Hi, Is there any R package to fit Richards' curve in the form of https://en.wikipedia.org/wiki/Generalised_logistic_function I found there is one package grofit, but currently defunct. Any pointer appreciated.
Hi Christofer Try FlexParamCurve or maybe drc package. Cheers Petr> -----Original Message----- > From: R-help <r-help-bounces at r-project.org> On Behalf Of Christofer Bogaso > Sent: Wednesday, May 13, 2020 11:26 AM > To: r-help <r-help at r-project.org> > Subject: [R] Fitting Richards' curve > > Hi, > > Is there any R package to fit Richards' curve in the form of > https://en.wikipedia.org/wiki/Generalised_logistic_function > > I found there is one package grofit, but currently defunct. > > Any pointer appreciated. > > ______________________________________________ > R-help at 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.
Shouldn't be hard to set up with nls(). (I kind of suspect that the Richards curve has more flexibility than data can resolve, especially the subset (Q,B,nu) seems highly related, but hey, it's your data...) -pd> On 13 May 2020, at 11:26 , Christofer Bogaso <bogaso.christofer at gmail.com> wrote: > > Hi, > > Is there any R package to fit Richards' curve in the form of > https://en.wikipedia.org/wiki/Generalised_logistic_function > > I found there is one package grofit, but currently defunct. > > Any pointer appreciated. > > ______________________________________________ > R-help at 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.-- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
The Richards' curve is analytic, so nlsr::nlxb() should work better than
nls() for getting derivatives --
the dreaded "singular gradient" error will likely stop nls(). Also
likely, since even a 3-parameter
logistic can suffer from it (my long-standing Hobbs weed infestation problem
below), is
that the Jacobian will be near-singular. And badly scaled. Nonlinear fitting
problems essentially
have different scale in different portions of the parameter space.
You may also want to "fix" or mask one or more parameters to reduce
the dimensionality of the problem,
and nlsr::nlxb() can do that.
The Hobbs problem has the following 12 data values for time points 1:12
# Data for Hobbs problem
ydat <- c(5.308, 7.24, 9.638, 12.866, 17.069, 23.192, 31.443,
38.558, 50.156, 62.948, 75.995, 91.972) # for testing
tdat <- seq_along(ydat) # for testing
An unscaled model is
eunsc <- y ~ b1/(1+b2*exp(-b3*tt))
This problem looks simple, but has given lots of software grief over nearly 5
decades. In 1974 an
extensive search had all commonly available software failing, which led to the
code that evolved
into nlsr, though there are plenty of cases where really awful code will luckily
find a good
solution. The issue is getting a solution and knowing it is reasonable. I
suspect a Richards'
model will be more difficult unless the OP has a lot of data and maybe some
external information
to fix or constrain some parameters.
JN
On 2020-05-13 5:41 a.m., Peter Dalgaard wrote:> Shouldn't be hard to set up with nls(). (I kind of suspect that the
Richards curve has more flexibility than data can resolve, especially the subset
(Q,B,nu) seems highly related, but hey, it's your data...)
>
> -pd
>
>> On 13 May 2020, at 11:26 , Christofer Bogaso <bogaso.christofer at
gmail.com> wrote:
>>
>> Hi,
>>
>> Is there any R package to fit Richards' curve in the form of
>> https://en.wikipedia.org/wiki/Generalised_logistic_function
>>
>> I found there is one package grofit, but currently defunct.
>>
>> Any pointer appreciated.
>>
>> ______________________________________________
>> R-help at 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.
>
Hi Christofer, This doesn't really answer your question. But if the goal is to fit an S-shaped curve to data, with increased flexibility... (I'm assuming that's the goal). ...then I'd like to note the option of splines (or smoothing), subject to shape constraints... My guess, is it's probably easier to model the inverse of a growth curve this way, than to model the growth curve directly. In which case, a 4-piece to 10-piece spline should give considerably flexibly. It's possible that Martin's package, cobs, can do this, but not sure, I haven't tried it. And there may be other R packages for fitting splines/smoothers to data, subject to shape constraints. If not, I'm guessing it wouldn't be too difficult to implement, via extensions to the quadprog package, for quadratic programming. On Wed, May 13, 2020 at 9:26 PM Christofer Bogaso <bogaso.christofer at gmail.com> wrote:> > Hi, > > Is there any R package to fit Richards' curve in the form of > https://en.wikipedia.org/wiki/Generalised_logistic_function > > I found there is one package grofit, but currently defunct. > > Any pointer appreciated. > > ______________________________________________ > R-help at 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.
> It's possible that Martin's package, cobs, can do this, but not sure, > I haven't tried it. > And there may be other R packages for fitting splines/smoothers to > data, subject to shape constraints.Further to my previous post. I read through the documentation for the cobs package. And (someone please correct me if I'm wrong) I don't think it can produce a smoother with an S-shaped shape constraint. I found two other packages for smoothing under shape constraints, but doesn't look like they can either. I have code that could be adapted for this purpose. But one it's incomplete, two it (currently) requires the user to specify a smoothness parameter, and three doesn't produce any kind of inference...
I have been using nlsr() to fit s curves to Covid-19 data over the past few weeks and I have not had any issues. Bernard Sent from my iPhone so please excuse the spelling!"> On May 13, 2020, at 5:16 PM, Abby Spurdle <spurdle.a at gmail.com> wrote: > > ?Hi Christofer, > > This doesn't really answer your question. > But if the goal is to fit an S-shaped curve to data, with increased > flexibility... > (I'm assuming that's the goal). > > ...then I'd like to note the option of splines (or smoothing), subject > to shape constraints... > > My guess, is it's probably easier to model the inverse of a growth > curve this way, than to model the growth curve directly. > In which case, a 4-piece to 10-piece spline should give considerably flexibly. > > It's possible that Martin's package, cobs, can do this, but not sure, > I haven't tried it. > And there may be other R packages for fitting splines/smoothers to > data, subject to shape constraints. > > If not, I'm guessing it wouldn't be too difficult to implement, via > extensions to the quadprog package, for quadratic programming. > > >> On Wed, May 13, 2020 at 9:26 PM Christofer Bogaso >> <bogaso.christofer at gmail.com> wrote: >> >> Hi, >> >> Is there any R package to fit Richards' curve in the form of >> https://en.wikipedia.org/wiki/Generalised_logistic_function >> >> I found there is one package grofit, but currently defunct. >> >> Any pointer appreciated. >> >> ______________________________________________ >> R-help at 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 at 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.