---
title: "Geostatistical inference under preferential sampling"
author: "Daniel Dinsdale & Matias Salibian"
date: "`r format(Sys.Date())`"
output: github_document
---


```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## Geostatistical inference under preferential sampling

This repository contains `R` code illustrating the 
computations in [Dinsdale, D. and Salibian-Barrera, M. (2018) Methods for preferential sampling in geostatistics](https://doi.org/10.1111/rssc.12286), *Journal of the Royal Statistical Society Series C*,
68(1), 181-198. 

We use 
[TMB](https://github.com/kaskr/adcomp/wiki) and 
[INLA](http://www.r-inla.org/). For the latter we adapted the scripts 
publicly available [here](http://www.r-inla.org/examples/case-studies/diggle09/simulation1),
with contributions from an anonymous referee. 

Please note that the TMB code below was last tested with the `R` INLA package "INLA_19.09.03". 


In this repository you will find:

* A script to generate synthetic data following the Poisson preferential sampling model [here](RFiles/dataExample.R)
* A script to obtain parameter estimates using INLA in R [here](RFiles/INLAExample.R)
* A script to obtain parameter estimates using TMB in R [here](RFiles/TMBExample.R) and [here](RFiles/TMBExample.cpp)