clusso: Regularized Spatial and Spatio-Temporal Cluster Detection

clusso

clusso is an R package based on Regularized Spatial and Spatio-Temporal Cluster Detection (Kamenetsky, Lee, Zhu, Gangnon). clusso implements Poisson and quasi-Poisson regression with the Lasso (least absolute shrinkage and selection operator) penalty to identify a parsimonious set of disease clusters with elevated or depressed risk relative to the background rate in a study region. The number of clusters and tuning parameters are selected based on (quasi-)information criteria.

The companion website and vignettes can be found here. Vignettes use simulated data with added noise based on the breast cancer incidence data set explored in Regularized Spatial and Spatio-Temporal Cluster Detection.

Code developed by and repository maintained by M.Kamenetsky.

Please report bugs or constructive tips to issues here

The main function in this package is clusso(), which performs both spatial and spatio-temporal cluster detection using the Lasso. Cluster detection can be performed across both space and space and time. Diagnostic tools are also provided for further analysis as well as plotting functions.

Installation

clusso was built on R version 4.0.2 “Taking Off Again”

Package dependencies:

glmnet (>= 3.0.1)
Matrix (>= 1.2-17)

Package imports:

ggplot2 (>= 3.2.1),
dplyr (>= 0.8.3),
tidyr (>= 1.0.0),
magrittr (>= 1.5),
data.table (>= 1.12.6),
geosphere (>= 1.5-10),
MASS (>= 7.3-51.4),
RColorBrewer (>= 1.1-2),
Rcpp (>= 1.0.3),
SOAR (>= 0.99-11),
stringi (>= 1.4.3)

To download the latest version of clusso:

library("devtools")
devtools::install_github("mkamenet3/clusso")