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Questions tagged [nested-data]

Refers to nested experimental design, nested random effects in mixed models, nested factors in ANOVA.

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Nested ANOVA (half sibling design) using binomial data?

Short question: I was wondering what kind of nested ANOVA-style analyses are available for binomial data? I would like to specifically compare the variances between Level A groups, but also between ...
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How to build a LME with nested random effects? A study with a very comlicated experimental design

I am trying to analyse the data on the climbing behaviour of flies. The design of the experiment was rather complicated, so I am currently struggling to build a propper LME model. The flies have ...
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What are some good examples of working through a multilevel model by hand?

I've been learning about multilevel models lately, and I understand the concept of shrinkage and partial pooling (I think), but I'm still confused to some extent on how partial pooling actually ...
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Comparing groups of empirical probability density functions

I'm a neuroscientist approaching doing some complex statistics and can't find anyone to point me in the right direction of what I need. I'm happy to read around the subject, I just don't know enough ...
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Right model approach for repeated observations

The problem: Panel Data, nested data or repeated observations for the same individual over eleven years. All independent variables are fixed effects and could be categorical or continuous variables. ...
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Stats for habitat preferences

I have what I think is a three level contingency table, with time spent in three habitats for two species, and whether their 'condition' was in the presence of a competitor species or not. example ...
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1answer
28 views

Nesting in experimental desing

Suppose I have following results from my 2 experiments that contain 3 Block each and there are 4 treatments per Block (the example is R based) ...
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1answer
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Can someone confirm if I am running this generalized linear model in R correctly? Multiple observations in each experimental unit

I'm a grad student and stats beginner just trying to make sure I'm using the right model and using it correctly. I'm using R version 3.5.0. My data look like this: ...
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Is lmer or glmer appropriate for nested continuous proportion data

I have a reviewer that wants me to analyze my data along the lines: Con_Ratio ~ Range * Latitude * Longitude + (1 | Genotype/Pair). But I'm not sure if this can be done and how. My experimental ...
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Nested models and ANOVA: F ratios

I have some commuting data involving a factor B (district) that is nested inside another factor A (city). I am assuming both factors are fixed. I have calculated F ratios involving $MS_A/MS_R$ and $...
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1answer
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Which stats can test differences between two experiments?

I have an experiment to look at habitat preferences of beetles and the effect of competition. In the first test, a beetle is on his own in an arena and I measured the % of time he spends in each of ...
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1answer
25 views

Nested design with “lmer” function

I have a nested data which I cannot model properly. The data satisfies all the assumptions of ANOVA. Data description: 4 varieties of plants planted in 4 blocks and in each block the same variety has ...
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Hierarchical model for identical dependent variable

I want to estimate a model with fixed-effects regressions. LMER in R and SEM (lavaan) do not converge and I wonder if the data structure itself is the problem. The dataset contains individual-level ...
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F ratios, ANOVA, and 2 stage nested (mixed) models in R

I have data relating to strength of fabric. Each fabric comes from one of 4 batches (B), and batches come from one of 3 suppliers (A). My question relates to the calculation and interpretation of F ...
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Mathematical description of covariance matrix

Using the nlme R package, I specified a model of the form ...
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2answers
81 views

Covariance structure with one or more random intercepts

I need to choose a suitable covariance structure including one or more random intercepts: If one factor B is nested in another factor ...
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1answer
55 views

Mixed effects model failing to converge - better to remove the random intercept? slope?

I have data for classes that are nested within schools There are two classes for most schools (n = 240), but I also have some schools with which I have more than two classes. i.e., 20 schools with ...
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Variable selection with nested data

I am interested in creating a risk score for a binary event. We have large pool of patient-level candidate predictors -- about 30 plus some expected interactions. The data set is large in terms of ...
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1answer
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Mixed Effects Model: How to Specify a Random Effect Nested Within 2 Factors in R

I have some example data that I need to fit using a mixed effects model. I can do this in Minitab, but struggling to specify the model correctly in R. I need 2 factors treated as fixed effects "...
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Logistic regression with separation and nested design in R

Data: An item can be in the state 0 or 1 (binary). Each year, it starts in the state 0 and then changes to state 1. I have data of 4 seasons (2010 -2013). Each year I sampled the (same) individuals ...
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What is the correct number of measurements and groups in the following Design?

I using GPOWER: "Anova repeated measures within factors" and need help in giving a correct number to the following inputs: Number of groups. Number of measurements. The design is as follows: I have ...
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2answers
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Actual meaning of anova table

I am having trouble understanding this simple example form the book Applied Survival Analysis in R. The example is as follows, Consider three cox models Model A only contains ageGroup Model B only ...
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1answer
70 views

Mathematical notation / formula of a mixed effect model

I am unsure how to define the mathematical notation of a mixed model of R. I built the model in this way: ...
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1answer
375 views

How do you deal with “nested” variables in a regression model?

Consider a statistical problem where you have a response variable that you want to describe conditional on an explanatory ...
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1answer
40 views

Imputing nested time series data with R

Does anyone know what is the superior algorithm to impute data in time series? I had strong dropouts over time because it was free to participants how many times to participate in my study (otherwise ...
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Time Series sampled at varying frequency - Employ Linear Mixed Model to compare trends?

