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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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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
18 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
78 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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Estimation of Random effects in lmer(): Defining model correctly

We have analyzed the levels of a protein in 500 samples, analyzing 100 samples in 5 consecutive experiments. 10 of the samples were included in all five experiments, which means there are 460 samples ...
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1answer
35 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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15 views

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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15 views

Power analysis nested design

I have some pilot data and I want to use it to do a power analysis and find out how many replicates I need. The design is: 4 locations (IV, ID, KV, KD) -> 3 containers per location (L, M, R) -> 4 sets ...
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23 views

How interpret the results of nested ANOVA?

I have nested ANOVA with three variables (impact -> amount -> item). amount is nested within ...
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1answer
37 views

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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32 views

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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nested data, one type of measurement, t-test?

I have data with the following variables: mutant | wild-type, treated | untreated, and one type of measurements (size) for time point 1 and 2. The data is roughly normal. My ultimate H1 is that there ...
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23 views

Pairwise comparisons for a nested effects

This is basically a theoretical question which is based on the following R output. I have the following R output which contains both crossed and nested effects. The group(3 levels) and phase(2 levels)...
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2answers
52 views

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
56 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
188 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
30 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
36 views

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
48 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
42 views

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
90 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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GLMM nested design

First time asking, really need some help to fit a model. I have a large dataset to investigate if the number of plant individuals (response variable) in a community is related to pollination mode (...
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0answers
23 views

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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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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48 views

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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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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48 views

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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15 views

Theory about LMM -design matrices for nested and crossed effects

I want to explore the details of the design matrices involved in Linear Mixed Models (LMM) with random effects associated with crossed and nested grouping factors. Of great interest to me, is also, ...
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16 views

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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19 views

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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125 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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90 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
73 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
51 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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132 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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134 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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48 views

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
206 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, ...
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108 views

notation for the regression equation in a nested and repeated measures random effects model

I'm looking for help with regard to the notation for a regression equation in a repeated measures model with nested data, $\eqref{eq:2}$, and connecting the notation back to my model specification, <...
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Use of bootstrap b632 instead of 10 cross validation

Well I have data that have 300 samples of case A and 300 of case B and 8 predictors ...I trained SVM,GLM and Rf models but I nested the data resampling by outer 5cv and an inner resample of 10cv for ...
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56 views

Season nested within a year. Is it repeated measures with nested effect?

I have a data set where I have years from 2010 to 2016. I have 2-3 different seasons for each year, where productivity is measured (for 5-10 days) for all the years. I want to check if the ...