Intensity Analysis of Spatial Point Patterns on Complex Networks.

intensitynet

The intensitynet package provides tools to analyze point patterns in space over planar network structures derived from graph-related intensity measures for undirected, directed, and mixed networks. This package is based on the research done by Eckardt, M., Mateu, J. presented in the following papers:

Eckardt, M., Mateu, J. Point Patterns Occurring on Complex Structures in Space and Space-Time: An Alternative Network Approach. Journal of Computational and Graphical Statistics 27. 312-322 (2017). 10.1080/10618600.2017.1391695

Eckardt, M., Mateu, J. Second-order and local characteristics of network intensity functions. TEST 30, 318-340 (2021). 10.1007/s11749-020-00720-4

Installation

You can install the released version of intensitynet from CRAN with:

install.packages("intensitynet")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("LlagosteraPol/intensitynet")

Example

This is an example that shows you how to set up intensitynet and calculate and plot the Geary-c correlation:

library(intensitynet)
library(spatstat)
#> Loading required package: spatstat.data
#> Loading required package: spatstat.geom
#> spatstat.geom 2.3-1
#> Loading required package: spatstat.core
#> Loading required package: nlme
#> Loading required package: rpart
#> spatstat.core 2.3-2
#> Loading required package: spatstat.linnet
#> spatstat.linnet 2.3-1
#> 
#> spatstat 2.3-0       (nickname: 'That's not important right now') 
#> For an introduction to spatstat, type 'beginner'
data(chicago)


chicago_df <- as.data.frame(chicago[["data"]]) # Get as dataframe the data from Chicago

# Get the adjacency matrix. One way is to create an igraph object from the edge coordinates.
edges <- cbind(chicago[["domain"]][["from"]], chicago[["domain"]][["to"]])
chicago_net <- igraph::graph_from_edgelist(edges)

# And then use the igraph function 'as_adjacency_matrix'
chicago_adj_mtx <- as.matrix(igraph::as_adjacency_matrix(chicago_net))
chicago_node_coords <- data.frame(xcoord = chicago[["domain"]][["vertices"]][["x"]], 
                                  ycoord = chicago[["domain"]][["vertices"]][["y"]])
                                   
# Create the intensitynet object, in this case will be undirected 
intnet_chicago <- intensitynet(chicago_adj_mtx, 
                               node_coords = chicago_node_coords, 
                               event_data = chicago_df)

intnet_chicago <- RelateEventsToNetwork(intnet_chicago)
#> Calculating edge intensities...
#> ================================================================================
#> Calculating node intensities...
#> ================================================================================

data_geary <- NodeLocalCorrelation(intnet_chicago, dep_type = 'geary', intensity = igraph::vertex_attr(intnet_chicago$graph)$intensity)
geary_c <- data_geary$correlation
intnet_chicago <- data_geary$intnet

PlotHeatmap(intnet_chicago, heattype='geary')