Hi, I want to fit some psychophysical data with cumulative gaussians. There is quite a convenient toolbox for matlab called 'psignifit' (formerly known as 'psychofit'). It allows the lower bound of the sigmoid to vary slightly from zero, aswell as the upper bound to vary from one. with these two free parameters, the fitted function is less sensitive to noisy data and outliers. Apart from advertising this toolbox I want to ask for possibilities in R to fit psychometric functions, as I would rather use R than matlab. Is there a comparable package specific for psychophysics in R? otherwise: which function would be a good choice? Can I have functionality equal to 'psignifit' with glm() from MASS. I would be grateful for some suggestions of people who have experience in sigmoid-fitting in R. Best, Mario. __________________________________________________________________ Mario Maiworm Biological Psychology and Neuropsychology University of Hamburg Von-Melle-Park 11 D-20146 Hamburg Phone: +49 40 42838 8265 Fax: +49 40 42838 6591 http://bpn.uni-hamburg.de/Maiworm_e.html http://cinacs.org
I am pretty certain a function for this model does not exist. Jan Deleeuw or Dimitris Rizopolous may suggest otherwise. There is a package for a model that would allow for the lower asymptote of the function to be > 0; it does not however, allow the upper asymptote to vary from 1 (well, it tends to 1) and this is in the ltm package.> -----Original Message----- > From: r-help-bounces at r-project.org > [mailto:r-help-bounces at r-project.org] On Behalf Of Mario Maiworm > Sent: Thursday, August 21, 2008 7:05 AM > To: r-help at r-project.org > Subject: [R] psychometric functions > > Hi, > I want to fit some psychophysical data with cumulative > gaussians. There is quite a convenient toolbox for matlab > called 'psignifit' (formerly known as 'psychofit'). It allows > the lower bound of the sigmoid to vary slightly from zero, > aswell as the upper bound to vary from one. with these two > free parameters, the fitted function is less sensitive to > noisy data and outliers. > Apart from advertising this toolbox I want to ask for > possibilities in R to fit psychometric functions, as I would > rather use R than matlab. Is there a comparable package > specific for psychophysics in R? otherwise: which function > would be a good choice? Can I have functionality equal to > 'psignifit' with glm() from MASS. I would be grateful for > some suggestions of people who have experience in > sigmoid-fitting in R. > Best, > Mario. > > > __________________________________________________________________ > > Mario Maiworm > Biological Psychology and Neuropsychology University of > Hamburg Von-Melle-Park 11 > D-20146 Hamburg > > Phone: +49 40 42838 8265 > Fax: +49 40 42838 6591 > > http://bpn.uni-hamburg.de/Maiworm_e.html > http://cinacs.org > > ______________________________________________ > R-help at r-project.org mailing list > 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. >
Hi Mario, in many applications there is not much difference between logistic and Gaussian distributions (just as logit and probit models often produce similar fits)... Moreover it's possible to fit sigmoidal curves using models such as the (log-)logistic where the lower and/upper limits are estimated rather than fixed at 0 and 1, respectively. Have a look at the package 'drc' to see how! Also the following talk at the recent user! 2008 conference might be of interest to you: http://www.statistik.uni-dortmund.de/useR-2008//slides/Haubo.pdf Best wishes Christian
There is a nice paper by Yssaad-Fesselier and Knoblauch on "Modelling Psychometric Functions in R". http://hal.archives-ouvertes.fr/docs/00/13/17/99/PDF/B125.pdf You might also be interested in this: http://www.journalofvision.org/5/5/8/article.aspx which comes from the same group as the psignifit toolbox for matlab (methinks), but is a step ahead. Best wishes Paul -- View this message in context: http://www.nabble.com/psychometric-functions-tp19086590p19091317.html Sent from the R help mailing list archive at Nabble.com.
Paul, thanks a lot for your advice! I got that kuss et al. paper and started to read, this is more than I had expected! Very cool paper, and an algorithm implemented in R that seems to be even superior to psignifit in matlab. So thanks again! mario __________________________________________________________________ Mario Maiworm Biological Psychology and Neuropsychology University of Hamburg Von-Melle-Park 11 D-20146 Hamburg Phone: +49 40 42838 8265 Fax: +49 40 42838 6591 http://bpn.uni-hamburg.de/Maiworm_e.html http://cinacs.org __________________________________________________________________>>> -----Original Message----- >>> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r- >>> project.org] On Behalf Of Paul Artes >>> Sent: Thursday, August 21, 2008 5:37 PM >>> To: r-help at r-project.org >>> Subject: Re: [R] psychometric functions >>> >>> >>> There is a nice paper by Yssaad-Fesselier and Knoblauch on "Modelling >>> Psychometric Functions in R". >>> http://hal.archives-ouvertes.fr/docs/00/13/17/99/PDF/B125.pdf >>> >>> You might also be interested in this: >>> http://www.journalofvision.org/5/5/8/article.aspx >>> which comes from the same group as the psignifit toolbox for matlab >>> (methinks), but is a step ahead. >>> >>> Best wishes >>> >>> Paul >>> -- >>> View this message in context: http://www.nabble.com/psychometric- >>> functions-tp19086590p19091317.html >>> Sent from the R help mailing list archive at Nabble.com. >>> >>> ______________________________________________ >>> R-help at r-project.org mailing list >>> 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.
Hi, 2008/8/21 Mario Maiworm <mario.maiworm@uni-hamburg.de>> Hi, > I want to fit some psychophysical data with cumulative gaussians. There is > quite a convenient toolbox for matlab called 'psignifit' (formerly known as > 'psychofit'). It allows the lower bound of the sigmoid to vary slightly > from > zero, aswell as the upper bound to vary from one. with these two free > parameters, the fitted function is less sensitive to noisy data and > outliers.you might also check the function psyfun.2asym from the psyphy package http://cran.r-project.org/web/packages/psyphy/index.html best Víctor H> > Apart from advertising this toolbox I want to ask for possibilities in R to > fit psychometric functions, as I would rather use R than matlab. Is there a > comparable package specific for psychophysics in R? otherwise: which > function would be a good choice? Can I have functionality equal to > 'psignifit' with glm() from MASS. I would be grateful for some suggestions > of people who have experience in sigmoid-fitting in R. > Best, > Mario. > > > __________________________________________________________________ > > Mario Maiworm > Biological Psychology and Neuropsychology > University of Hamburg > Von-Melle-Park 11 > D-20146 Hamburg > > Phone: +49 40 42838 8265 > Fax: +49 40 42838 6591 > > http://bpn.uni-hamburg.de/Maiworm_e.html > http://cinacs.org > > ______________________________________________ > R-help@r-project.org mailing list > 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]]