Questions tagged [blup]
Best linear unbiased prediction (BLUP) aka "conditional mode" is the most likely value of a random effect in a linear mixed model.
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How to compare plant response to stress?
I am looking for advice on analysis of a greenhouse experiment.
I had 3 levels of stress (drought) treatments, and seeds were from 4 enviromental "Sources". I grew 5 plants per "Line&...
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Relationship between BLUP and variance parameter
When performing a mixed-effects analysis, one gets the mean (beta coefficients) of the fixed effects and the variance parameter for each of the random effects included in the model. Additionally, ...
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Simplistic linear estimator for a probability vector
I am working on a problem where the unknown probabilities $p_i$ are related to observed rates/frequencies $\pi_\alpha$ as
$$
\pi_\alpha = \sum_iW_{\alpha i}p_i,
$$
where $W_{\alpha i}$ is known (...
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Why not us conditional modes (BLUPs) for further analyses?
De Waters et al. (2017 ;2019) used conditional modes (BLUPs) from a generalized linear mixed model to further examine individual differences. In their experiment, they performed a temporal delay task (...
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Making inferences on BLUPs/conditional means from multilevel model
We're currently running a conjoint experiment in 26 countries with 2000 participants per country and would like to use a multilevel model. We've done up most of the pre analysis plan and run some ...
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Mixed model via ridge regression
A mixed model can be recast as a ridge regression for a specific regularization parameter $\lambda$ that penalizes only the random effects -- aka dummy variables for the grouping levels.
Fitting a ...
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Should GBlup method and Bayesian Ridge Regression give the same results?
I am working on genomic selection and I am comparing the performance of two models, one of them is a likelihood method (GBlup) and the other is a Bayesian meyhod (Bayesian Ridge Regression). I am ...
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Parameter estimation in the linear mixed effects model
In Parameter estimation and inference in the linear mixed effects model, page 1923, the variance
\begin{equation}
\begin{aligned}
\text{var}(\tilde{u} - u) & = \sigma^2G - \text{var}(\tilde{u}) \...
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Repeated Measures Linear mixed model notation
Not sure the right place to ask this question but struggling with specifying the correct notation and wording for my linear mixed model.
Problem set up:
I have a set number of biological replicates (...
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Interpreting BLUPs or VarCorr estimates in mixed models?
I am referring to the question. When estimating random effect (RE) variance or correlation, the estimations are different in VarCorr(mod) function and when ...
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Intuition about parameter estimation in mixed models (variance parameters vs. conditional modes)
I have read many times that random effects (BLUPs/conditional modes for, say, subjects) are not parameters of a linear mixed effects model but instead can be derived from the estimated variance/...
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BLUP formula for random coefficient models, in form that allows for convenient derivatives WRT loss function
In Semiparametric Regression, Ruppert et al assert that the BLUP for $U_i$ in the model
$$
\begin{equation}
y_{it} = \beta_0 + U_i + \beta_1x_{it} + \epsilon_{it}
\end{equation}
$$
reduces to
$$
\...
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Mixed model by gradient descent?
I can't be the first person to think about estimating variance components of mixed models by gradient descent, and then computing BLUP's at each update. Googling, I find little on the topic. But the ...
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Why is the estimated variance of a random effect not equal to the variance of its BLUP estimates? [duplicate]
I am learning mixed effect model from here.
I built a simplified model and trying to extract the $\gamma$ vector from linear mixed effect model
$$y=X\beta+Z\gamma+\epsilon$$
then calculate ...
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Negative BLUP in Linear Poisson Mixed Model
For school, I'm tasked with investigating the effect of beta carotene on the prevention of skin cancer.
For this, I have data on several patients that are examined over the course of 5 years in ...
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Why do the estimated values from a Best Linear Unbiased Predictor (BLUP) differ from a Best Linear Unbiased Estimator (BLUE)?
I understand that the difference between them is related to whether the grouping variable in the model is estimated as a fixed or random effect, but it's not clear to me why they are not the same (if ...
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Calculated breeding values using markers using animal model in R
Animal model (frequently used in animal science and sometime in human or plants) is mixed model with:
$y$ = $X$$b$ + $Z$$u$ + $e$
y is observed values for any quantitative variable, $Xb$ is fixed ...
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