From: A Singh [mailto:aditi.si...@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
<wdun...@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.si...@bristol.ac.uk]
>> Sent: Friday, September 18, 2009 9:03 AM
>> To: William Dunlap; r-help@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
>> <wdun...@tibco.com> wrote:
>>
>> >> From: r-help-boun...@r-project.org
>> >> [mailto:r-help-boun...@r-project.org] On Behalf Of A Singh
>> >> Sent: Friday, September 18, 2009 4:42 AM
>> >> To: r-help@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.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.
>> >>
>>
>>
>>
>> ----------------------
>> A Singh
>> aditi.si...@bristol.ac.uk
>> School of Biological Sciences
>> University of Bristol
>>
>>
>>
>>
>>
----------------------
A Singh
aditi.si...@bristol.ac.uk
School of Biological Sciences
University of Bristol
