similar to: help with nlme function

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

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…

I am having difficulty understanding the syntax of the nlme() function for nonlinear mixed models. The data frame is called Marouane.chlorophyll. The model involves a dependent variable (Absorb) and an independent variable (Ch.surf), which are both numeric variables in the data frame. The data are hierarchically grouped as Espece, Plante nested within Espece, and Feuille nested within Plante

Hello. I am working on an analysis involving the nonlinear mixed model function (nlme) in R. The data consist of measures of carbon fixation by leaves as a function of light intensity and the parametric function (standard in this area because it has a biological interpretation) is a non-rectangular hyperbola. I cannot get the nonlinear mixed model (nlme) function to converge cleanly. I am

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

Hello. I am trying to understand the syntax of the nonlinear least squares function (nls) when the function definition is made outside of the call. Here is the context. 1. If I specify the following command, it works fine: > fit2<-nls( + A~Am*(1-exp(-alpha*(I-LCP))),data=dat1, + start=list(Am=3.6,alpha=0.01,LCP=20)) 2. Now, I want to be able to specify the function definition

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

Dear R users, I want to do a fitted.contour plot of selected columns of a dataframe M with M$AM and M$Irradiance as x and y axes respectively. The level of the contour shall be determined by M$PR. Some words on my data first. Dataframe M looks like: head(M$Irradiance) [1] 293 350 412 419 477 509 head(M$AM) [1] 2.407 2.161 1.964 1.805 1.673 1.563 head(M$PR) [1] 70.102 72.600 75.097 80.167

I would like to wrap a y-axis label onto two lines. My label is an expression containing both text and math symbols. I have looked at plotmath, strsplit(), strwrap(), deparse(), do.call(), substitute() and bquote(). Based on previous posts, I can get plain text to wrap. However, when I try these methods on my label, the exact string is returned, rather than evaluating the math symbols. My

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: >

I'm wondering if I'm seeing a regression of 5616 with 3.4.8. I'm trying to set-up pptpd with winbind, which I'm doing on two machines on Debian lenny, and I'm trying on Debian Squeeze now. The Windows client is saying "Error 778: It was not possible to verify the identity of the server." The logs say that everything is ok, and that the client is hanging up the

Hi: I am using the following command: xyplot(dat6$CO3*1e6 ~ dat6$irradiance, data=dat6, group=ref, xlab=list(label=expression(paste("Irradiance (", mu, "mol photons", m^"-2", " ", s^"-1", ")")), cex=1.3), ylab=list(label=expression(paste("Carbonate concentration (x ", 10^"6", " ", kg^"-1",

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 using the nonlinear least squares function (nls). The function that I am trying to fit seems to be very sensitive to the starting values and, if these are not chosen properly, the nls function stops and gives an error message: Error in numericDeriv(form[[3]], names(ind), env) : Missing value or an Infinity produced when evaluating the model In addition: Warning

My goal is to make VPN access to our Samba PDC (FreeBSD 7.0) so that users can access there home shares from Windows clients. I have read the instructions at http://samba.org/ftp/unpacked/lorikeet/pppd/final-report.pdf, but I can't make it work. Don't know if is due to my lack of skills or has something to do with the Popop functionality in FreeBSD. Following the instructions, i made a

I am trying to set up a secure PPP tunnel between an OpenSSH client and server, and am having problems establishing the tunnel. ----------------------------------------------------------------------------- Server information: Stock Redhat 6.1 machine running a 2.2.12 kernel OpenSSH version 2.2.0p1 (downloaded as Redhat RPMs, revision 2) OpenSSL version 0.9.5a (downloaded as Redhat RPMs, revision

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

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

After upgrading to R 2.6.0, I'm having trouble running lmer: model <- lmer(primed ~ log(dist.time)*role + 1|target.utt, data=data.utts) Error in UseMethod("as.logical") : no applicable method for "as.logical" So I thought I'd upgrade lme4 to the latest version, but unfortunately the compilation fails - perhaps there's a missing #include: R CMD INSTALL

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