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Questions tagged [random-effects]

238 questions
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understanding lmer random effects in R

What is the point of the "1 +" in (1 + X1|X2) structure of the random effect of an lmer function in lme4 package of R, and how does this differ from (1|X1) + (1|X2)?
kriggs
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Species-by-year random effects in a GLMM (point count data)

SUMMARY I'm analyzing avian point count data using glmmTMB. I'm trying to estimate year-specific mean abundance for each species. Models with interactions of fixed terms are not working, I think because limited data are split across several…
G. Channing
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What is the difference between 1|block:run and 1|(block:run)?

Study design is an incomplete randomized block design. Fixed effects are maturity (covariate/continuous variable) and type (A, B, or C). There are 20 total samples with 7 of two types and 6 of one type. Samples were put into blocks with at least one…
yaynikkiprograms
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How to compare the slope of interaction variables in mixed effect model in r

I want to test the effects of island area and land use, and the interaction between island area and land use on species richness. For land use, I have three groups, namely forest, farmland and mix. The data is based on transects on different…
Yuhao Zhao
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Dropping Random effect term in predict() from glmmTMB

I am running a generalized linear mixed effect model using the glmmTMB package to analyse number of bite wounds in a wild predator. my model: Mod<-glmmTMB(all~Sex+class+sseason+timeR+class:timeR+(1|Microchip)+(1|olre), data = mydata_select, family =…
Sofie Scheuer Didriksen Nagly
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lme4::lmer() With A -1?

I am looking at an lmer model that's been coded, and I don't quite understand what the -1 is / is doing. The code looks like fit = lmer(resids ~ -1 + (1|loc/time)) I believe the (1|loc/time) piece can be equivalently written as (1|loc) +…
Ryan S
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Two fixed effects variables and one random effect? plm in r

I believe I have found a way of having three variables (ID, Time and type) as fixed effect using the plm function (where I have previously indexed the ("ID","Time") in pdata.frame): FixedEffects <- plm(Y ~ x1 + X2 + factor(type), …
Lucas Gomes
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How to include nested effects in mixed effect model with lme4 package

I am studying mixed models and have a doubt about nested random effects.. In the example, we tested subjects variable X and outcome Y and want to see if X is correlated with Y. The data were collected on 8 different mountains in 3 different site…
FrAiello
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Split plot design with nested random effects and interactions between random effects

I am trying to analyse a split plot design for a plant growth experiment with these variables: Biomass (dependent variable) Transect (sub plot factor with three levels) Treatment (main plot factor with two levels) Block (2 blocks in total, serving…
Ecologist
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Generalized Additive Mixed Model (GAMM) in R mgcv Package Formula Implementation for Grouping Variable

I am attempting to use mgcv to model a non-linear multilevel model with Time as the primary independent variable + a level 2 covariate (Xc). Because these data are within-person, I would like the model to reflect the within-person responses at level…
aspark2020
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R: Plotting Mixed Effect models plot results

I am working on linguistic data and try to investigate the realisation of the vowel in words such as NURSE. There are more less 3 categories that can be realised, which I coded as . I then measured Formant values (F1 and F2). Then I…
Tomikichi
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what do the us, idh, idv stand for in the MCMCglmm in R

I am having hard time remembering the meaning of the us, idh, and idv functions in the MCMCglmm. I understand that these are the functions taking random variance-covariance structure into account, but are they abbreviations of some words in English?…
user11806155
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R / PLM Package: How to include a nested effect for the same brands across countries?

I am currently analyzing a panel data set, which tracks brands across countries over time.In particular, I am interested in how certain variables are impacting future market share. Using the head() function, my data set looks as followed: # A…
Sven
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Check for statistically significant differences between groups after running a logistic regression w/ interaction & random effect?

I ran an ordinal logistic regression (using the function clmm from the R package ordinal) with a two-factor interaction and a random effect. The response is a factor w/ 5 levels (Liker scale: 1 2 3 4 5), the independent variables are a factor w/ 2…
elena_m
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ICC per random factor for multilevel negative binomial regression

I have a multi-level negative binomial model fit with brms (library(brms)) fit1 <- brm(TOTAL_VIOLATIONS ~ LN_POP + Source_binary + Source_purchased + (1|TYPE_consolidated) + (1|COUNTY), data = Data, family = negbinomial()) This is what the data…
KDobb
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