[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 __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Re: [R] Ordinal regression with some categories combined for some data
Dear Bob, I don't know any package that handles ordinal data the way you are looking for. I'd just would comment on the ordinal regression. Would the time of loss be the ordinal response? That seems inefficient to me when you have a lot of time points (= lots of ordinal classes). IMHO the survival analysis would make more sense. Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey 2016-01-15 16:48 GMT+01:00 Bob O'Hara : > 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 > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Re: [R] Ordinal regression with some categories combined for some data
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: mac...@northnet.com.au -Original Message- From: R-help [mailto:r-help-boun...@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 __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Re: [R] Ordinal regression with some categories combined for some data
This does seem to be a good situation for ordinal regression. The R rms package's orm function allows for thousands of categories in Y. But it doesn't handle censoring. This discussion would be better for stats.stackexchange.com Frank -- Frank E Harrell Jr Professor and Chairman School of Medicine Department of *Biostatistics* *Vanderbilt University* [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Re: [R] Ordinal regression with some categories combined for some data
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 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: mac...@northnet.com.au > > > > -Original Message- > From: R-help [mailto:r-help-boun...@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 > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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. > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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. -- 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 __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.