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

Matthias Kuhn lenz99 at gmail.com
Tue Sep 30 10:13:15 CEST 2014

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..


ps> This is my setting:

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

[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’


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,


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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