Dear Steve et al, 
Congratulations on putting together a self-start function for the Richards models. They are so flexible that it can be a real bear to get them to fit to data. I just wanted to mention a new paper that may be of interest to you and to the list: "How to fit nonlinear plant growth models and calculate growth rates: an update for ecologists". (I'm the first author). It's recently been published (early view) in Methods in Ecology and Evolution. http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2011.00155.x/abstract
It summarizes how to fit non-linear models to growth data, calculate absolute & relative growth rates, and how to propagate uncertainty into confidence intervals around those estimates. It's full of trouble-shooting advice and is implemented in R. I hope you might find it useful!

best-
tim




On Oct 3, 2011, at 8:17 PM, Steve Oswald wrote:

> Dear list,
> 
> Just to let you know that the package FlexParamCurve (<http://cran.r-project.org/web/packages/FlexParamCurve/index.html>) is now available on CRAN for fitting non-linear positive-negative Richards models (ie the union of positive and negative trajectory Richards curves) in nls, nlsList and nlme. It includes a flexible selfStart function and model selection routines for assessing the curve that best suits your dataset. This was designed with growth analysis in mind but provides support for any curve-fitting requiring combined positive-negative trajectories. As always, I welcome questions and comments that could improve this package.
> Thanks
> 
> Steve
> 
> Dr. Steve Oswald
> Penn State Berks
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Tue, 2 Aug 2011 15:45:27 -0400
> From: "Steve Oswald" <<A onclick="addTo('steve.oswald@psu.edu')"
> 
> Hi Nils
> 
> My colleagues and I are currently putting the final touches on a flexible selfStart function that should be able to do what you are looking for. It is based on a "double"-Richards model (using your terminology) and uses a similar formulation (A / ([1+ m exp(-k (t-i))]1/m) – Aʹ / ([1+ mʹ exp(-kʹ (t-iʹ ))]1/mʹ ) 
> 
> in which the exponents are raised to 1/m (or 1/m' in the second part of the curve). The package includes reduced parameterizations of this general curve and thus you could remove k and k' and simply convert estimates for m and m' to give scale1 and scale2. 
> 
> We are aiming to submit it to CRAN within the next week and hope to have an Application paper to Methods in Ecology and Evolution submitted in the same timeframe. If you are interested I will let you know as soon as it is available.
> 
> Thanks
> 
> Steve
> 
> 
> Dr. Steve Oswald
> Penn State Berks
> 
> 
>> 
>> Message: 1
>> Date: Mon, 1 Aug 2011 10:32:12 +0000
>> From: "Bunnefeld, Nils" 
>> 
>> Dear All,
>> 
>> We have recently used a double logistic model to quantify migration patterns of moose in Sweden. You can find some more information on the biology in our paper <http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2656.2010.01776.x/abstract> .
>> 
>> The model consists of two logistic non-linear models, one for the spring migration and one for the autumn migration. We used net squared displacement of GPS collared moose, for which we have data for three years  and both sexes, males and females. The model looks like this
>> 
>> M1<-nlme(moosensd ~ asym/(1+exp(xmidA-jday21March)/scale1) + (-asym /(1 + exp(xmidB-jday21March)/scale2),
>> 	fixed = list(asym+ xmidA + xmidB + scale1 ~	factor(yearnsd)+factor(sexn),scale2~factor(yearnsd),
>>  	random = asym ~ 1|mooseID,
>> 	start = c(asym =6490,0,0,0, xmidA =71,0,0,0, xmidB = 254,0,0,0, scale1 =8,0,0,0,scale2=15,0,0)
>> 	,data=datansd)
>> 
>> If you want to see what I mean with double logistic, copy and paste the code below
>> nsd1<-10000/(1+exp(80-(0:365)/5) + (-10000)/(1+exp(240-(0:365)/5)
>> plot(0:365,nsd1,type="l", lty=1, tcl=0.5,ylab=expression(paste('Net squared displacement ',' ', (km^2),
>> 	xlab="Months of the year",cex=2.5,xaxt="n",lwd=2.5)
>> axis(1,at = c(11,72,133,194,255,317), labels=c("April","June","Aug","Oct","Dec","Feb"),tcl=0.5)
>> 
>> The problem is that it can be quite hard to find the right starting values for the above model. Even for a model without fixed effects it can take a while to find the right starting values, which is difficult to handle when one aims to automate the model fitting.
>> I have seen the selfstarter model for the logistic model (SSlogis) but I couldn't find one for a double logistic model that we use. Does anyone know of a function in R that provides starting values for a double logistic model?
>> 
>> Many thanks,
>> Nils
>> 
>> ------------------------------------------------------------------------
>> Nils Bunnefeld
>> Postdoctoral Research Associate
>> Imperial College London
>> Silwood Park
>> SL5 7PY, Ascot, UK
>> <http://www.iccs.org.uk/><<http://www.iccs.org.uk/>>
>> <http://fp7hunt.net/>
>> Tel: +44 20 7594 2253
>> 
______________________
C. E. Timothy Paine
Institut für Evolutionsbiologie und Umweltwissenschaften
Universität Zürich
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
timothy.paine@ieu.uzh.ch
office: ++41 (0)44 635 4740

skype: cetimothypaine
lots of rainforest trees… manuplants.org


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