Questions tagged [inla]

Integrated Nested Laplace Approximation

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Is the term “latent effect” in statistics has the same meaning as “latent variable”?

Is the term “latent effect” in statistics has the same meaning as “latent variable”? If not, then what would be its substantive interpretation? UPDATE: There is a whole class of models called “Latent ...
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4 votes
1 answer
188 views

How to interpret the standard deviation of the slope random effect in a multilevel model

How do you interpret the standard deviation of the slope random effect in multilevel models? Suppose I want to show how Urbanization percentage changed across time in Western and Eastern Europe, so it ...
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1 vote
1 answer
30 views

Zero and One tricks for INLA?

The Zero and One tricks are used to sample from a model not included in the basic functions in BUGS: http://www.medicine.mcgill.ca/epidemiology/Joseph/courses/common/Tricks.html I have a general and ...
0 votes
0 answers
25 views

Convert a simple phylogenetic model example from BRMS to INLA

I am trying to convert the simple phylogenetic model described here in BRMS into INLA. Although I think I have implemented the model in INLA correctly, I can't seem to figure out how to translate the ...
0 votes
0 answers
49 views

Specify nested random effect in INLA

I am trying to understand how to specify nested random effect in INLA, but I do not succeed to reproduce the results of glmmTMB. My final goal is to build a model with random intercept and slope on ...
0 votes
0 answers
51 views

How to fit overdispersed count data in R using INLA package?I have tried the Neg Binomial family already! I would like to use other family in R?

I would like to know how to fit a spatial conditional Poisson and Neg Binomial in R using INLA to cater for overdispersed counts data.
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0 votes
1 answer
41 views

What means that the model is "singular"?

My question might be rather basic, theoretical. I am running spatial and spatial-temporal bayesian models in INLA. I have areal data and a continuous response variable with spatial and temporal ...
0 votes
0 answers
31 views

Can we use INLA for the following model?

Suppose that we have the following model $$Y_{i}\sim Pois(N_{j}e^{x})$$ $$N_{j}\sim Pois(\xi_{j})$$ $$log(\xi_{j})= a+bz_{j} + \epsilon_{j}$$ With $i=1,...I, j=1,...,J$ where $x$ is a random parameter ...
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0 votes
0 answers
54 views

INLA model with spatial autocorrelation - binary response, binomial predictor

I have a binary response variable (0/1) and a predictor distributed continuously on 0-1 scale. There is significant spatial autocorrelation in data, thus I am running an INLA model to account for that....
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2 votes
1 answer
153 views

How to model spatial data using SPDE and finite element method

Suppose we want to model a stochastic process using Gaussian processes. We have data on $z$ (dependent variable) at some spatial points $(x_{i},y_{i})$. If our dataset is large then calculating the ...
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0 votes
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178 views

Variable selection in Bayesian hierarchical models with R-INLA

I'm working with Bayesian hierarchichal regressions fitted with R-INLA. I would like to simplify my model by reducing the number of covariates. According to my understanding, Bayesian variable ...
1 vote
0 answers
41 views

How to validate or make predictions from a spatial Cox PH survival model built with R-INLA?

I'm trying to model deforestation as a survival analysis. I have a raster map where unaffected areas are zero and deforested pixels have values 1-20 depending on the year of deforestation (2001-20). I ...
1 vote
0 answers
283 views

INLA Fitting logistic regression using bym or besag smoothing using neighboring spatial points instead of neighboring polygons

Ordinarily, if you want to account for the effect spatial boundaries have on certain variables. You could fit as follows as highlighted in Virgilio Gómez-Rubio's Bayesian inference with INLA article. <...
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0 votes
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124 views

Model comparison: WAIC value is large between nested random effect models

I have computed two models using INLA and following the proceedure laid out in this paper. As in the paper, the model has two random effects, one representing temporal relationships between data ...
0 votes
1 answer
379 views

How to combine complex surveys from different populations?

I have 4 national representative surveys (DHS) and let us assume one survey belong to one country (e.g. Lesotho, Namibia, South Africa, and Zimbabwe). The sampling method used in these surveys is ...
0 votes
1 answer
249 views

Neighborhood matrix in spatio-temporal model

I am attempting to create a neighborhood matrix (poly2nb in spdep) in R to use either for a GAM or an INLA. As I have spatio-...
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1 vote
0 answers
229 views

Bayesian spatial autoregressive (SAR) model with heteroskedasticity in R

In socio-economic data, I always found heteroskedasticity that can't be solved using transformation.I had read a paper "Spatial autoregressive models with unknown heteroskedasticity:A comparison of ...
1 vote
1 answer
348 views

How can I interpret the estimated random coefficients (e.g. random intercept) in a mixed model?

We know that random effects are estimated as a probability distribution rather than each individual random coefficients. Take the simplest random intercept model as an example: $biomass_{i,j}$ ~ $...
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2 votes
1 answer
177 views

Who invented INLA?

I am trying to do a literature review on integrated nested Laplace approximations (INLA). Most papers cite a popular paper by Rue and Chopin, however, this does not seem to be the seminal paper. Can ...
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0 votes
1 answer
1k views

In R and INLA, how do I graph results of 'rw2' model?

I'm working with model 2 of INLA's Zambia example in R: ...
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4 votes
2 answers
627 views

Is there an R package for MCMC estimation of Generalized Method of Moments?

I'm looking for an R package (or a combination of packages) that would allow me to perform MCMC estimation of a GMM model, with a user-specified moments function. I've looked at the CRAN Bayesian ...
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2 votes
1 answer
891 views

How to specify the unit information prior

Continuing on from this question and this question re BIC and its approximation to the Bayes factor with a unit information prior (Kass & Wasserman, 1995), I'm trying to quantify this relationship ...