"Mixed effects models" refers to models that have both fixed effects and random effects. They are used to model longitudinal data or data that are clustered & thus do not have independent errors.

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Problems with curve fitting

I have a longitudinal dataset to which I am trying to fit the following model : $$ y_{i,j} = \frac{1}{1+a_{i} \exp(-r_{i}t_{i,j})} + \varepsilon_{i,j} \tag{1}$$ The setting : $i$ ($1 \leq i \leq ...
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Residual structure in Linear Mixed Models with Random effects

You can further improve a linear mixed model with random intercept and slope by specifying a structure in the residuals (for example AR(1)). In SAS it is possible, but I hope this is also already ...
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Specifying variance structure in mixed effects Cox model in R [migrated]

I am fitting a mixed effects Cox model in R using the function coxme() in the coxme package. In my model I have a censored survival time $X$, a single covariate ...
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Identifiability in nonlinear mixed-effects models

I am interested in the identifiability of linear mixed effects models. Let's assume $p$ subject are observed at different instants in time. Let $\mathbf{y}_{i}$ $(1 \leq i \leq p)$ the vector ...
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Subjects:condition interaction random effect in a growth model

I'm investigating the effect of 'Condition' (3 levels: Quiet, Intelligible, Unintelligible) on pupil response over time (intercept, linear, cubic, quadratic, quartic and quintic terms). When I use ...
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178 views

lme4: glmer problems with offset()

this is my first post, so I hope everything is in the right format. I have some problems with glmer and don't know how to fix it, so I hope somebody can help me out with this. I could not find an ...
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50 views

Repeated measures mixed modeling. Why is Time (day, second etc.) a fixed effect?

Let's say I have an experiment where I repeatedly measure something over Time (1:10), say 10 days. Here I simulate some data... ...
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Correlation of fixed effects with multiple response variables in MCMCglmm

I'm working with a mixed model for which I have several response measurements for every individual. One goal is to determine the sampling variance/covariance of the fixed effect estimates for a ...
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Adjusting data for measurement errors

I have approximately 500,000 data points that were mechanically measured over about 2000 days. The equipment is manually set up each day, which likely induces some error. What I am attempting to do ...
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26 views

calculate VIF for glmm

If we have colinearity among our axplanatory variables we can calculate a varianvce inflation factor to estimate the effects on our standard errors $$ VIF = 1/(1-R^2) $$ I am unsure how to calcuate ...
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134 views

Trouble finding good model fit for count data with mixed effects - ZINB or something else?

I have a very small data set on solitary bee abundance that I am having trouble analysing. It’s count data, and almost all the counts are in one treatment with most of the zeroes in the other ...
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198 views

Calculate log-likelihood “by hand” for generalized nonlinear least squares regression (nlme)

I'm trying to calculate the log-likelihood for a generalized nonlinear least squares regression for the function $f(x)=\frac{\beta_1}{(1+\frac x\beta_2)^{\beta_3}}$ optimized by the ...
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51 views

Multivariate multi-level analysis in nlme

The question I have a dataset which I think requires a multivariate multilevel analysis. I am unsure both of the appropriate model and of how to fit it with R. I ...
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77 views

Negative values for AIC in General Mixed Model

I'm trying to select the best model by the AIC in the General Mixed Model test. The best model is the model with the lowest AIC, but all my AIC's are negative! So is the biggest negative AIC the ...
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60 views

Different degrees of freedom when using the same mixed effect model (SPSS)

I have a question regarding mixed effect models. Is it possible that the degrees of freedom differ when I use the same model with different dependent variables? Or does that indicate that something ...
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83 views

Non-converging heteroscedastic linear mixed-effects model (R lme)

I'm working on a project where I try to determine the influence of consulting expenditures companies made the year before on several economic figures. My dataset consists of roughly 2'000 different ...
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36 views

comparing results of lmer using geom_area plots

I was wondering if somebody could help with trying to visualise some data. I have 11 groups of organisms and have related them to levels of a specific bacteria in water samples. I have a strong ...
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54 views

Repeated measures approach or not?

The basic question here is whether the following situation would warrant a repeated measures approach with a mixed effects model or not. Let's say I have a set of grocery stores in 5 different ...
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35 views

should both scores of 2 time points be of same scale in mixed ANOVA

I am running mixed ANOVA as repeated measurement analysis for cognitive score at 2 time points for 2 groups (blood pressure low vs. High). The the score at time 1 was normally distributed and at time ...
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55 views

Generalized Linear Mixed Model

I have three independent variables (all binary) and two interaction variables that I would like to test for their effect on the dependent variable "Awareness_level". This dependent variable is also ...
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42 views

Why do I have 0 degrees of freedom for my group mean variables in my mixed model? nlme package

I am trying to run a mixed effects model in the R package 'nlme'. I have 3 groups and 294 observations, and am using the following model: ...
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101 views

How to specify mixed ANOVA with multiple repeated measures and covariate in R

Working in R, how can I specify a mixed ANOVA with multiple between- and within-subjects factors in such a way that it's amenable to adding a covariate in a subsequent analysis? Also, ideally, I would ...
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36 views

Mixed-model specification in R - exploring individual differences

My current experiment aims to explore the effect of viewing condition, difficulty and depth perception on object grasping. I'm mostly interested in the effect of individual differences in depth ...
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244 views

Changing reference level for contrasts changes results in R 3.0.2/lme4 1.1-2 vs. R 2.15.0/lme4 .999999-0

