knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "README_figure/README-" )
Package of data and methods for spatial epidemiology.
Get the released version from CRAN:
install.packages("SpatialEpi")
Or the development version from GitHub:
# If you haven't installed devtools yet, do so: # install.packages("devtools") devtools::install_github("rudeboybert/SpatialEpi")
Note: In order for all C++ code to compile correctly you may need to
cpp11
packageRcppArmadillo
by runningr
packageurl <- "https://cran.r-project.org/src/contrib/Archive/RcppArmadillo/RcppArmadillo_0.9.900.3.0.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
We load the data and convert the coordinate system from latitude/longitude to a grid-based system.
library(SpatialEpi)
data(NYleukemia) sp.obj <- NYleukemia$spatial.polygon centroids <- latlong2grid(NYleukemia$geo[, 2:3]) population <- NYleukemia$data$population cases <- NYleukemia$data$cases
We plot the incidence of leukemia for each census tract.
plotmap(cases/population, sp.obj, log=TRUE, nclr=5) points(grid2latlong(centroids), pch=4)
We run the Bayesian Cluster Detection method from Wakefield and Kim (2013):
y <- cases E <- expected(population, cases, 1) max.prop <- 0.15 shape <- c(2976.3, 2.31) rate <- c(2977.3, 1.31) J <- 7 pi0 <- 0.95 n.sim.lambda <- 10^4 n.sim.prior <- 10^5 n.sim.post <- 10^5 # Compute output output <- bayes_cluster(y, E, population, sp.obj, centroids, max.prop, shape, rate, J, pi0, n.sim.lambda, n.sim.prior, n.sim.post)
plotmap(output$post.map$high.area, sp.obj)
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