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

Duncan Mackay dulcalma at bigpond.com
Sun Jan 17 01:38:12 CET 2016


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 



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


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 O'Hara

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

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

R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

More information about the R-help mailing list