Hi,
I have fixed this. I replaced the "=" with "<<-". I do not think this
is the most elegant way, so if anyone else has any better ideas they
would be very much apperitiaded.
New lines:
formulaGenotype <<- test_variable~Genotype + Gender
formulaNull <<- test_variable~Gender
Cheers,
Hugh
On 01/29/2012 07:46 PM, Hugh Morgan wrote:
> Hi,
>
> I have what I suppose is the same problem as this. I am using the
> linear mixed model function lme, and this does not seems to take the
> attribute "model=TRUE" at the end of the function.
>
> Is there a more general way of solving this problem?
> Is my description of the problem below correct (from my understanding
> of cran.r-project.org/doc/contrib/Fox-Companion/appendix-scope.pdf)?
>
> Using the test script:
>
> calculate_mixed_model_p <- function() {
> dataObj=read.csv('dataMini.csv', header=TRUE, sep=",", dec=".")
> colnames(dataObj)
> attach(dataObj)
> library(nlme)
>
> formulaGenotype = test_variable~Genotype + Gender
> formulaNull = test_variable~Gender
> finalModelGenotype = lme(formulaGenotype, random=~1|Date, dataObj,
> na.action="na.omit", method="ML", keep.data = TRUE)
> finalModelNull = lme(formulaNull, random=~1|Date, dataObj,
> na.action="na.omit", method="ML")
> anovaModel = anova (finalModelGenotype,finalModelNull)
> print(anovaModel)
> }
>
> Fails with:
>
> Error in eval(expr, envir, enclos) : object 'formulaGenotype' not found
>
> I THINK function lme(...) constructs an object (finalModelGenotype)
> that has as part of it a link (pointer?) to object formulaGenotype.
> During construction this is in the function scope as it was passed to
> it. When finalModelGenotype is later passed to function anova(...)
> the link is still there but as the lme(...) scope no longer exists the
> link is now broken.
>
> Any help greatly apperitiated,
>
> Hugh
>
> PS, I tried to make this script self contained, and generated the data
> object with the following lines. It looks identical when you print
> it, but the lme function fails with error at [2]. If someone was to
> tell me what I am doing wrong I may be able to post easier scripts.
>
> [1]
>
> dataObj=data.frame(test_variable=c("23.0","20.2","23.8","25.6","24.6","22.7","27.7","27.5","23.5","22.8","22.3","20.9","26.6","23.8","24.5","26.8","23.2","29.9","23.3","22.5","22.2","27.2","28.1","24.5","22.7","20.7","26.2","27.1","22.0","22.2","26.7","28.5","22.2","22.1","25.3","21.7","29.3"),
>
> Gender=c("Female","Female","Male","Male","Male","Female","Male","Male","Female","Female","Female","Female","Male","Male","Male","Male","Female","Male","Female","Female","Female","Male","Male","Male","Female","Female","Male","Male","Female","Female","Male","Male","Female","Female","Female","Female","Male"),
>
> Genotype=c("10028","10028","10028","10028","10028","10028","10028","10028","10028","10028","10028","10028","10028","10028","10028","10028","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0"),
>
> Assay.Date=c("01/07/2009","01/07/2009","01/07/2009","01/07/2009","01/07/2009","01/07/2009","01/07/2009","01/07/2009","01/07/2009","07/07/2010","07/07/2010","07/07/2010","01/07/2009","07/07/2010","07/07/2010","07/07/2010","02/06/2010","02/06/2010","02/06/2010","02/06/2010","02/06/2010","02/06/2010","02/06/2010","02/06/2010","17/06/2010","17/06/2010","17/06/2010","17/06/2010","16/06/2010","16/06/2010","16/06/2010","16/06/2010","22/06/2010","22/06/2010","22/06/2010","22/06/2010","22/06/2010"),
>
> Weight=c("9.9","9.5","9.9","10","9.9","9.8","10.2","10.4","9.9","9.8","9.9","9.5","9.8","9.5","9.8","9.9","9.5","10","9.8","9.5","9.7","10","10.2","9.9","9.9","9.5","10","10","9.8","9.9","10.2","10.1","9.8","9.9","10.2","9.8","10")
> )
>
> [2]
>
> Error in `rownames<-`(`*tmp*`, value = c("1", "2", "3", "4", "5", "6", :
> attempt to set rownames on object with no dimensions
> In addition:Warning message:
> In Ops.factor(y[revOrder], Fitted) : - not meaningful for factors
>
>
>
> On 01/25/2012 01:25 PM, Terry Therneau wrote:
>>> I want use survfit() and basehaz() inside a function, but it doesn't
>>> work. Could you take a look at this problem. Thanks for your help.
>> Your problem has to do with environments, and these lines
>>
>> fmla<- as.formula("Surv(time, event) ~ Z1 + Z2")
>> BaseFun<- function(x){
>> start.coxph<- coxph(x, phmmd)
>> ...
>> survfit(start.coxph)
>> }
>> Basefun(fmla)
>>
>> The survfit routine needs to reconstruct the model matrix, and by
>> default in R this is done in the context where the model formula was
>> first defined. Unfortunately this is outside the function, leading to
>> problems -- your argument "x" is is unknown in the outer envirnoment.
>> The solution is to add "model=TRUE" to the coxph call so that the model
>> frame is saved and survfit doesn't have to do reconstruction.
>>
>> If you think this should work as is, well, so do I. I spent a lot of
>> time on this issue a few months ago and finally threw in the towel. The
>> interaction of environments with model.frame and model.matrix is subtle
>> and far from obvious. (Just to be clear: I didn't say "broken". Each
>> aspect of the process has well thought out reasons.) The standard
>> modeling functions lm, glm, etc changed their defaults from model=F to
>> model=T at some point. This costs some space& memory, but coxph may
>> need to do the same.
>>
>> Terry T
>>
>> ______________________________________________
>> 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.
>
>
> ______________________________________________
> 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.
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