search for: nlslist

Dear listers, I am trying to fit a model using nlsList() using alternately a SSfol() selfstart function or its developped equivalent formulae. This preliminary trial works well mydata<-groupedData(Conc~Tps|Organ,data=mydata) mymod1<-nls(Conc~SSfol(Dose,Tps,lKe,lKa,lCl),data=mydata) as well as a developped form: mymod2<-nls(Conc~Dose * exp...

Hello, nls-users, is it possible to pass additional parameters to the model function that are known and groupwise constant with nlsList? I could not find something like a "keep this fixed" option in the documentation and the code (my fault...?) The current workaround is to break the problem down into groups and use globals to pass the constant parameters, but it is ugly code and won't work when an over-all nlme is ne...

Hi All I'm analysing growth rates using a gompertz (logistic) curve and am attempting to fit parameters for all of my study birds using nlsList. I've been looking for an option in nlsList to set min and max limits for parameter values during estimation, although I have failed to find any under 'control'. Other users seem to have reported that using control in the port algorithm (as in an nls fit) failed to work and it didn...

...propriate, or there is another way to do it that does not involve changing the source code. I don't have enough experience to start changing the sorurce code of a library function. Calling nlme from within a function as done below will give an error: testfunc<- function(dat=v) { test<-nlsList(result~a+(b-a)/(1+(conc/(c+z*cdiff))^d) |rep,start=dat$init,data=dat$mixeddat) return(nlme(test,random=b~1)) } Here, v is an appropriate data frame in the main workspace. Inserting two lines in nlme.nlsList will fix it: Replacing line 21 from bottom "mData<-eval(mData) " by "...

Hi All. I'm trying to run nlsList an getting an error that makes no sense to me. I have accuracy and reaction time data over many trials for each person (id) When I use nlsList code that is virtually identical to the example in the doc file I get the following error. I've tried everything I could think of and can't get a...

DeaR I am trying to use a dynamically create formula with nlsList and nlme, but I cannot get the environment of the string-generated formal to work similarly to the manually entered one. Any idea? Dieter #----- library(nlme) # Pinheiro/Bates p 280 fm1Indom.lis = nlsList(conc~SSbiexp(time,A1,lrc1,A2,lrc2), data=Indometh) nlme(fm1Indom.lis,random=pdDiag(A1+lrc...

Hello together, Is there a tool to test the statistical differences between parameter estimates of a nlsList fit? I fitted degradation data using the nlsList method and want to find out whether derived rate constants are significantly different from each other at the grouping factors soil and temperature. Regards Frank Scherr +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++...

Dear R users, Does anybody have a function to calculate logLik or AIC for nlsList objects? After receiving error messages, another user helped me ascertain that this function is not currently written into R. Many thanks Lindsay

Dear R-helpers, I'm using R 2.5.0 under Windows and am trying to use nlsList from nlme 3.1-80 with the selfstart function for the four parametric logistic function. My first test went well, but now I'm trying to do some more sophisticated things and it does not work anymore. I simulate my data from a five parametric logistic function like this: Y<-as.data.frame(a...

Hi All. I'd like to send some control arguments to the nls function when performing a nlsList analysis. I'm fitting a power model to some grouped data and would like to impose lower bounds on the estimates using the "port" algorithm. Obtaining the lower bound constraint works fine with a direct call to nls for a single level of the grouping variable. ?However, the bounds aren...

Hi Rick Thanks to Dieter Menne I did manage to solve the problem of imposing bounds on the parameter space duirng an nlsList fit. He suggested using optim to optimize the parameters prior to each fit. This worked well for me as I had a customized selfStart function that then optimized the parameters for each individual separately. if you rewrote your selfStart function as: powrDpltInit <- function(mCall, LHS, dat...

...lar hyperbola. I have already searched the archives and have read the book by Pinheiro & Bates (2000) and, although they give many useful suggestions, none seem to work in my case. Details: In particular, I can obtain convergence for each group (plant) separately using either nls or nlsList, but cannot get convergence using nlme. My function is a non-rectangular hyperbola with 4 parameters (theta, Am, alpha, Rd): #Nonrectangular hyperbola for photosynthesis # myfunct (1/(2*theta))*( alpha*Irr + Am -sqrt((alpha*Irr+Am)^2-4*alpha*theta*Am*Irr))-Rd I have written a self-st...

Dear all, is there a way to extract the individual variance-covariance matrix of the parameter estimates of the i-th individual using nlsList ? Thanks a lot Peter -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To:...

I hope that the mailing list is the correct forum for the question below. I have trouble calling functions nlsList and nlme from another function. Any help would be greatly appreciated. Jens Praestgaard Human Genome Sciences Rockville MD. I have a data set v with two components, v$mixeddat and v$init. They are listed below: > v$mixeddat conc result rep sample z 11 20.00000000 11141 1 vial...

...hile using the nonlinear mixed model (nlme) function in R with a self-starting function. Thanks for those who responded. This posting is to explain what (I think) it causing the error. Pinheiro & Bates (2000, pages 342-347) describe how to construct a self-starting function for use in nls, nlsList and nlme. A self-starting function provides, not only the function to be evaluated, but also estimates of initial values of the parameters that are to be estimated. I have written a self-starting function (NRhyperbola) for a non-rectangular hyperbola with 4 parameters (theta, Am, alpha, Rd). The...

Howdee, I am able to fit a 4-parameter logistic growth curve to a dataset which comprise many individuals (using R v. 2.3.1). Yet, if I want to obtain the parameters for each individual (i.e., for each 'id') using nlsList, then I obtain an Error message which I have trouble interpreting. Any advice as to how I can solve this problem? Thanks for your time, Marc > reg <-nls(mass ~ SSfpl(age, A, B, xmid, scal), + na.action=na.omit, + data=data) > summary(reg) Formula: mass ~ SSfpl(age, A, B, xmid, sca...

Hi list, In the object returned by summary.nlsList, what's the difference between "coefficients" and "parameters"? The have the same "Estimate", different se (therefore t value), but same p values. R.2.8.0 on winxp with nlme_3.1-89 Thanks, ...Tao +++++++++++++++++++++++++++++++++++++++++++++++++ > library(...

...ecause logLike() subsumes logLike.nls() and logLike.nlme() as special cases? Did/does logLike.nls() and logLike.nlme() have any advantages above and beyond logLike() when applying them to nls and nlme objects? On a related note, is there a way to get the log likelihoods of each individual from an nlsList object? On p. 349 of Pinheiro and Bates (2000) the logLik() function is said to give the sum of the individual nls log-likelihoods. However, logLike(some.nlsList.object) does not work for me (even when there are no NAs). Any ideas? Thanks for any thoughts or feedback. Have a good day, Ken

Hi I am using nlsList from the nlme package to estimate group specific coefficient sets to get a first impression of the structure of coefficients in relation to potential predictor variables. In some cases I got coefficients in other there are conversion problems due to bad start values I guess, resulting in typical er...

Hello. I am trying to fit a nonlinear mixed model involving 3 parameters. I have successfully made a self-starting function. getInitial() correctly outputs the initial estimates. I can also use the nlsList with this function to get the separate nonlinear fits by group. However, I get an error message when using the nlme function. Here is the relevent code: fit<-nlsList(photosynthesis~photo(irradiance,Q,Am,LCP)|species/plant/leaf,da ta=marouane.data, + na.action=na.omit) This works, showing tha...