Perhaps I should have added the following: To see that it "works," run the
following:
famfit<-lmer(peg.no~1 + (1|family), na.action=na.exclude, vcdf)
resfam<-residuals(famfit)
for( i in 1:length(colms))
{
print(coef(lm(resfam~colms[,i])))
}
Regards, Mark.
A Singh wrote:
>
>
> Dear All,
>
> I am quite new to R and am having a problem trying to run a linear model
> with random effects/ a regression- with particular regard to my variable
> lengths being different and the models refusing to compute any further.
>
> The codes I have been using are as follows:
>
> vc<-read.table("P:\\R\\Testvcomp10.txt",header=T)
>>> attach(vc)
>>
>> family<-factor(family)
>> colms<-(vc)[,4:13] ## this to assign the 10 columns containing marker
>> data to a new variable, as column names are themselves not in any
>> recognisable sequence
>>
>> vcdf<-data.frame(family,peg.no,ec.length,syll.length,colms)
>> library(lme4)
>
>>> for (c in levels(family))
>> + { for (i in 1:length(colms))
>> + { fit<-lmer(peg.no~1 + (1|c/i), vcdf)
>> + }
>> + summ<-summary(fit)
>> + av<-anova(fit)
>> + print(summ)
>> + print(av)
>> + }
>>
>> This gives me:
>>
>> Error in model.frame.default(data = vcdf, formula = peg.no ~ 1 + (1 + :
>> variable lengths differ (found for 'c')
>
>
> I had posted a similar message on the R mixed model list a few days ago,
> with respect to my fundamental methods, and Jerome Goudet had kindly
> referred me to an alternative approach using residuals obtained from a
> random effects model in lmer(), and then doing regressions using those
> [residuals being the dependent variable and my marker data columns the
> independent variable].
>
> The code for that is as follows:
>
> vc<-read.table("P:\\R\\Text
> Files\\Testvcomp10.txt",header=T,sep="",dec=".",na.strings=NA,strip.white=T)
>> attach(vc)
>>
>> family<-factor(family)
>> colms<-(vc)[,4:13]
>>
>> names(vc)
> [1] "male.parent" "family" "offspring.id" "P1L55" "P1L73"
>
> [6] "P1L74" "P1L77" "P1L91" "P1L96" "P1L98"
>
> [11] "P1L100" "P1L114" "P1L118" "peg.no"
> "ec.length"
> [16] "syll.length"
>>
>> vcdf<-data.frame(family, colms, peg.no, ec.length, syll.length)
>>
>> library(lme4)
>
>> famfit<-lmer(peg.no~1 + (1|family), na.action=na.omit, vcdf)
>> resfam<-residuals(famfit)
>> for( i in 1:length(colms))
> + {
> + print ("Marker", i)
> + regfam<-abline(lm(resfam~i))
> + print(regfam)
> + }
>
> This again gives me the error:
>
>
> [1] "Marker"
> Error in model.frame.default(formula = resfam ~ i, drop.unused.levels =
> TRUE) :
> variable lengths differ (found for 'i')
>
>
> My variables all have missing values somewhere or the other. The missing
> values are not consistent for all individuals, i.e some individuals have
> some values missing, others have others,
> and as much as I have tried to use na.action=na.omit and na.rm=T, the
> differing variable length problem is dogging me persistently..
>
> I also tried to isolate the residuals, save them in a new variable (called
> 'resfam' here), and tried to save that in the data.frame()->vcdf, that I
> had created earlier.
>
> The problem with that was that when the residuals were computed, lmer()
> ignored missing data in 'peg.no' with respect to 'family', which is
> obviously not the same data missing for say another variable E.g.
> 'ec.length'- leading again to an inconsistency in variable lengths.
> Data.frame would then not accept that addition at all to the previous set.
> This was fairly obvious right from the start, but I decided to try it
> anyway. Didn't work.
>
> I apologise if the solution to working with these different variable
> lengths is obvious and I don't know it- but I don't know R that well at
> all.
>
> My data files can be downloaded at the following location:
>
> <http://www.filesanywhere.com/fs/v.aspx?v=896d6b88616173be71ab> (excel-
> .xlsx)
>
> <http://www.filesanywhere.com/fs/v.aspx?v=896d6b88616174a76e9e>
> (.txt file)
>
>
> Any pointers would be greatly appreciated, as this is holding me up loads.
>
> Thanks a ton for your help,
>
> Aditi
>
>
>
> ----------------------
> A Singh
> aditi.si...@bristol.ac.uk
> School of Biological Sciences
> University of Bristol
>
> ______________________________________________
> 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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