I hope that this question has not be asked like this elsewhere, if so I could not find it during my google research.. I have the following problem: I have data sampled from different sensors("ID") ...
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1answer
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Specifying random slope in a nested random effects

I collected crop yield and rainfall data from multiple counties and year ( > 30 years). Each county can only belong to one province and each province can only belong to one region. I am interested in ...
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1answer
57 views

Linear Mixed Model in R: Rep. Measures, Nested, Random Effects

I ran a study with the following design: Subjects were presented 100 different stimuli and asked to indicate their liking (scaled from 0-10) for each stimulus. Each stimulus was part of only one of 4 ...
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1answer
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Nested mixed model with longitudinal data and variables with very few observations

I am doing my first data analysis and I have a hard time translating the experiment design to the model I want to fit. I have a couple of basic questions about the overall coding of the model, and a ...
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1answer
172 views

Multilevel nested glmer model (logistic regression) with 4 groups

I have 3 level nested data that is causing convergence problems (glmer function in lme4, R for multilevel logistic regression). The Data Country(4 groups) -> School(100 groups) -> respondent A ...
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Which statistical test to use in R? Unbalanced design with one dependent variable and multiple independent variables

it's been a while since I've had to do any statistics and I need a little help determining which statistical model/test to use in R. My background is more with multivariate stats, so it's been a while ...
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43 views

Linear Mixed Model for partially nested AND crossed factors

We are struggling with random effects for a linear mixed effects model that has partial nesting AND crossing. In our data, all individuals are coupled (male and female only, one couple per case). 2/...
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Interpreting interacting random effects in lme4

My questions is about how to interpret the output from lme4 for interacting random effects. Our model is as follows: ...
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Can this be solved using a binary logistic multi-level model?

Is it possible to solve the following task by using a binary logistic multi level regression? If not, how can you solve it? The concept as a diagram: I have the location of individual stores and ...
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50 views

Multi-level modeling using lmer in R

I have nested data as followed: 'Learning group sessions' in 'students' in 'learning groups' (each learning group consisted of different students and the learning groups chose to have between 3 and 10 ...
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AR1 Correlation and nested random variable using glmmPQL

I'm new using nested factors and temporal autocorrelation and I din't find many literature with both themes at the same. I'm running a model with negative binomial distribution where response variable ...
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Specification of partially nested / partially crossed longitudinal 3-level model

I am analyzing how properties of brain hemispheres change over time under different conditions. Each subject has a left (L) and a right (R) hemisphere for each of which I measure the property of ...
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Experimental design comparing two different drugs

I'm planning a study evaluating the effect (behavior, memory task) of two different drugs at multiple doses (+vehicle control). Ideally I'd like to compare the effects against the control and each ...
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211 views

Error when using lmer but not lme (specifying nested data in random-effects structure)

I have a dataset with participants' scores on three exams. Each participant completed each of the three exams. So the dataset looks something like (for a total of 945 rows): ...
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is it correct to nest fixed effects within random factors?

In this post @Ben Bolker wrote in his answer that for the interaction between station and day we could write ...
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1answer
118 views

What approach can I use to analyse zero-inflated, overdispersed, count data with very low replicates and a nested random effect?

I am having trouble with analysing some of my data. I'm trying to test the effect of a treatment with two levels (Treatment/Control) on the abundance of ants belonging to different dominance ...
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1answer
80 views

Modeling repeated measures with a second layer of nesting using lmer

I am doing a longitudinal repeated measures study looking at the effect of age (maturation) on my test result (Y - a type of hearing test). My outcome Y, is numeric, and the main effect is age (age....
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comparing groups in repeated measures FE models, with a nested error component, estimated using plm

I have estimated some repeated measures Fixed Effects models, with a nested error component, based on on grouping variables, i.e. non-nested models, using plm. I am now interested to test if the ...
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1answer
56 views

Is a linear mixed-effects model appropriate for my nested dataset?

I'm not entirely confident in the statistical method I am using for my study design, and would like some feedback/advice. I am primarily looking at the effect of land use on stream chemistry ...
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164 views

Specifying nested random factor in emmeans from a gamlss object

I am trying to use the package emmeans with a gamlss object with a mixed model using a beta distribution. I am unsure as to the best way to use the emmeans function to include my nested random effects....
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Is it necessary to include all levels as random intercepts in a multilevel model when they are perfectly nested?

I am running a mixed-effects model in R and I want to have random intercepts for two sampling levels, country and site. The ...
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187 views

Mixed Effects Model with Nesting - RNAseq differential expression

I'm new in the RNAseq differential expression analysis and I'd like to know which is the best way to treat my data. I have RNAseq data collected from iPSCs organized as follows: I have 2 groups of ...
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Nested Anova with continuous variable

I want to perform a two way Anova with two independent (categorical) variables, but add a correction (continuous) on one of them. In more details, the idea would be to explain the biomass of one ...
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1answer
254 views

Crossed or nested random effects structure or both for mixed effects model using glmer?

I conducted an experiment where i walked transects down polytunnels on a farm. On each transect i was recording the number of flower visitation events that i saw. The farm is divided up into 3 fields, ...