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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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How I extract the SE values of delta and sigma from gls object?

How can I extract the SE of delta (power function) and sigma of a gls objective? If I do the summary I have this output: > summary(l3s) Generalized least squares fit by REML Model: biom.kg ~ I(dbh^2 * h) Data: ssf AIC BIC logLik …
Dea
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How to model fixed effects in lme?

I have a longitudinal measurements and basic demographic variables age and gender and ı'd like to model the measurements with lme. What are the things that I must take account of when modeling fixed effects part in lme? I've read so many questions…
eee
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Visualize Multilevel Growth Model with nlme/ggplot2 vs lme4/ggplot2

I am trying to visualize the results of an nlme object without success. When I do so with an lmer object, the correct plot is created. My goal is to use nlme and visualize a fitted growth curve for each individual with ggplot2. The predict()…
Santi Allende
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Non-linear mixed effect model, nlme model formulation in R

I have a data set which collected biomass of a species from 7 trees repeatedly. I assumed the biomass would change as a Gaussian peak function through time. Since it's non-linear with nested repeated measure and I would like to add tree group as a…
lamushidi
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Mac versus PC differences with lsmeans/nlme in R?

I am having two problems, that are apparently related: Firstly, lsmeans in R is giving me two different outputs when run on Mac versus PC. Secondly, the script works outside of a function on both PC and Mac. However, it will not work inside a…
Nic George
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How to translate glmer() call to lme(); and including list() for random effects

I have previously run mixed model analyses using glmer() in package lme4. I would now like to run the very same analyses using lme() in package nlme instead. This is because a subsequently used function requires the output or call of a lme() mixed…
tabtimm
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Wald Chi-Squared Test between two variable in one mixed effect model in r

I tried to finish a homework in longitudinal data analysis. the question is to compare the difference in the cross-sectional and longitudinal effects of age (baseline cross-sectional:baseage, longtitudinal age: agechange) within a model. the model…
Zhenyu Zhang
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Why can I not use the function read.affybatch() in biocLite("affy") using RStudio?

I have some Affymetrix data that I would like to open using the read.affybatch() command in affy. I have downloaded the biocLite and affy packages with no issues, but as soon as I try and read my .CEL files using the read command it comes up with…
RLiu
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Adding confidence bands for log growth curve

I'm working with data that shows a log growth curve. I was able to fit a non-linear mixed effects regression using the nlme package nicely. However, I am uncertain as to how to add confidence bands around the estimated lines. Can anyone help? …
David
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Multilevel models in R using nmle package

I am using the nlme package to learn multilevel models, and following examples from the textbook "Discovering Statistics Using R" when it happened. Mixed Models Code The data set is Honeymoon Period.dat, also downloadable under their companion…
bzzbzzRzzbzz
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Meaning of predict.fixed and predict.Subject in predict function of nlme

I am trying to understand what the predicted values represent in the predict function in nlme I am using the data and code given in the nlme manual for the predict function as an example library(nlme) fm1 <- lme(distance ~ age, Orthodont, random = ~…
llewmills
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glmmPQL crashes on inclusion of corSpatial object

Link to data (1170 obs, 9 variables, .Rd file) Simply read it in using readRDS(file). I´m trying to setup a GLMM using the glmmPQL function from the MASS package including a random effects part and accounting for spatial autocorrelation. However, R…
pat-s
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Using Non-Linear Mixed Models instead of Sqrt-transformed Dependent Variable in Linear Mixed Model

I am running a Random Coefficient Mixed Model in R using lme in {lme4}. I had to transform my dependent variable by square-root because of problems of uniqual variance of the errors. However, with this formulation of the DV, the interpretation of my…
Caserio
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Extract fixed effect from nlme model

I am trying to extract the fixed effect Intercept (1.807425) and Residual (1.431592) from an nlme model, but nothing in the structure seems to have these values, despite the fact they show up in the summary. How can I get them? library(nlme) fm2 <-…
Rilcon42
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Why does a linear mixed model work in SAS and nlme but not lme4?

My data consists of 20 subjects in a control group and 20 in an experimental group. The DV of interest is a change score of peak power measured on each participant. There is also a dummy variable xVarExp that includes a 1 for subjects in the…
user2716568
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