[R] ..nlme: start values necessary even though using self-start function?..

[Prof Brian Ripley]

This seems to be a bug in the package.  Maybe the code was written for 
S, or maybe R has changed in the many years since the former maintainer 
decided to be unhelpful.

I'll put this on the list for the next release.


On 30/09/2014 09:13, Matthias Kuhn wrote:
> Dear list.
>
> I am stuck with an "subscript out of bounds" error when I play with an
> nlme-example from the yellow Pinheiro/Bates book. It is about using
> nlme() using the formula interface for non-linear mixed models.
>
> The following code snippet is inspired by the book (in section 8.2),
> using the Orange-example data from R datasets containing repeated
> measures of trunk circumferences over time for 5 trees. It is a
> nfnGroupedData with structure circumference ~ age | Tree.
>
>
> nlme( circumference ~ SSlogis(age, Asym, xmid, scal), data=Orange,
>                        fixed= Asym + xmid + scal ~ 1)
>
> It results in the following error:
> Error in nlme.formula(circumference ~ SSlogis(age, Asym, xmid, scal),  :
>    subscript out of bounds
>
> Specifiying the grouping as in groups=~Tree does not help, either.
>
> When I do provide start values, it works, though.
>
> nlme( circumference ~ SSlogis(age, Asym, xmid, scal), data=Orange,
>                        start=c(Asym = 200, xmid=725, scal=350),
>                        fixed= Asym + xmid + scal ~ 1)
>
> Beginning of result output:
>
> Nonlinear mixed-effects model fit by maximum likelihood
> Model: circumference ~ SSlogis(age, Asym, xmid, scal)
> Data: Orange
> Log-likelihood: -129.9907
> Fixed: Asym + xmid + scal ~ 1
>      Asym     xmid     scal
> 192.0959 727.5887 356.6011
> ...
>
>
>
> SSlogis() is a selfStart object and should be able to get its own
> starting values like so:
> getInitial(circumference ~ SSlogis(age, Asym, xmid, scal), data=Orange)
>
>
> So start= argument should not be necessary.
> What am I missing here? Any ideas?
>
> Thanks in advance..
>
> -m
>
>
>
> ps> This is my setting:
>
>> sessionInfo()
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-apple-darwin13.1.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] nlme_3.1-117 devtools_1.5
>
> loaded via a namespace (and not attached):
>   [1] digest_0.6.4    evaluate_0.5.5  grid_3.1.1      httr_0.5
> lattice_0.20-29 memoise_0.2.1   parallel_3.1.1  RCurl_1.95-4.3
> stringr_0.6.2   tools_3.1.1     whisker_0.3-2
>
>
>
> And regarding my nlme-package from CRAN:
>
> Information on package ‘nlme’
>
>
> Description:
>
>
> Package:            nlme
>
> Version:            3.1-117
>
> Date:               2014-03-31
>
> Priority:           recommended
>
> Title:              Linear and Nonlinear Mixed Effects Models
>
> Authors at R:          c(person("José", "Pinheiro", role = "aut", comment
> = "S version"), person("Douglas", "Bates", role = "aut", comment = "up
> to 2007"), person("Saikat", "DebRoy", role = "ctb", comment = "up
>                to 2002"), person("Deepayan", "Sarkar", role = "ctb",
> comment = "up to 2005"), person("EISPACK authors", role = "ctb",
> comment = "src/rs.f"), person("R-core", email =
>
>                      "R-core at R-project.org", role = c("aut", "cre")))
>
> Description:        Fit and compare Gaussian linear and nonlinear
> mixed-effects models.
>
> Depends:            graphics, stats, R (>= 3.0.0)
>
> Imports:            lattice
>
> Suggests:           Hmisc, MASS
>
> LazyData:           yes
>
> ByteCompile:        yes
>
> Encoding:           UTF-8
>
> License:            GPL (>= 2)
>
> BugReports:         http://bugs.r-project.org
>
> Packaged:           2014-03-31 07:56:40 UTC; ripley
>
> Author:             José Pinheiro [aut] (S version), Douglas Bates
> [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar
> [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), R-core [aut,
>
>                      cre]
>
> Maintainer:         R-core <R-core at R-project.org>
>
> NeedsCompilation:   yes
>
> Repository:         CRAN
>
> Date/Publication:   2014-03-31 10:16:43
>
> Built:              R 3.1.1; x86_64-apple-darwin13.1.0; 2014-07-11
> 12:37:41 UTC; unix
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK