Questions tagged [inla]

Integrated Nested Laplace Approximation

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Error when adding factor variables into R-INLA stack [closed]

I am running a joint hurdle model with R-INLA, the model has two liklihoods, a binary part and a count part modelled with a truncated negative binomial distribution. There are 8 covariates, 2 factors ...
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14 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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19 views

Setting priors for a beta distribution in R-INLA

I'm running a regression in R-INLA, where the response variable is proportion of grid squares suffering deforestation (by year, over a 20-year period). Setting the response for the last 5 years to NA ...
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48 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 ...
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20 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 ...
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66 views

Spatial modelling of sparse count data

I am trying to model claim counts over for a given region. The data is very sparse. I am using the BESAG model from R INLA package. I am having a tough time to model the data. I am able to reproduce ...
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95 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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14 views

Modelling a multivariate spatial response to understand movement processes

I have position data for fish in a river relative to a point-source pollutant coming from upstream. When pollution levels are high, I expect the fish to either move downstream, deeper, or both. My ...
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32 views

INLA in R for fitting parametric and semiparametric (Cox-like) survival models with frailties

I am exploring different methods of fitting survival models in R. One method of interest utilizes INLA for fitting Cox-type semi-parametric survival models. I would like to compare fits from INLA to ...
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69 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 ...
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1answer
173 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 ...
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1answer
175 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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197 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 ...
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1answer
280 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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1answer
158 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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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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597 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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1answer
831 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 ...