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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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Specifying a continuous covariate - R

I am looking to identify differential gene expression with age. I would like to do this with a linear mixed model with specifying the age as continuous covariate. The expression of the genes are from different tissues. Tissue acts as a fixed effect…
Sudharshan Ravi
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Extracting elements from output in of mixed-effects model using nlme

I am trying to extract individual elements from the random effects table contained within the object created by the summary call of a mixed-effects model. Specifically I want to extract each of the level-2 random effects. Toy…
llewmills
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convert a SAS code mixed model in R

am trying to perform a linear mixed model via R. I have a SAS code existing and I am trying to translate it in R. Here is my data: 2 groups products: treated, témoin 5 times: T0, T1, T2, T4 et T6 vol (Subjets) = 12 Subjets 1 response : y Here is my…
Maïna Kerbrat
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using the augPredict and predict functions after nlme with fixed effects

Since I updated R to version 3.2.3 and the package 'nlme' to version 3.1-124 I am unable to use the augPredict (and predict) functions for models including mixed effects. Below you can find an example of my code using the Soybean data that are…
Tanja Milotić
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correlation in multivariate mixed model in r

I am running multivariate mixed model in R by using nlme package. Suppose that x and y are responses variables for longitudinal data which assumed that the error within group is correlated. The residual error matrix is presented as: So my question…
R. Saeiti
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simulate a data based on lme in r

I am trying to simulate data based on two models of linear mixed model. The first model is included random intercept and for fixed there are intercept and slope library(nlme) library(mixAK) fm1 <- lme(distance ~ age , data = Orthodont, random =…
R. Saeiti
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lme: NA/NaN/Inf in foreign function call (arg 3)

I am trying to simulate a data based on multivariate linear mixed effects model by using package lme in R. The data is > data_simO[1:10,] pat time outcome csse vase 1 1 0 0 35.94075 -0.08586536 2 1 3 0 …
R. Saeiti
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Predict with gls

I'm learning how to predict with gls but I keep getting an error when I try to do that. Here's the code I'm…
user5594581
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reduce variation on simulated data

I am running simulation on bivariate longitudinal data. I will describe my code which I hope to reduce variation on csse for group 0. So, there is tow classes Y= (0,1) and for each class I generate linear mixed effects model. There are 4 random…
R. Saeiti
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Warning messages: 1: In logLik.reStruct(object, conLin)

I am running multivariate linear mixed effects model on lme function on simulated data as: lme(value ~-1 + cs_d0 + va_d0 + as.numeric(times):cs_d0 + as.numeric(times):va_d0 , random = ~ -1 + (cs_d0 + va_d0) + as.numeric(times):va_d0 +…
R. Saeiti
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Using R to calculate between- by within-subj ANOVA interaction contrasts using car or lme

Psychology student here. As part of my thesis I have some data from an experiment with two between-subjects IVs, classification and condition, and a within-subjects IV, trial_type. The data are of the form: test = data.frame( …
user16324262
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Step halving factor reduced below minimum in PNLS step

I am running a self-starting logistic model in nlme, and have received the classic error message: Error in nlme.formula(model = MASS.CUL ~ SSlogis(GD10C, Asym, xmid, scal), : step halving factor reduced below minimum in PNLS step I first put in…
Michael
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Why does gnls (from nlme package for R) estimate a curve that doesn't necessarily fit my data?

I'm trying to fit nonlinear curves while specifying a covariance structure based on a phylogeny. To do this, I am using gnls from nlme to fit my model, while the covariance structure is created using corBrownian from ape. The analysis runs fine, but…
g.m
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Piecewise HLM model using nlme package in R

I have two time periods of interest and four observation points(0 months, 4 months, 12 months, 16 months) for my subjects. The first time period of interest is between observation 1 and observation 3. The second time period of interest is between…
user61578
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Simbiology Population PK using NLME: Missing values in covariates result in "no valid value" error

Would really appreciate some advice on using MatLab Simbiology for Population PK modelling! Basically, when I try to fit parameters using the population fit (NLME) method, I encounter an error/warning message "Covariate 'Potassium' has no valid…
Nicholas Syn
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