Package: gsClusterDetect 1.0.2

gsClusterDetect: Utilities for Geo-Spatial Cluster Detection and Significance Classification

Provides utilities for manipulating time series of location-based counts of events to detect geo-spatial clusters. Significance of these clusters is determined using a set of models that classify based on a learned relationship between observed and the log(observed/expected) ratio of counts. The approach implemented here is similar to prospective space-time estimation of clusters using the scan statistic.

Authors:Luke C. Mullany [aut, cre], Howard S. Burkom [aut]

gsClusterDetect_1.0.2.tar.gz
gsClusterDetect_1.0.2.zip(r-4.7-any)gsClusterDetect_1.0.2.zip(r-4.6-any)gsClusterDetect_1.0.2.zip(r-4.5-any)
gsClusterDetect_1.0.2.tgz(r-4.6-any)gsClusterDetect_1.0.2.tgz(r-4.5-any)
gsClusterDetect_1.0.2.tar.gz(r-4.7-any)gsClusterDetect_1.0.2.tar.gz(r-4.6-any)
gsClusterDetect_1.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gsClusterDetect/json (API)

# Install 'gsClusterDetect' in R:
install.packages('gsClusterDetect', repos = c('https://lmullany.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lmullany/gsclusterdetect/issues

Pkgdown/docs site:https://lmullany.github.io

Datasets:

On CRAN:

Conda:

6.18 score 5 stars 6 scripts 283 downloads 31 exports 14 dependencies

Last updated from:e1bd0ae1a6. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK202
source / vignettesOK314
linux-releaseOK209
macos-releaseOK210
macos-oldrelOK248
windows-develOK166
windows-releaseOK151
windows-oldrelOK139
wasm-releaseOK136

Exports:add_location_countsadd_spline_thresholdcompress_clusterscompress_clusters_fastcounty_distance_matrixcreate_custom_dist_listcreate_dist_listcustom_distance_matrixfind_clustersfind_clusters_by_dfgen_nearby_case_infogenerate_case_gridsgenerate_heatmapgenerate_heatmap_datagenerate_observed_expectedgenerate_summary_tablegenerate_time_series_datagenerate_time_series_plotget_baseline_datesget_nearby_locationsget_test_datesidentify_statesinject_countsmap_clustersprepare_map_datareduce_clusters_to_minstate_distance_matrixtract_distance_matrixtract_generatorus_distance_matrixzip_distance_matrix

Dependencies:classclassIntclidata.tableDBIe1071jsonliteKernSmoothproxyRcpps2sfunitswk

Vignette 1: Package Overview
Overview: Package Purpose | Package functionality | Technical Requirements to Enable Cluster Detection in User Data | Distance Structures for Geographic Scanning | Full Distance Matrix Functions: | Limited Distance Lists | Main Wrapper: find_clusters() | Preparing Inputs | Key Parameters in find_clusters() | Required: | Optional: | Running find_clusters() | Built-In Spline Tables and Example Data | Example Cluster Map | Summary and Plotting Utilities
Rendered fromv01_basic_demo.Rmdusingknitr::rmarkdown

Last update: 2026-08-06
Started: 2026-08-06

Vignette 2: Creating Distance Objects
Overview | Types of Distance Objects: | Square pairwise distance matrices | Example: county distance matrix: | Example: zip code distance matrix: | Example: tract distance matrix: | Custom Distance Matrices | Distance Lists | Custom Distance Lists | Other Functions
Rendered fromv02_distance_objects.Rmdusingknitr::rmarkdown

Last update: 2026-08-06
Started: 2026-08-06

Vignette 3: Accessing Interim Objects from Cluster Estimation
Overview | Functions called by find_clusters() | Example Usage:
Rendered fromv03_interim_objects.Rmdusingknitr::rmarkdown

Last update: 2026-08-06
Started: 2026-08-06

Vignette 4: Artificial Cluster Injection
Overview: Creation of artificial target signals | Available options for signal injections | Generating Cluster Signals for Detection | Example Cluster Signal Generation | Example with multiple artificial signals
Rendered fromv04_artificial_cluster_injection.Rmdusingknitr::rmarkdown

Last update: 2026-08-06
Started: 2026-08-06

Readme and manuals

Help Manual

Help pageTopics
Add location counts to cluster location listadd_location_counts
Use spline lookup to restrict `ObservedExpectedGrid` to potential clustersadd_spline_threshold
check for variables in framecheck_vars
Compress a cluster_alert_tablecompress_clusters
Fast version of compress clusterscompress_clusters_fast
County Location Datasetcounties
Get distance matrix for counties within a statecounty_distance_matrix
Create a sparse distance list from custom location datacreate_custom_dist_list
Generalized distance list as sparse listcreate_dist_list
Build a Distance Matrix from a Custom Data Framecustom_distance_matrix
Example Count Datasetexample_count_data
Find clustersfind_clusters
Wrapper: Find clusters by data frame onlyfind_clusters_by_df
Return baseline and test period case grids restricting by distancegen_nearby_case_info
Get test period and baseline period case countsgenerate_case_grids
Generate heatmap of datagenerate_heatmap
Get heat map data from a set of location, date, count datagenerate_heatmap_data
Generate the observed and expected informationgenerate_observed_expected
Summary count-by-location-and-date data, given baseline and test interval lengths, and an end-date for the test intervalgenerate_summary_table
Generate time series datagenerate_time_series_data
Generate timeseries plot datagenerate_time_series_plot
Generate baseline dates vectorget_baseline_dates
Get nearby locationsget_nearby_locations
Generate test dates vectorget_test_dates
Identify states from location frameidentify_states
Add data counts for parameterized injected clustersinject_counts
Map Clustersmap_clusters
Prepare cluster result and shape file for mappingprepare_map_data
Filter clusters on minimum overall countreduce_clusters_to_min
Spline Lookup Table - 0.001spline_001
Spline Lookup Table - 0.005spline_005
Spline Lookup Table - 0.01spline_01
Spline Lookup Table - 0.05spline_05
Get distance matrix for states in the USstate_distance_matrix
State Location Datasetstates
Build a Tract Distance Matrix for a Statetract_distance_matrix
Generate Census Tract Centroids for a Statetract_generator
Get distance matrix for all counties in the USus_distance_matrix
Get distance matrix for zip codes within a statezip_distance_matrix
Zipcode Location Datasetzipcodes