Questions tagged [nested-data]

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

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ANOVA: crossed or nested

I wish to run a factorial design of experiment (DoE) to investigate the effect sizes of many factors. In my opinion the evaluation of the data depends on what I am comfortable to assume. If I am ...
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Correctly specifying nested random effects and fixed effects with the same variable: how do I specify without running in convergence issues in lmer?

This question is a follow-up question on nested random effects and fixed effects in lmer from the following answer. https://stats.stackexchange.com/a/228814/257284 ...
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Options for investigating hierarchical covariance structures

In many distinct contexts in biology, one covariance structure will emerge in a dataset of some kind if another covariance structure is present. As an example, we may consider proteins produced by ...
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Field study with subsampling but no replication of treatment

I keep running into the same type of analysis problem with large-scale field studies where researchers apply treatments (e.g., pesticides) to experimental plots, with one plot per each treatment and ...
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Mixed model from SPSS doesn't produce same results in R? Am I miscoding something?

TL/DR: I'm trying to convert a model from SPSS to R and I'm getting different results (Estimates of Fixed Effects), and I haven't been able to figure out what I'm doing wrong. Syntax, code, and ...
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Are my random effects nested or crossed?

I am using the R package lme4 to build a mixed-effects model. My data is set up in the following way: ...
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Nested random effects for testing individual choices when choices are made in a group

I'm planning an experiment where individuals' choices will be measured. I want to test individuals' choices before and after an intervention. The problem is the individuals are in groups and cannot be ...
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Repeated measures with nested data in R

Previously, I conducted a model like the following. I have repeated measures (Time factor: pre-post) of depressive mood in two different groups (Group factor: neutral and experimental). Each ...
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Mixed effects model: nesting when having a maximum of 2 cases per multiple nests?

Hello everyone and thank you in advanced for your willingness to help: it's been years since I've been reading and learning from this community. I hope to get some light with my question. I have 50 ...
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What to use for nested subjects with repeated measures, ANCOVA or LME or even SEM?

I have a dataset like: I grouped the subjects based on their initial depressive mood (first step (pre-treatment) of repeated measures level) as 1 low, 2 high. I have two conditions (1 control, 2 ...
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Non-orthogonal Nested ANOVA

I am running a nested statistical analysis of variance on a field study I preformed. Unfortunately due to the conditions of the field it is non-orthogonal nested design where the number of sub-factors ...
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How do I make a mixed model in SPSS when treatment is intertwined with subgroups?

I'm experiencing difficulties with running a mixed model in SPSS (version 26). My experiment is a 2x2 factorial design in which we provide light and/or larvae to chickens. I have individual (...
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Correctly specify nested error structure for a split-plot ANOVA

I would like to check we are thinking about an approriate model structure for an experiment we have run, and whether I have specified this correctly in R. I have data from an experiment using plants ...
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Linear mixed model with several nested levels and grouping factor in R

I am in need of help concerning linear mixed model in R. The design I am trying to analyse is a bit complex and I am struggling in how to correctly fit the model to answer my research question. Design:...
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Grouped/Nested data in logistic regression

Update: Added more meaningful example data Setting: In my study, each of three randomly chosen readers (A, B,...
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Make predictions (classification) with nested? data

The goal of this small project is the predict one week in advance whether this athlete is sustaining an injury (binary classification). The data I have is questionnaire data from 29 athletes, with ...
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How are regression coefficients calculated in linear models with nested factors?

I would like to know how to calculate "by hand" the regression coefficients and the intercept in linear models with nested factors. Using a subset of the iris dataset in R, I am trying to ...
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Feature not applicable to some samples

I am working with a private medical dataset including categorical features coming from patients examinations. However, the problem is that some patients underwent MRI, others scanner, and some ...
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How do you perform a mixed model ANOVA with nested and crossed factors?

I have a dataset where measurements were made on individuals from three different genotypes at two different temperatures. Thus, I have two crossed factors- Temperature and Genotype. However, separate ...
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mixed-effect model with nesting. What to nest within?

I collected data as following: 14 mice were observed for their behavior with manipulating the enrichment at 3 contexts: Context 1,2 and 3. Within each context each mouse was recorded twice for 1hour (...
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How to specify my permutation scheme?

I am studying the biofilm microbiome of mountain lakes and plan to use PERMANOVA with adonis2 to assess the importance of some grouping variables (e.g. lakes with introduced fish vs. lakes without ...
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The optimal sample size for variance component analysis

I am trying to perform a variance component analysis (nested ANOVA) to quantify the contribution of several factors to the variation in my data. Those data are measured on samples taken from several ...
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Violation of normality in mixed effect model with nested random structure

I have the following data: DV: d15N (numeric) IVs: Two factors used as fixed effects: Treatment (2 levels), Sampling_Date (6 levels). Two factors used as nested random effects: Enclosure - the ...
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Randomization of two-factor nested design

In an experiment I surveyed the growth rate of a particular species (a bacterium) under different treatment conditions. Although I performed the experiments on 1 biological species, I used different ...
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How to nest independent variables/factors in a logistic regression?

I am running a logistic regression in R using the function glm and the package I am using is ggplot2. My dependent variable is ...
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How to choose the right analysis for a partially nested design?

I am not even sure if it is appropriate to call this scenario a partially nested design, but I settled for it for lack of a better term. My design is similar to the following in terms of its overall ...
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Machine learning (CNN) - What questions can I answer while violating assumption of independence?

