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inlabru

The goal of inlabru is to facilitate spatial modeling using integrated nested Laplace approximation via the R-INLA package. Additionally, implements a log Gaussian Cox process likelihood for modeling univariate and spatial point processes based on ecological survey data. See Yuan Yuan, Fabian E. Bachl, Finn Lindgren, David L. Borchers, Janine B. Illian, Stephen T. Buckland, Havard Rue, Tim Gerrodette (2017), arXiv.

Installation

You can install the current CRAN version of inlabru:

install.packages("inlabru")

You can install the latest bugfix release of inlabru from GitHub with:

# install.packages("devtools")
devtools::install_github("fbachl/inlabru", ref="master")

You can install the development version of inlabru from GitHub with:

# install.packages("devtools")
devtools::install_github("fbachl/inlabru", ref="devel")

Example

This is a basic example which shows you how to solve a common problem:

## basic example code

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Version

Install

install.packages('inlabru')

Monthly Downloads

1,705

Version

2.1.13

License

GPL (>= 2)

Maintainer

Fabian Bachl

Last Published

February 16th, 2020

Functions in inlabru (2.1.13)

cprod

Cross product of integration points
bru.components

bru components
deltaIC

Summarise DIC and WAIC from lgcp objects.
bru.options

Poisson3_1D

1-Dimensional NonHomogeneous Poisson example.
Poisson1_1D

1-Dimensional Homogeneous Poisson example.
bru

Convenient model fitting using (iterated) INLA
devel.cvmeasure

Variance and correlations measures for prediction components
bincount

1D LGCP bin count simulation and comparison with data
Poisson2_1D

1-Dimensional NonHomogeneous Poisson example.
gg

ggplot2 geomes for inlabru related objects
generate.inla

Sampling based on bru posteriors
gg.matrix

Geom for matrix
gg.prediction

Geom for predictions
glplot.inla.mesh

Visualize SpatialPoints using RGL
generate.bru

Sampling based on bru posteriors
gm

ggplot geom for spatial data
generate

Generate samples from fitted bru and inla models
gg.SpatialPixels

Geom for SpatialPixels objects
gg.SpatialLines

Geom for SpatialLines objects
glplot.SpatialLines

Visualize SpatialLines using RGL
gg.SpatialPixelsDataFrame

Geom for SpatialPixelsDataFrame objects
int

Weighted summation (integration) of data frame subsets
gg.SpatialPoints

Geom for SpatialPoints objects
gg.SpatialGridDataFrame

Geom for SpatialGridDataFrame objects
gg.inla.mesh.1d

Geom for inla.mesh.1d objects
globe

Plot a globe using rgl
gg.RasterLayer

Geom for RasterLayer objects
glplot

Render Spatial* and inla.mesh objects using RGL
init.tutorial

Global setting for tutorial sessions
int.polygon

Integration points for polygons inside an inla.mesh
gg.data.frame

Geom for data.frame
gg.SpatialPolygons

Geom for SpatialPolygons objects
gg.inla.mesh

Geom for inla.mesh objects
glplot.SpatialPoints

Visualize SpatialPoints using RGL
gmap

Plot a map using extend of a spatial object
import.mrsea

MRSea data import
import.gorillas

Gorilla data import
ipoints

Generate integration points
mexdolphin

Pan-tropical spotted dolphins in the Gulf of Mexico.
mrsea

Marine renewables strategic environmental assessment
spatial.to.ppp

Convert SpatialPoints and boundary polygon to spatstat ppp object
inlabru

inlabru
import.seals

Seal pup edata import
import.mexdolphin

Mexdolphin data import
spde.posterior

Posteriors of SPDE hyper parameters and Matern correlation or covariance function.
integration_weight_construction

Safe(?) way to construct integration weights for mesh/polygon intersections
is.inside

Query if a point is inside the mesh boundary
gorillas

Gorilla Nesting Sites.
like

predict.inla

Prediction from fitted inla model
predict.bru

Prediction from fitted bru model
lgcp

Log Gaussian Cox process (LGCP) inference using INLA
multiplot

Multiple ggplots on a page.
make_stable_integration_points

Basic robust integration weights for mesh/polygon intersections
split_lines

Split lines at mesh edges
pixels

Generate SpatialPixels covering an inla.mesh
plotsample

Create a plot sample.
point2count

Convert a plot sample of points into one of counts.
intersection_mesh

Construct the intersection mesh of a mesh and a polygon
stransform

Coordinate transformation for spatial objects
sample.lgcp

Sample from an inhomogeneous Poisson process
vertices

Vertices
materncov.bands

Matern correlation or covariance function approximate credible bands.
vertices.inla.mesh

Extract vertex locations from an inla.mesh
spoly

Convert a data.frame of boundary points into a SpatialPolgonsDataFrame
summary.bru

plot.prediction

Plot prediction using ggplot2
plot.bru

seals

Seal pups
refine.inla.mesh

Refine an inla.mesh object
sline

Convert data frame to SpatialLinesDataFrame
toygroups

Simulated 1D animal group locations and group sizes
tsplit.inla.mesh

Split triangles of a mesh into four triangles