search for: nlme

I am having trouble fitting correlation structures within nlme. I would like to fit corCAR1, corGaus and corExp correlation structures to my data. I either get the error "step halving reduced below minimum in pnls step" or alternatively R crashes. My dataset is similar to the CO2 example in the nlme package. The one major difference is that in...

Dear list, Has anyone created a version of SSmicmen that allows testing for group differences? The basic Michaelis-Menten equation is: (Bmax * X) / (Kd + X). The nlme package allows modeling of random effects for Bmax and Kd as needed, but I curious how I can build in group differences? I have receptor binding data for strains of mice, and following Pinheiro and Bates' lead in their book, a random effort for animal differences in Bmax seems reasonabl...

I've moved nlme from Depends to Imports in my coxme package. However, a few of the examples for lmekin use one of the data sets from nlme. This is on purpose, to show how the results are the same and how they differ. If I use data(nlme::ergoStool) the data is not found, data(nlme:::ergoStool) does no bett...

Hello all! R2.0.1, W2k. All packages updated. I?m heavily dependant on using mixed models. Up til?now I have used lme() from nlme as I have been told to. Together with estimable() from gmodels it works smooth. I also often run Rcmdr, mostly for quick graphics. After using Rcmdr, on reopening the R workspace all help libraries for Rcmdr (22 !) loads, among them nlme, but not Rcmdr itself. Why? Now I saw on the list yesterda...

How to set the nlme() function to return the answer without the intercept parametrization? #========================================================================================= library(nlme) Soybean[1:3, ] (fm1Soy.lis <- nlsList(weight ~ SSlogis(Time, Asym, xmid, scal),                        data = Soybean)...

Sorry, I forgot to be more specific. I am using Windows XP. I am using R.12.2 I installed both packages from the install packages menu. I always write library(name.of.library), and it is enough. But when I write library(nlme), R does not find nlme right away I load nlme first and it says package was downloaded succesfully. However, when I try to do this again in another day, R cannot find nlme, so I try to load mgcv with library(mgcv), then I get this message: Error: package 'nlme' could not be loaded In add...

Dear All: I updated my R program as well as associated packages yesterday. Currently my R version is 2.2.1 running under WINXP SP-2. When I tried to list (summary) an nlme object that I developed before, I got the following error message: [ Error in .C("ARMA_constCoef", as.integer(attr(object, "p")), as.integer(attr(object, : C entry point "ARMA_constCoef" not in DLL for package "nlme" ] The nlme object was fitted w...

Hello, I was relying on withTimeout (from R.utils) to help me stop nlme when it ?hangs?. However, recently this stopped working. I am pasting a reproducible example below: withTimeout should stop nlme after 10 seconds but the code will generate data for which nlme does not converge (or takes too long) and withTimeout does not stop it. I tried this both on a linux (6...

Could someone explain the meaming of this error message from augPred: > augPred(area3.pen.nlme, primary=~day) Error in predict.nlme(object, value[1:(nrow(value)/nL), , drop = FALSE], : Levels 1,2,3 not allowed for block > predict.nlme(area3.pen.nlme) does not produce an error. area3.pen.nlme was created with: > area3.pen.nlme <- nlme(area ~ SSlogis(day, Asym, xmid, scal...

...; > Did you at least try to use search possibilities in R to find it? It shall > > be a part of basic R installation, however it is not loaded automatically > > when starting R (there are only few packages loaded on start). > > > > If you tried > > > > > ?nlme > > No documentation for 'nlme' in specified packages and libraries: > > you could try 'help.search("nlme")' > > > > and help.search(nlme) gives > > > > BIC(nlme) Bayesian Information > > Criter...

This is only partly a question about R, as I am not quite sure about the underlying statistical theory either. I have fitted a non-linear mixed-effects model with nlme. In the fixed part of the model I have a factor with three levels as explanatory variable. I would like to use Tukey HSD or a similar test to test for differences between these three levels. I have two grouping factors: 'plant' to which the treatments were assigned at random, and '...

Hello, I would like to fit correlation structures with nlme, but R crashes. My data is similar to the "growth of orange trees" example from Pinheiro and Bates (2000), but data are not equally spaced in time, as the last observation is taken after 6 days ( and not 2 as the others). This is the code I'm using: library(nlme) DO<-c(0.107,0.1...

Hello all. I was wondering if the logLike.nls() and logLike.nlme() functions are still being used. Neither function seems to be available in the most recent release of R (1.9.1). The following is contained in the help file for logLik(): "classes which already have methods for this function include: 'glm', 'lm', 'nls' and 'gls'...

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 experienc...

Hi out there, I am trying to fit a species accumulation curve (increase in number of species known vs. sampling effort) for multiple regions and several bootstrap samples. The bootstrap samples represent different arrangements of the actual sample sequence. I fitted a series of nlme-models and everything seems OK, but since the observations are correlated I tried to include some correlation structure. Since the ARMA classes were not succesful in reducing this correlation, I tried spatial correlation functions with sampling effort (measured in time units) as a distance measure....

Hi, I am trying to convert the following NLMIXED code to NLME, but am running into problems concerning 'Singularity in backsolve'. As I am new to R/S-Plus, I thought I may be missing something in the NLME code. NLMIXED *********** proc nlmixed data=kidney.kidney; parms delta=0.03 gamma=1.1 b1=-0.003 b2=-1.2 b3=0.09 b4=0.35 b5=-1.43 varu=0.5; eta=b1*a...

Dear All, let E(Y | t, b, theta) be the conditional expectation of Y where b is a vector of random effects , theta is a vector of fixed effects and t is the time of observation (t =1,2, ...,n). I wonder if nlme has a function to compue E(Y | t, theta). I know that it can be done by approximating the integrals over b of E(Y | t, b, theta). But I am wondering if nlme has a function to do that directly. Thank you, Bernard --------------------------------- [[alternative HTML ve...

...4). In fact, three times now, with separate clean source and build directories each time, just to be sure that the issue is predictable. I would be happy to have somebody tell me that I am missing something fundamental here also... After running make check-all, I get the following error for 'nlme': * using log directory ?/Users/marcschwartz/R.Files/SourceCode/32bitR/tests/nlme.Rcheck? * using R version 2.12.0 Patched (2010-10-15 r53323) * using platform: i386-apple-darwin10.4.0 (32-bit) * using session charset: UTF-8 * checking for file ?nlme/DESCRIPTION? ... OK * this is package ?nlme...

Dear R Helpers, I try to write a small package that based on nlme however my code does not work. R always appears this message: Error in eval(expr, envir, enclos) : object "y" not found where y is the response variable. Please help me out! This is my code: require(nlme) AMPmixed<-function(y, x, S1=c("asymptotic","logistic"), ran...

...o 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 that the function "photo" works as a self-starting function. nlme(model=photosynthesis~photo(irradiance,Q,Am,...