instead of a 
>> groupedData object? 
>> > 
>> >Best regards, 
>> > 
>> >Thierry 
>> > 
>> >------------------------------------------------------------- 
>> ---------- 
>> >----- 
>> >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.Onkelinx at 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-sig-mixed-models-bounces at r-project.org 
>> >> [mailto:r-sig-mixed-models-bounces at r-project.org] Namens nrm2010 
>> >> Verzonden: donderdag 24 februari 2011 23:16 
>> >> Aan: r-sig-mixed-models at r-project.org 
>> >> Onderwerp: [R-sig-ME] NLME model syntax 
>> >> 
>> >> 
>> >> Hello, 
>> >> 
>> >> I'm trying to use NLME for a non-linear model with one 
>> random effect 
>> >> that is the same as the one grouping level (chamber). 
>> >> Using the following 
>> >> statement: 
>> >> 
>> >> test <- nlme(flux ~ b0 * exp((b1*soiltemp) - (b2*soiltemp^2)) 
>> >> * vpd^b3 * mstsoil2^b4 * airtemp^b5, data = ac5, fixed = 
>> list(b0 + b1 
>> >> + b2 + b3 + b4 + b5 ~ 1), random = chamber ~ 1, start = 
>> c(b0 = 570, 
>> >> b1 = 0.08, b2 = 0.002, 
>> >> b3 = -0.06, b4 = 3, b5 = 0.3), subset = airtemp > 0) 
>> >> 
>> >> I always get the error message 
>> >> "Error in eval(expr, envir, enclos) : object 'chamber' not found" 
>> >> 
>> >> Data "ac5" is a groupedData object with chamber as the grouping 
>> >> factor: 
>> >> 
>> >> > head(ac5) 
>> >> Grouped Data: flux ~ soiltemp + vpd + mstsoil2 + airtemp | chamber 
>> >> 
>> >> I've tried many variations such as 
>> >> random = list(chamber ~ 1) or random = ~1|chamber or adding the 
>> >> "groups" statement or trying to put chamber on the RHS of 
>> the model 
>> >> statement, after the fixed effects, but I always get the 
>> same error 
>> >> message. 
>> >> 
>> >> What is the correct way to formulate the call to nlme? Or 
>> is this not 
>> >> a syntax error? 
>> >> 
>> >> Thank you in advance. 
>> >> 
>> >> Toby Gass 
>> >> 
>> >> tobygass at cnr dot colostate dot edu 
>> >> 
>> >> _______________________________________________ 
>> >> R-sig-mixed-models at r-project.org mailing list 
>> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models 
>> >> 
>> 
>> 
>> 
>>