[R] Error: length(f1) == length(f2) is not TRUE
A Singh
Aditi.Singh at bristol.ac.uk
Fri Sep 18 21:26:36 CEST 2009
Bill,
It worked!!!
> lmer(data=vcdf, peg.no~1 + (1|family/P1L55))
Linear mixed model fit by REML
Formula: peg.no ~ 1 + (1 | family/P1L55)
Data: vcdf
AIC BIC logLik deviance REMLdev
2981 2997 -1487 2976 2973
Random effects:
Groups Name Variance Std.Dev.
P1L55:family (Intercept) 4.6659e-11 6.8308e-06
family (Intercept) 8.7571e+01 9.3579e+00
Residual 9.2269e+01 9.6057e+00
Number of obs: 390, groups: P1L55:family, 82; family, 57
Fixed effects:
Estimate Std. Error t value
(Intercept) 96.577 1.376 70.2
It seems as if all along it was the na.action=na.exclude that was working
against me, because it probably threw out NAs in a way that made column
lengths incompatible.
It seemed to work with some other models I had tried, but here it was
clearly a problem.
Your example was brilliant for breaking it down.
Thanks a huge bunch, and cheers!
Aditi
--On 18 September 2009 11:40 -0700 William Dunlap <wdunlap at tibco.com> wrote:
>> From: A Singh [mailto:Aditi.Singh at bristol.ac.uk]
>> Sent: Friday, September 18, 2009 11:24 AM
>> To: William Dunlap
>> Subject: RE: [R] Error: length(f1) == length(f2) is not TRUE
>>
>> Yup, they are all factors- and its still doesn't work.
>> Getting to the stage where I can use 'summary()' is the
>> problem- the error
>> stalls the process before a summary can be output.
>
> I meant to get a summary of the input, vcdf, not of
> the output of lmer. Make sure that vcdf$family and
> all the vcdf$P* things are factors.
>
> Here is a short example that gives an error like yours.
> Without seeing your data I can't say for sure yours
> is similar. You need to at least show the output of
> summary(vcdf).
>
>> library(lme4)
>> d <- data.frame(y=log(1:36), expand.grid(g2=1:2,g3=11:13,g6=101:106))
>> sapply(d,class)
> y g2 g3 g6
> "numeric" "integer" "integer" "integer"
>> lmer(data=d, y~1 + (1|g2))
> Linear mixed model fit by REML
> Formula: y ~ 1 + (1 | g2)
> Data: d
> AIC BIC logLik deviance
> 98.784754747615 103.53531156298 -46.392377373808 90.735690977203
> REMLdev
> 92.784754747615
> Random effects:
> Groups Name Variance Std.Dev.
> g2 (Intercept) 0.000000000000000 0.000000000000000
> Residual 0.748809753022119 0.865337941513094
> Number of obs: 36, groups: g2, 2
>
> Fixed effects:
> Estimate Std. Error t value
> (Intercept) 2.65888040394842 0.14422299035915 18.435898446754
>> lmer(data=d, y~1 + (1|g2/g6))
> Error: length(f1) == length(f2) is not TRUE
> In addition: Warning messages:
> 1: In g6:g2 : numerical expression has 36 elements: only the first used
> 2: In g6:g2 : numerical expression has 36 elements: only the first used
>
> Now change the d$g* columns to be factors with
>> d[2:4] <- lapply(d[2:4],factor)
>> # and check with summary(d)
>> summary(d) # or sapply(d,class)
> y g2 g3 g6
> Min. :0.00000000000 1:18 11:12 101:6
> 1st Qu.:2.27624496408 2:18 12:12 102:6
> Median :2.91740536853 13:12 103:6
> Mean :2.65888040395 104:6
> 3rd Qu.:3.30492877705 105:6
> Max. :3.58351893846 106:6
>> lmer(data=d, y~1 + (1|g2))
> Linear mixed model fit by REML
> Formula: y ~ 1 + (1 | g2)
> Data: d
> AIC BIC logLik deviance
> 98.784754747615 103.53531156298 -46.392377373808 90.735690977203
> REMLdev
> 92.784754747615
> Random effects:
> Groups Name Variance Std.Dev.