I hope this is an appropriate forum to post this question. I recently upgraded my R software from 2.15.0 to 3.0.2. I also upgraded the lme4 package from .999999-0 to 1.1-2. After doing so, the results ...
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Power analysis for log-gamma model

I fitted a generalized linear mixed log-gamma model in SPSS with 1 fixed factor (binary), patient ID as a random intercept and a continuous variable as (fixed) covariate. How can I calculate the ...
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124 views

Mixed effect logistic regression in R: choosing random effects

I conducted an experiment which measured a binary response for each subject. The subjects were in 1 of 3 groups. There were two other fixed factors, each of which were continuums (cont1, cont2) ...
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124 views

Convert nonlinear mixed model to log-linear mixed model in R (nlme)

I want to analyze fish aquaculture data comparing growth rates by state and controlling for tank effects as a mixed effect. I will use the equation $$ w = aL^b $$ but I want ...
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126 views

How to simplify coxme survival models?

I have some questions about specifying a coxme (mixed-effects Cox proportional hazards) model in R and then simplifying it after reading the ...
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76 views

How to write a (mixed effect?) model for a hypothetical experiment studying exam scores

Consider the following slightly unrealistic experiment: I have an infinitely large pool of questions to write exams from, and suppose that the questions are continuously rated in difficulty from 0 to ...
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linear (?) mixed models help?! - simple question from a simple mind

I have a stunningly simple data set and, unfortunately, an equally simple mind when it comes to stats. This is how my data are set up: I asked people to sit small exams on different days of the week ...
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102 views

Theory behind non-linear mixed effect models

I'm fairly new to this site. I'm currently doing some research work that involves the use of non-linear mixed effect model on longitudinal data (R). I'm presently using Pinheiro and Bates' book, ...
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140 views

glmm unbalanced nested random factors

imagine you have the following data structure ...
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62 views

How to fit a mixed model to this advertising data?

I have data on about 20000 consumers who were exposed to some form of advertising. The data is in the following form. ...
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165 views

How to specify partially crossed random effect in lme?

I am new to R and would like your help with lme formula for partially crossed random effect in a random-intercept, random-slope model. In the longitudinal data I have, each subject (barring some ...
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115 views

Leave-one-subject-out cross validation for mixed effects models

I am doing a leave-one-subject-out for a mixed-effects model for a longitudinal data analysis, in which the model is fitted to all subjects minus one at a time, and the left-out subject becomes ...
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Degree of freedom with mixed model , using nlme package?

I am conducting a mixed model, but do not well understand how df is calculated, can someone help me to clarify it? I have been searching very hard on the internet but could not find the right answer. ...
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Correct model to use in travel speed analysis

I am attempting to analyse downstream travel speed of fish within two different rivers, however, I am getting lost on which model I should use. Please see working below data: ...
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90 views

Mixed-model or not? Case-study in R

I performed some observations of clownfishes. For each individual fish (each observation), I recorded the anemone species where it lives, the size of the anemonea and the size of the fish (and many ...
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148 views

Account for both between and within variance in panel data

I have a general question on fixed-effects and mixed-effects models for panel data. I am doing a logistic regression on panel data, with data measured on the individual level. I understand that by ...
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428 views

Nested random effects group size using lme (in nlme)

I'm wrestling with a question regarding random effects that I haven't been able to figure out with my regular resources. I am examining the effects of two treatments (heat and water) on plant biomass ...
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Can and should you use data from repeated responses in a linear mixed-effects model?

When you collect data from participants in an experiment, sometimes you can collect repeated responses for the same condition, e.g., in R: ...
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How to analyze this incomplete block design in R?

I was just wondering if you could point me in the right direction. I have a dataset with 5 tree clones planted at 10 different sites, i.e. same clones are replicated twice at different sites. ...
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Equations from linear regression

Notation. Let $y$, $a$, and $b$ be $n\times 1$, $p\times 1$, and $q\times1$ real vectors. Let also $X$ and $Z$ be $n\times p$ and $n \times q$ real matrices. Suppose that there is no solution, $a$, ...
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Did anyone know how to fit factor analytic covriance struture either in R or SAS?

I would like to make meaningful interpretation from a two-way interaction data using factor analytic covariance structure. I have a genotype x environment matrix and I would like to know which ...
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70 views

Translating R lme comand to mathematical equation

I would appreciate if someone could help me in translating the following R command into a mathematical equation: ...
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2answers
358 views

Alternatives to pvals.fnc to compute confidence intervals for fixed effects?

Lately I keep encountering the same problem and I'm wondering whether other people have been able to get around it. I'm running a mixed effects model using lmer(). My model has by-subject and by-item ...
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60 views

Modeling time in multilevel logistic regression

I conducted an experiment in which participants listened to sentences while looking at pictures about the sentences on a computer screen. Whether at a given time point a participant looked at the left ...
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132 views

Relative variances of higher-order vs. lower-order random terms in mixed models

TL, DR summary: Is there any theoretical or empirical basis to support the following statement being true as a general rule of thumb? "When estimating a mixed model, typically the estimated ...
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1answer
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Comparings BIC of lme models with and without a correlation function

I have created an lme model using the same predictors both with and without a specified correlation structure based upon distance between the points (lat/long). I ...
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Convergence problems created by jittered coordinates

I am creating a mixed model and including a spatial correlation. My data points include lat long values although some are duplicated. I have two questions about dealing with these. To specify the ...