Introduction to the experiment and data type: Suppose that I have 20 or so participants exposed to visual stimuli in several trials in two different conditions: Simple, and Complex, of 3 flavors each. ...
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What is the correct nesting structure for calculating the Inter-rater reliability or intra class correlation (ICC) with multiple raters?

I need to figure out which inter-rater reliability for multiple raters I should calculate. I'm trying to figure out how I should nest or structure certain observations within my dataset in order to ...
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Model specification of Linear Mixed effect model

I've got data with which I am trying to find causality of a dependent variable "relative growth rate" of corals on different types of reefs. The data originate from an unbalanced design, ...
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Mixed-effects model: Combined analysis of two separate within-subject data sets?

I have conducted two separate experiments, let's call them Exp. I and Exp. II. Both experiments were carried out applying a within-subject design, but different individuals were used in Experiment I ...
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Why does removing nesting from a factor in general linear model change the outcome of the model?

I am using SPSS to perform general linear models. I have some general questions about my results. My variable is reproduction and my factors are lineage (aka family), ploidy, and treatment. When I run:...
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Mixed effects model for longitudinal data with nested random effects?

I have three groups, one control, a low dose treatment, and a high dose treatment. These groups are composed of 6 subjects nested in each group, for a total of 18 subjects. Each of these 18 subjects ...
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How to make relationships between dataframes rows?

I have a such big json file with many nested dictionaries, lists etc. My approach is to divide them to standalone dataframes. There occurs a problem - how can I make relationships between them? Lets ...
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Differences between nested ANOVA and two-way ANOVA, without a repeated measures structure and a small number of levels per factor

My question is rather simple, and it's not so much about R, but about how to analyse a very simple dataset. I have 6 sites, and 2 ecosystem type (3 sites per ecosystem). From each site I have 3 ...
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How to calculate sample size for a biomarker discovery nested case-control study (approach by M. Pepe)?

I'm about to design a nested case-control study in which I will try to identify a biomarker (or biomarker panel) from protein expression levels (determined with mass spectronomy). I've got a cohort of ...
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Estimating the mean and variance for a set of probabilities (bounded by 0 and 1) based on Image Segmentation results

Data My data is from a set of images wherein I am computing the Sensitivity of an image segmentation algorithm. Sensitivity is computed as: $$Sensitivity=\frac{TP_{pixels}}{TP_{pixels}+FN_{pixels}}$$ ...
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Linear mixed models nested random effects: can you nest within a factor that has just 2 observations?

I'm working in the context of a twin study where I have to account for the relatedness between twins in the same family. The way I usually do this is by specifying a linear mixed model with ...
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LMER random effects

I have a question regarding a linear mixed-effects model, specifically the random effects. I have taken one core in each zone (three Zones (U,L,P)) across five transects (T1-T5) and three ...
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How to calculate denominator degrees of freedom in a repeated measures design?

I'm trying to understand how to calculate error (denominator) degrees of freedom in a model for my dataset. The data are from an experiment conducted on 30 individuals. There were three treatments. ...
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specifying random effects in an intensive longitudinal design

I conducted a study where participants made 15 decisions (which could be correct or incorrect) per trial (or block). There were 10 identical trials (so the same 15 decisions were made 10 times). All ...
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GLMM with a fixed effect 'nested' within a random effect

I am working on a GLMM regarding some organism occurrence data in relationship to climate data (over time) and habitat data (static) - my main question is how to best handle a habitat measurement that ...
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Random effects structure for nested, repeated measures in clmm?

I'm trying to code a clmm model in R to analyze 1-5 Likert data. Respondents in different cities were asked to take a survey twice: once before a treatment, then again afterwards (Treatment). The ...
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Mixed effects model specification lmer

I am quite new to mixed effects modelling but am starting to explore more complex designs for hypothesis testing using lmer in R. The model specification is ...
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How to interprate random effects in an lme model in R [closed]

I am having trouble understanding the results of my lme model. Could someone tell me how to understand the random effects? Here is my model: ...
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Testing L2 effects without any L2 variance?

I'm testing a hypothesized effect of an L2 variable on L1 outcomes (students nested in classrooms), but a few of my outcome variables have no L2 (classroom-level) variance (i.e. the within-classroom, ...
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Crossed random effects: how do we model multiple reciprocal transplants in lme4?

I saw the previous post on "Crossed vs nested random effects: how do they differ and how are they specified correctly in lme4?" with a very nice descriptive response from @RobertLong (...
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Is it correct to have nested random effects when you have multiple questions per item?

Let's imagine a study where people study 50 images. After each image they get get 5 true/false questions about the image (different questions for each image; e.g., was there a tree in the image you ...
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Modeling nested data using linear mixed modeling (specifically lme4)

I'll appreciate your help with conceptually understanding the models below. I have data for 150 subjects who completed a cognitive task. Each subject responded to four types of stimuli (A, B, C, D), ...
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Nested linear mixed modeling including a factor applicable to one subject group only

I am trying to build a nested linear mixed model (LMM) where 2 subject groups are compared, each with a set of measurements (time series). The outcome measure (dependent variable) is speech ...
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lmer applicable for nested unbalanced experimentel design?

My experimental design causes me some headache. It consists of three sites (A, B, C). Each site contains two treatments (Treat1 and Treat2). Obtained data (resp1 and resp2) were recorded at eight ...
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