> g2 (Intercept) 0.000000000000000 0.000000000000000
> Residual 0.748809753022119 0.865337941513094
> Number of obs: 36, groups: g2, 2
>
> Fixed effects:
> Estimate Std. Error t value
> (Intercept) 2.65888040394842 0.14422299035915 18.435898446754
>> lmer(data=d, y~1 + (1|g2/g6))
> Linear mixed model fit by REML
> Formula: y ~ 1 + (1 | g2/g6)
> Data: d
> AIC BIC logLik deviance
> 63.097147876589 69.431223630414 -27.548573938295 54.113964539198
> REMLdev
> 55.097147876589
> Random effects:
> Groups Name Variance Std.Dev.
> g6:g2 (Intercept) 0.6928532833231706 0.832378089165717
> g2 (Intercept) 0.0000000000000000 0.000000000000000
> Residual 0.0955486486847417 0.309109444509128
> Number of obs: 36, groups: g6:g2, 12; g2, 2
>
> Fixed effects:
> Estimate Std. Error t value
> (Intercept) 2.6588804039484 0.2457461012621 10.819623954533
>
>>
>> I tried the same code, but using 'family' and P1L55 as
>> independent random
>> factors, and that works.
>>
>> (I actually tried this with a new marker P1L74)
>>
>> > try(fit<-lmer(peg.no~1 + (1|family) + (1|P1L74),
>> na.action=na.exclude))
>> > summary(fit)
>>
>> Linear mixed model fit by REML
>> Formula: peg.no ~ 1 + (1 | family) + (1 | P1L74)
>> AIC BIC logLik deviance REMLdev
>> 2981 2997 -1487 2976 2973
>> Random effects:
>> Groups Name Variance Std.Dev.
>> family (Intercept) 87.86380 9.37357
>> P1L74 (Intercept) 0.48815 0.69868
>> Residual 92.11681 9.59775
>> Number of obs: 390, groups: family, 57; P1L74, 2
>>
>> Fixed effects:
>> Estimate Std. Error t value
>> (Intercept) 96.40 1.49 64.71
>>
>> ..but the nested random effect ..(1|family/P1L74).. is where
>> the error
>> occurs. And its the same error.
>>
>> Error : length(f1) == length(f2) is not TRUE
>> In addition: Warning messages:
>> 1: In P1L55:family :
>> numerical expression has 390 elements: only the first used
>> 2: In P1L55:family :
>> numerical expression has 390 elements: only the first used
>>
>> My design is a very unbalanced one. Do you think that can be
>> the problem?
>>
>>
>>
>>
>> --On 18 September 2009 09:11 -0700 William Dunlap
>> <wdunlap at tibco.com> wrote:
>>
>> > Look at the output of summary(vcdf) and make sure
>> > that 'family' and 'P1L55' columns are factors. Perhaps
>> > columns 4:13 did not include them.
>> >
>> > Bill Dunlap
>> > TIBCO Software Inc - Spotfire Division
>> > wdunlap tibco.com
>> >
>> >> -----Original Message-----
>> >> From: A Singh [mailto:Aditi.Singh at bristol.ac.uk]
>> >> Sent: Friday, September 18, 2009 9:03 AM
>> >> To: William Dunlap; r-help at r-project.org
>> >> Subject: RE: [R] Error: length(f1) == length(f2) is not TRUE
>> >>
>> >> Hi Bill,
>> >>
>> >> Thanks, I did try out what you suggested but it doesn't
>> seem to work.
>> >> I get the same error again.
>> >>
>> >> There's obviously something here that I don't get. Need to
>> >> figure it out.
