similar to: Warning message

Hope one of you could help with the following question/problem: We would like to explain the spatial distribution of juvenile fish. We have 2135 records, from 75 vessels (code_tripnr) and 7 to 39 observations for each vessel, hence the random effect for code_tripnr. The offset (‘offsetter’) accounts for the haul duration and sub sampling factor. There are no extreme outliers in lat/lon. The model

Dear Reader, Is it possible to extract the random part of nlme fitting analysis (non linear mixed effect model) i.e.sigma(b), in R? Thank you for respond Farinaz

Perdón por anticipado ante una pregunta sólo achacable a mi ignorancia en programación. Estoy creando un nuevo paquete con una estructura "decente", en vez de las chapuzas que hacía hasta ahora. Defino una función que ajusta unos datos a una distribución que podemos llamar ND. La sintaxis de esta función sería, de forma resumida: ND.fit<-function(x, start, ...){ ...

Hi everyone. I'm working with nlme and I have a question regarding nlme fits that fail because of singularity issues. Specifically, there a way to return an nlme object when the estimation process runs into a singular matrix? For example, can the results up to the point of an error such as "Error in solve.default(pdMatrix(a, fact = TRUE)) : system is computationally singular" or

Hi I have found some postings referring to the fact that one can try and understand why a particular model is failing to solve/converge from the verbose output one can generate when fitting a nonlinear mixed model. I am trying to understand this output and have not been able to find out much: **Iteration 1 LME step: Loglik: -237.4517 , nlm iterations: 22 reStruct parameters: subjectno1

Hello: I am new to R Help so hopefully I will have included enough information to allow for valuable feedback on an error message I am receiving. I am trying to a fit a mixed effects cox model to binary elk telemetry data to look at movement decisions relative to other possibilities (specifically selection or avoidance of risk <- kauf_avg ) in a matched-case-control framework. >

Hello, Excuse me for posting two questions in one day, but I figured it would be better to ask my questions in separate emails. I will again give the caveat that I'm not a statistician by training, but have a fairly decent understanding of probability and likelihood. As before, I'm trying to fit a nonlinear model to a dataset which has two main factors using nlme. Within the dataset

Hello, I'm running a number of arima models using the "arima" function. Often, when lag length gets too high, these model don't converge and an error message appears as this: > reg <- arima(y,order=c(7,0,7),xreg=isr) Warning message: In arima(y, order = c(7, 0, 7), xreg = isr) : possible convergence problem: optim gave code=1 In this case, when you print the results

Hi I'm encountering an error/warning when doing multiple comparisons with the package multcomp on a coxme model. My data: I'm looking at the removal of brood from the nest according to three treatments I applied on the brood. The brood and the workers caring about the brood in the nest, belonged to different colonies. Factor: treatment (3 levels: tx,uv,meta) Random effect 1: origin of

Hi, I want to fit multiple cox models using the coxph() function. To do this, I use a for-loop and save the relevant results in a separate matrix. In the example below, only two models are fitted (my actual matrix has many more columns), one gives a warning message, while the other does not. Right now, I see all the warning message(s) after the for-loop is completed but have no idea which model

Thanks a lot to everybody that helped me out with this. Conclusions: (1) In order to edit arima in R: >fix(arima) or alternatively: >arima<-edit(arima) (2) This is not contained in the "Introduction to R" manual. (3) A "productive" fix of arima is attached (arma coefficients printed out and error catched so that it doesn't halt parent loops to search for

Dear list, I was trying to create a VarClass for nlme to work with Fay-Herriot (FH) models. The idea was to create a modification of VarComb that instead of multiplying the variance functions made their sum (I called it varSum). After some fails etc... I found that the I was not getting the expected results because I needed to make sigma fixed. Trying to find how to make sigma fixed I run into

Good day R help list!!! I've been trying to do Bootstrap in R on Censored data. I encountered WARNING/ERROR messages which I could not find explanation. I've been searching on the literature for two days now and still can't find answers. I hope there's anyone out there who can help me with these two questions: 1. If the "Loglik converged before variable..." message

I use lmer to fit a mixed effect model.It give some warnings.what does this warnings mean? and what should I do? > (fm2.mlm <- lmer(qd ~ edu + jiankang + peixun +hunyin + cadcj + age + age2 + sex + dangyuan + Comp.1 + Comp.2+trust.cz1 +(trust.cz1|commid), data = individual,na.action = "na.exclude",family="quasibinomial")) Generalized linear mixed model fit using PQL

I'm getting an error from nlme that has me stymied. I have a data set ,'mydata', with variables: AChE, Dose, sex, set, and mrid; 'set' and 'mrid' indicate two levels of nesting, with 'set' nested within 'mrid'. I want to fit the model: mod <- nlme(AChE ~ Cexp(Dose, A, B, m), data=mydata, fixed = A+B+M~sex, random=A+B+m~sex | mrid/set,

This is a simple R program that I have been trying to run. I keep running into the "singular matrix" error. I end up with no sensible results. Can anyone suggest any changes or a way around this? I am a total rookie when working with R. Thanks, Rasika > library(survival) Loading required package: splines > args(coxph) function (formula, data, weights, subset, na.action, init,

Dear R-help folks: Here is my platform: > version platform sparc-sun-solaris2.7 arch sparc os solaris2.7 system sparc, solaris2.7 status major 1 minor 5.0 year 2002 month 04 day 29 language R I have a

Hi, I've been trying to work with the gnls() function in the "nlme" package. My decision to use gnls() was so that I could fit varPower and such to some of the data. However, in working with a small dataset, I've found that the results given by gnls() don't seem to make any sense and they differ substantially from those produced by nls(). I suspect that I am just

Dear R users, I have been using the pdMat class "pdIdnot" (from the mgcv package)instead of "pdIdent" to avoid overflow in GLMM fits with the MASS package function glmmPQL, of the following form: fit1 <- glmmPQL(fixed=y0~-1+xx0, random=list(gp=pdIdent(~-1+zz0)), family=binomial) # vulnerable to overflow fit2 <- glmmPQL(fixed=y0~-1+xx0,

Dear R users, I want to conduct a small simulation study and I have to use the lme function in a loop to save the restricted log likelihood. However, for one simulated data set the lme function gives this error Error en lme.formula(yboot ~ X[, -1], data = data.fr, random = Z.block) : nlminb problem, convergence error code = 1 message = singular convergence (7) and then, the