similar to: strategies to obtain convergence using nlme

Hello. I am having a problem setting up a self-starting function for use in nonlinear regression (and eventually in the mixed model version). The function is a non-rectangular hyperbola - called "NRhyperbola" - which is used for fitting leaf photosynthetic rate to light intensity. It has one independent variable (Irr) and four parameters (theta, Am, alpha and Rd). I have created this

A few days ago I posted a question to this discussion group concerning to origin of an error message < subscript out of bounds > while 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

Hello. Following pages 342-347 of Pinheiro & Bates, I am trying to write a self-starting nonlinear function (a non-rectagular hyperbola) to be used in nonlinear least squares regression (and eventually for a mixed model). When I use the getInitial function for my self-starting function I get the following error message: > getInitial(photo~NRhyperbola(Irr,theta,Am,alpha,Rd),dat) Error

This may appear too elementary to some on this list, but not to me. My apologies if this is the case. I have mastered the lme function but the nlme function has me stumped. I am attempting to fit a nonlinear mixed model with 4 levels of nesting. I am getting a cryptic error message and do not know what is wrong with the syntax of the call. This is the call: >

Following on my posting of this morning, concerning a problem that I am having constructing a self-starting function for use with nls (and eventually with nlsList and nlme), the following is the self-starting function called NRhyperbola: > NRhyperbola function (Irr,theta,Am,alpha,Rd) { # Am is the maximum gross photosynthetic rate # Rd is the dark resiration rate (positive value) #

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:

Hello. I am trying to fit a non-rectangular hyperbola function to data of photosynthetic rate vs. light intensity. There are 4 parameters that have to be estimated. I find the nls function very difficult to use because it often fails to converge and then gives out cryptic error messages. I have tried playing with the control parameters but this does not always help. Is there another

Earlier, I posted a question concerning the syntax of nls() when the nonlinear function within the call is specified outside of nls(). Sundar showed me how to do this. Now I have a slightly more complex problem that is analogous to a broken-stick regression but in a non-linear context. I want my data to be fit to a non-rectangular hyperbola if the value of the independent variable (I) is less

Hi, I am new to R, and as a first exercise, I decided to try to implement an XIRR function using the secant method. I did a quick search and saw another posting that used the Bisection method but wanted to see if it was possible using the secant method. I would input a Cash Flow and Date vector as well as an initial guess. I hardcoded today's initial date so I could do checks in Excel.

I am getting an error message in a call to nlme and cannot understand what is happening. I explain the steps below in the hope that someone can explain the error and how to correct it. STEP 1: Data set: name: marouane.data. This is a data frame whose first few lines are as follows: > marouane.data[1:13,] species plant leaf irradiance photosynthesis chlorophyll 1

Howdee, My question appears at #6 below: 1. I want to model the growth of each of a large number of individuals using a 4-parameter logistic growth curve. 2. nlme does not converge with the random structure that I want to use. 3. nlsList does not converge for some individuals. 4. I decided to go around nlsList using: t(sapply(split(data, list(data$id)), function(subd){coef(nls(mass ~

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(lKe+lKa-lCl) *

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

I have a need to call and pass arguments to nlme() from within another function. I use R version 1.8. I have found an apparent way to make this work, but I would appreciate some comments on whether this fix is really appropriate, 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

The irr package seems to install correctly: > install.packages("irr") trying URL 'http://cran.us.r-project.org/src/contrib/irr_0.61.tar.gz' Content type 'application/x-tar' length 13848 bytes opened URL ================================================== downloaded 13Kb * Installing *source* package 'irr' ... ** R ** data ** help >>>

Hello. I have a script in which I repeatedly fit a nonlinear regression to a series of data sets using nls and the port algorithm from within a loop. The general structure of the loop is: for(i in 1:n){ … extract relevant vectors of dependent and independent variables … … estimate starting values for Amax and Q.LCP…

Dear all, in the package its the print() method does not seem to correctly work in all circumstances: > selectMethod(print, "its") Method Definition: function (x, ...) { print(x@.Data <mailto:x@.Data> , ...) } <environment: namespace:its> Signatures: x target "its" defined "its" > fundPME.lst[[1]]$irr An object of

Hi, I am new to R, and I suspect I am missing something simple. I have a data set that performance data that correlates request rate to response times http://pastebin.com/Xhg0RaUp There is some jitter in the data, but mostly it looks like a hockey puck curve. It does not get converted into a straight line when I tried log conversions, so it does not seem to be a

Dear R-Users, I have been using R for about 1 week and recently learned about the Aggregate function, and from reading online it seems like it is comparable to a SQL group by to perform summary functions. I am looking to do a summary function, such as SUM/MIN, but instead of these basic functions, I would like to calculate the IRR. Assuming I have a data set DS01: FirstName LastName

hi: could someone please point me to a function that allows me to solve general non-linear functions? > irr.in <- function(r, c1, c2, c3 ) { return(c1+c2/(1+r) + c3/(1+r)^2); } > solve.nonlinear( irr.in, -100, 60, 70 ); 0.189 If someone has written an irr function, this would be helpful, too---though not difficult to write, either. thanks for any pointers. Regards, /iaw