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Questions tagged [nlme]

An R package for fitting Non-Linear Mixed Effects statistical models.

An package for fitting Non-Linear Mixed Effects statistical models ().

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494 questions
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Getting NaNs from nested LME

Having some issues with a subset of my data (subset still has 600 values). For the experiment, I have two time points, nested within each are three treatments (TT), with 5 replicate cultures nested within them (A through E). Within each of these…
Jackson Sage
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R language: Can the function rfe of the package caret be used with a mixed effect model

I would like to do feature selection with a mixed effect model in R, but I cannot manage to combine the function rfe of the package caret with the function me of the package nlme. Here is a example that works but does not use a mixed effect…
fstevens
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R: lme, cannot evaluate groups for desired levels on 'newdata'

I'm running an lme -model from the package nlme on R v.3.0.2. I'm trying to extract the model estimates with predict.lme, but it returns an error. Here's the code to replicate the error: my.model = lme(fixed = Maxi ~ Time*Origin, random = ~ 1…
tuhinokkaeläin
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lme summary in nlme-package (r) interpretation / fails to display all levels of fixed effects

Need some help interpreting the summary() -function results. I am running a lme from the package nlme in R. I have a simple (and quite small) dataset with three grouping variables: origin, genotype and time, response is a continuous variable named…
tuhinokkaeläin
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nlme and differential equations in R

i have been trying to use the nlme package for differential equations and have struggled to get the code to work. I am aware there is an nlmeODE package but i was hoping to avoid using it. I was wondering if anyone knows of some example code…
Jitendra
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Resolving symmetry in gnls model

I'm trying to fit a logistic growth model in R, using gnls in the nlme package. I have previously successfully fit a model: mod1 <- gnls(Weight ~ I(A/(1+exp(b + v0*Age + v1*Sum.T))), data = df, start =…
Andrew
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Understanding error message "step halving factor reduced below minimum in NLS step"

I am trying to run a gnls model (package nlme) in R, and am troubleshooting error messages. My model so far is: Log13.5_Sum.T_gnls <- gnls(Weight ~ Asym/(1+exp((xmid-Age)*(v0 + v1*Sum.T))), data = WTS_w13.5, …
Andrew
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define nested design in R

I have three factors A,B,C. B and C are random. And B is nested with A. There is interacion between C and B , C and A. I try with lme function, but I don't know how to define nesting and the interacion C and B. lme(dades~A*C,random=list(~1|B,…
user_012314112
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Want to convert SAS code using proc nlmixed to R code using nlme

The question is similar to the one in the following post: " troubles converting proc nlmixed (SAS) to nlme (R) "
goren9
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Calculating the standard error of parameters in nlme

I am running a non-linear mixed model in nlme, and I am having trouble calculating the standard errors of the three parameters. We have our final model here: shortG.nlme9 <- update(shortG.nlme6, fixed = Asym + xmid + scal ~…
Michael
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How to add level2 predictors in multilevel regression (package nlme)

I have a question concerning multi level regression models in R, specifically how to add predictors for my level 2 "measure". Please consider the following example (this is not a real dataset, so the values might not make much sense in…
deschen
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Partially nested/blocked experimental design in R

The design of the experiment involves 10 participants. All of them go through conditions A, B, C, D for treatment, however for participants 1-5 go through conditions E,F and participants 6-10 go through conditions G,H. I'm using the nlme package…
adrienne
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error in nlme package

I was trying to use the nlme package in r to do a multilevel linear model. I have yield as response variable and rainfall as predictor variable for 60 years for 6 different locations (State). I am trying to see whether rainfall has same level of…
user3013423
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Nonlinear models with dicotomic affecting to a subset of parameters

I have been working in R with nonlinear models such us: Y = Alpha1*time + Alpha2*sin(2*pi*time/Alpha3) + Alpha4*(-1)^time And I would line whether a bernoulli variable affects to the Alpha1*time and intercept or not. Such bernoulli variable could…
Hector
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Make panels fill screen in lattice?

I am plotting out some grouped data from nlme and I have 120 panels. The default plotting plot(dataG) puts them in 2 rows, 60 columns, which fills up the screen, but is too difficult to read. When I specify the layout plot(dataG), layout=…
Nazer
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