>> >>
>> >> Aditi
>> >>
>> >> --On 18 September 2009 08:34 -0700 William Dunlap
>> >> <wdunlap at tibco.com> wrote:
>> >>
>> >> >> From: r-help-bounces at r-project.org
>> >> >> [mailto:r-help-bounces at r-project.org] On Behalf Of A Singh
>> >> >> Sent: Friday, September 18, 2009 4:42 AM
>> >> >> To: r-help at r-project.org
>> >> >> Subject: [R] Error: length(f1) == length(f2) is not TRUE
>> >> >>
>> >> >>
>> >> >> Dear R users,
>> >> >>
>> >> >> I am trying to fit an lmer model with only random effects
>> >> >> which is giving
>> >> >> me the following error:
>> >> >>
>> >> >> Error : length(f1) == length(f2) is not TRUE
>> >> >> In addition: Warning messages:
>> >> >> 1: In P1L55:family :
>> >> >> numerical expression has 390 elements: only the first used
>> >> >> 2: In P1L55:family :
>> >> >> numerical expression has 390 elements: only the first used
>> >> >>
>> >> >>
>> >> >> I am trying to extract variance components for a phenotype
>> >> >> 'peg.no', using
>> >> >> the variable 'family' and a marker column 'P1L55' (which is
>> >> >> categorical and
>> >> >> has 2 levels- 0 and 1), as random effects. There are no
>> >> fixed effects.
>> >> >>
>> >> >> The code I used is as follows:
>> >> >>
>> >> >> vc<-read.table(...)
>> >> >>
>> >> >> vcdf<-data.frame(vc)
>> >> >> colms<-(vc)[4:13] ##these are the markers
>> >> >> lapply(colms,factor)
>> >> >
>> >> > Note that you did not change columns 4:13 of vcdf to factors:
>> >> > you changed copies of them to factors. Do
>> >> > vcdf[4:13] <- lapply(vcdf[4:13], factor)
>> >> > and lmer should be happier.
>> >> >
>> >> > Bill Dunlap
>> >> > TIBCO Software Inc - Spotfire Division
>> >> > wdunlap tibco.com
>> >> >
>> >> >>
>> >> >> try(fit<-lmer(peg.no~1 + (1|family/P1L55),
>> >> >> na.action=na.include, data=vcdf))
>> >> >>
>> >> >>
>> >> >> I thought that putting the data into a dataframe would help,
>> >> >> along with the
>> >> >> na.exclude command, because there is a lot of missing data in
>> >> >> patches which
>> >> >> I have replaced with NA's, but I don't know how to fix this
>> >> >> error at all.
>> >> >>
>> >> >> Its a bit urgent, and any help is hugely appreciated.
>> >> >>
>> >> >> The data files are at:
>> >> >>
>> >> >>
>> >> >> <http://www.4shared.com/file/131980362/460bdafe/Testvcomp10.ht
>> >> >> ml> (excel)
>> >> >> http://www.4shared.com/file/131980512/dc7308b/Testvcomp10.html
>> >> >> (txt)
>> >> >>
>> >> >>
>> >> >> Cheers,
>> >> >> Aditi
>> >> >>
>> >> >> ----------------------
>> >> >> A Singh
>> >> >> Aditi.Singh at bristol.ac.uk
>> >> >> School of Biological Sciences
>> >> >> University of Bristol
>> >> >>
>> >> >> ______________________________________________
>> >> >> R-help at 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.
>> >> >>
>> >>
>> >>
>> >>
>> >> ----------------------
>> >> A Singh
>> >> Aditi.Singh at bristol.ac.uk
>> >> School of Biological Sciences
>> >> University of Bristol
>> >>
>> >>
>> >>
>> >>
>> >>
>>
>>
>>
>> ----------------------
>> A Singh
>> Aditi.Singh at bristol.ac.uk
>> School of Biological Sciences
>> University of Bristol
>>
>>
>>
>>
>>
----------------------
A Singh
Aditi.Singh at bristol.ac.uk
School of Biological Sciences
University of Bristol
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