[R] Ordinal regression with some categories combined for some data

[Bob O'Hara]

Thanks, Thierry & Duncan. I'll go down the survival analysis route.

The data are for central American epiphytes, so not your usual
species. Visually there's definitely differences in the times of
germination, but not in eventual germination, so that's
straightforward.

Bob

On 17 January 2016 at 01:38, Duncan Mackay <dulcalma at bigpond.com> wrote:
> Hi
>
> I have never seen germination experiments carried out as ordinal regression.
> Most germination tests are done using a nls model.
> For some species germination may only start a week after planting and then
> germinate over 2 or 3 days.
> If all germinated over the experimental period and  there is no change in
> germination between readings then read them accordingly.
> If there are ungerminated seeds at the end; have these then had germinable
> tests been applied to them?.
>
> I agree with Thierry about survival analysis.
> If however you are wanting to get into latency then ordinal models may be OK
> Another package to do ordinal regression is VGAM
>
> Regards
>
> Duncan
>
> Duncan Mackay
> Department of Agronomy and Soil Science
> University of New England
> Armidale NSW 2351
> Email: home: mackay at northnet.com.au
>
>
>
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Bob O'Hara
> Sent: Saturday, 16 January 2016 01:49
> To: r-help
> Subject: [R] Ordinal regression with some categories combined for some data
>
> Hi!
>
> I've been asked about a problem where I think I can see how to write
> the model, but don't know if it's been implemented in R. It's not
> something I work on a lot, so I'm hoping someone else can point me to
> an answer straight away.
>
> The researcher has been carrying out germination experiments: lost of
> seeds are put in several conditions (temperature humidity etc.), and
> every few days they are checked to see if they have germinated.
> Because the days are discrete I think it makes sense to view this as
> an ordinal regression problem (rather than as an interval censored
> survival analysis). But what makes this tricky is that there are days
> when the researcher only checked some seeds. So for some seeds the
> germination might fall into more than one category.
>
> Is there a package in R that can handle this, i.e. do an ordinal
> regression where for some observations the categories are interval
> censored? Or is it easier to go straight to a full interval-censored
> survival analysis?
>
> Bob
>
> --
> Bob O'Hara
>
> Biodiversity and Climate Research Centre
> Senckenberganlage 25
> D-60325 Frankfurt am Main,
> Germany
>
> Tel: +49 69 798 40226
> Mobile: +49 1515 888 5440
> WWW:   http://www.bik-f.de/root/index.php?page_id=219
> Blog: http://occamstypewriter.org/boboh/
> Journal of Negative Results - EEB: www.jnr-eeb.org
>
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> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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-- 
Bob O'Hara

Biodiversity and Climate Research Centre
Senckenberganlage 25
D-60325 Frankfurt am Main,
Germany

Tel: +49 69 798 40226
Mobile: +49 1515 888 5440
WWW:   http://www.bik-f.de/root/index.php?page_id=219
Blog: http://occamstypewriter.org/boboh/
Journal of Negative Results - EEB: www.jnr-eeb.org