Spatial and Spatio-Temporal Models using 'INLA'.
INLAspacetime
This is a R package to implement certain spatial and spatio-temporal models taking use to the cgeneric
interface in the INLA package. This interface is a way to implement models by writing C
code to build the precision matrix compiling it so that INLA can use it internally.
Installation
You can install the current CRAN version of INLAspacetime:
install.packages("INLAspacetime")
You can install the latest version of INLAspacetime from GitHub with
## install.packages("remotes")
remotes::install_github("eliaskrainski/INLAspacetime", build_vignettes=TRUE)
We have implemented
some of the models presented in https://arxiv.org/abs/2006.04917
the barrier model proposed in https://doi.org/10.1016/j.spasta.2019.01.002
Example
This is a basic example which fit a spacetime model for some fake data. The model fitting using inlabru facilitates coding.
set.seed(1)
n <- 5
dataf <- data.frame(
s1 = runif(n, -1, 1),
s2 = runif(n, -1, 1),
time = runif(n, 1, 4),
y = rnorm(n, 0, 1))
str(dataf)
#> 'data.frame': 5 obs. of 4 variables:
#> $ s1 : num -0.469 -0.256 0.146 0.816 -0.597
#> $ s2 : num 0.797 0.889 0.322 0.258 -0.876
#> $ time: num 1.62 1.53 3.06 2.15 3.31
#> $ y : num -0.00577 2.40465 0.76359 -0.79901 -1.14766
Loading the packages:
library(INLA)
#> Loading required package: Matrix
#> Loading required package: foreach
#> Loading required package: parallel
#> Loading required package: sp
#> The legacy packages maptools, rgdal, and rgeos, underpinning this package
#> will retire shortly. Please refer to R-spatial evolution reports on
#> https://r-spatial.org/r/2023/05/15/evolution4.html for details.
#> This package is now running under evolution status 0
#> This is INLA_23.05.30-1 built 2023-05-30 11:52:19 UTC.
#> - See www.r-inla.org/contact-us for how to get help.
#> - To enable PARDISO sparse library; see inla.pardiso()
library(INLAspacetime)
library(inlabru)
Define spatial and temporal discretization meshes
smesh <- inla.mesh.2d(
loc = cbind(0,0),
max.edge = 5,
offset = 2)
tmesh <- inla.mesh.1d(
loc = 0:5)
Define the spacetime model object to be used
stmodel <- stModel.define(
smesh = smesh, ## spatial mesh
tmesh = tmesh, ## temporal mesh
model = '121', ## model, see the paper
control.priors = list(
prs = c(1, 0.1), ## P(spatial range < 1) = 0.1
prt = c(5, 0), ## temporal range fixed to 5
psigma = c(1, 0.1) ## P(sigma > 1) = 0.1
)
)
Define the data model: the linear predictor terms
linpred <- ~ 1 +
field(list(space = cbind(s1, s2),
time = time),
model = stmodel)
Setting the likelihood
ctrlf <- list(
hyper = list(
prec = list(
initial = 10,
fixed = TRUE)
)
)
datalike <- like(
formula = y ~ .,
family = "gaussian",
control.family = ctrlf,
data=dataf)
Fitting
result <-
bru(
components = linpred,
datalike,
options = list(
control.inla = list(
int.strategy = "eb"
),
verbose = !TRUE)
)
#> Warning in inla.model.properties.generic(inla.trim.family(model), mm[names(mm) == : Model 'cgeneric' in section 'latent' is marked as 'experimental'; changes may appear at any time.
#> Use this model with extra care!!! Further warnings are disabled.
Summary of the model parameters
result$summary.fixed
#> mean sd 0.025quant 0.5quant 0.975quant mode kld
#> Intercept 0.5211454 3.49482 -6.328575 0.5211454 7.370866 0.5211454 0
result$summary.hyperpar
#> mean sd 0.025quant 0.5quant 0.975quant mode
#> Theta1 for field 1.202935 0.5125858 0.3321324 1.162519 2.324768 0.9707531
#> Theta2 for field 1.435746 0.1706775 1.1044643 1.434143 1.776487 1.4273398
Vignettes
Please check it out at the Tutorials.