[R] error in "predict.gam" used with "bam"
Simon Wood
s.wood at bath.ac.uk
Tue Jul 9 09:07:12 CEST 2013
Hi Julian,
Any chance you could send me (offline) a short version of your data,
which reproduces the problem? I can't reproduce it in a quick attempt
(but it is quite puzzling, given that bam calls predict.gam internally
in pretty much the same way that you are doing here).
btw (and nothing to do with the error) given that you are using R 3.0.1
it's a good idea to upgrade to mgcv_1.7-23 or above, for the following
reason (taken from the mgcv changeLog)
1.7-23
------
*** Fix of severe bug introduced with R 2.15.2 LAPACK change. The
shipped version of dsyevr can fail to produce orthogonal eigenvectors
when uplo='U' (upper triangle of symmetric matrix used), as opposed to
'L'. This led to a substantial number of gam smoothing parameter
estimation convergence failures, as the key stabilizing
re-parameterization was substantially degraded. The issue did not affect
gaussian additive models with GCV model selection. Other models could
fail to converge any further as soon as any smoothing parameter became
`large', as happens when a smooth is estimated as a straight line.
check.gam reported the lack of full convergence, but the issue could
also generate complete fit failures. Picked up late as full test suite
had only been run on R > 2.15.1 with an external LAPACK.
best,
Simon
On 08/07/13 10:02, julian.bothe at elitepartner.de wrote:
> Hello everyone.
>
>
>
> I am doing a logistic gam (package mgcv) on a pretty large dataframe
> (130.000 cases with 100 variables).
>
> Because of that, the gam is fitted on a random subset of 10000. Now when I
> want to predict the values for the rest of the data, I get the following
> error:
>
>
>
>
>
>> gam.basis_alleakti.1.pr=predict(gam.basis_alleakti.1,
>
> +
> newdata=activisale_join[gam.basis_alleakti.1.complete_cases,all.vars(gam.b
> asis_alleakti.1.formula)],type="response")
>
> Error in predict.gam(gam.basis_alleakti.1, newdata =
> activisale_join[gam.basis_alleakti.1.complete_cases, :
>
> number of items to replace is not a multiple of replacement length
>
>
>
>
>
> The following is the code:
>
> #formula with some factors and a lot of variables to be fitted
>
> gam.basis_alleakti.1.formula=as.formula( paste("verlängerung ~“,
>
> paste( names(activisale_join)[c(2:10)], collapse="+"), ##factors
>
>
> paste("s(",names(activisale_join)[c(17,19:29,31:42,44)],")",
> collapse="+")) # numeric variables, all count data
>
> )
>
>
>
> # complete cases
>
> gam.basis_alleakti.1.complete_cases =
> complete.cases(activisale_join[,all.vars(gam.basis_alleakti.1.formula) ])
>
>
>
> # modell fitting works on random subset
>
> gam.basis_alleakti.1=bam(gam.basis_alleakti.1.formula,
>
> data = activisale_join[subset.10000, ], family=
> "binomial")
>
>
>
> # error, no idea why
>
> gam.basis_alleakti.1.pr=predict(gam.basis_alleakti.1,
> newdata=activisale_join[gam.basis_alleakti.1.complete_cases,
> ],type="response")
>
>
>
>
>
> the prediction on the same subset (subset.10000) works.
>
>
>
>
>
> It could be that this error is somewhat similar to that described as
> sidequestion in
>
> http://r.789695.n4.nabble.com/gamm-tensor-product-and-interaction-td452618
> 8.html, where simon answered the following:
>
>
>
> “> Here is the error message I obtain:
>>
> vis.gam(gm1$gam,plot.type="contour",n.grid=200,color="heat",zlim=c(0,4))
>> Error in predict.gam(x, newdata = newd, se.fit = TRUE, type = type) :
> number of items to replace is not a multiple of replacement length
> - hmm, possibly a bug. I'll look into it.
>
> best,
> Simon“
>
>
>
> All the best
>
>
>
> Julian
>
>
>
> Ps.: > version
> _
> platform x86_64-w64-mingw32
> arch x86_64
> os mingw32
> system x86_64, mingw32
> status
> major 3
> minor 0.1
> year 2013
> month 05
> day 16
> svn rev 62743
> language R
> version.string R version 3.0.1 (2013-05-16)
> nickname Good Sport
>
>
>
> package mgcv version 1.7-22
>
>
>
>
> [[alternative HTML version deleted]]
>
>
>
> ______________________________________________
> 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.
>
--
Simon Wood, Mathematical Science, University of Bath BA2 7AY UK
+44 (0)1225 386603 http://people.bath.ac.uk/sw283
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