{ "_id": "6ae3cd08327abcdf86867867", "Package": "gsClusterDetect", "Type": "Package", "Title": "Utilities for Geo-Spatial Cluster Detection and Significance\nClassification", "Version": "1.0.2", "Authors@R": "c(\nperson(\"Luke C.\", \"Mullany\", email = \"luke.mullany@jhuapl.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Howard S.\", \"Burkom\", role = \"aut\")\n)", "Description": "Provides utilities for manipulating time series of\nlocation-based counts of events to detect geo-spatial clusters.\nSignificance of these clusters is determined using a set of\nmodels that classify based on a learned relationship between\nobserved and the log(observed/expected) ratio of counts. The\napproach implemented here is similar to prospective space-time\nestimation of clusters using the scan statistic.", "URL": "https://github.com/lmullany/gsClusterDetect,\nhttps://lmullany.github.io/gsClusterDetect/", "BugReports": "https://github.com/lmullany/gsClusterDetect/issues", "License": "Apache License (>= 2)", "Encoding": "UTF-8", "LazyData": "true", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.1.1", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibssl-dev libproj-dev libsqlite3-dev libudunits2-dev", "Repository": "https://lmullany.r-universe.dev", "Date/Publication": "2026-10-29 19:04:46 UTC", "RemoteUrl": "https://github.com/lmullany/gsclusterdetect", "RemoteRef": "HEAD", "RemoteSha": "e1bd0ae1a64c7425ffdca5b9824d192fde933ec8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-29 22:42:42 UTC", "User": "root" }, "Author": "Luke C. Mullany [aut, cre],\nHoward S. 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"_exports": [ "add_location_counts", "add_spline_threshold", "compress_clusters", "compress_clusters_fast", "county_distance_matrix", "create_custom_dist_list", "create_dist_list", "custom_distance_matrix", "find_clusters", "find_clusters_by_df", "gen_nearby_case_info", "generate_case_grids", "generate_heatmap", "generate_heatmap_data", "generate_observed_expected", "generate_summary_table", "generate_time_series_data", "generate_time_series_plot", "get_baseline_dates", "get_nearby_locations", "get_test_dates", "identify_states", "inject_counts", "map_clusters", "prepare_map_data", "reduce_clusters_to_min", "state_distance_matrix", "tract_distance_matrix", "tract_generator", "us_distance_matrix", "zip_distance_matrix" ], "_datasets": [ { "name": "counties", "title": "County Location Dataset", "object": "counties", "class": [ "data.table", "data.frame" ], "fields": [ "state_name", "state", "state_fips", "fips", "longitude", "latitude" ], "rows": 3144, "table": true, "tojson": true }, { "name": "example_count_data", "title": "Example Count Dataset", "object": "example_count_data", "class": [ "data.table", "data.frame" ], "fields": [ "location", "date", "count" ], "rows": 11264, "table": true, "tojson": true }, { "name": "spline_001", "title": "Spline Lookup Table - 0.001", "object": "spline_001", "class": [ "data.table", "data.frame" ], "fields": [ "observed", "spl_thresh" ], "rows": 399, "table": true, "tojson": true }, { "name": "spline_005", "title": "Spline Lookup Table - 0.005", "object": "spline_005", "class": [ "data.table", "data.frame" ], "fields": [ "observed", "spl_thresh" ], "rows": 399, "table": true, "tojson": true }, { "name": "spline_01", "title": "Spline Lookup Table - 0.01", "object": "spline_01", "class": [ "data.table", "data.frame" ], "fields": [ "observed", "spl_thresh" ], "rows": 399, "table": true, "tojson": true }, { "name": "spline_05", "title": "Spline Lookup Table - 0.05", "object": "spline_05", "class": [ "data.table", "data.frame" ], "fields": [ "observed", "spl_thresh" ], "rows": 399, "table": true, "tojson": true }, { "name": "states", "title": "State Location Dataset", "object": "states", "class": [ "data.table", "data.frame" ], "fields": [ "state_name", "state", "state_fips", "longitude", "latitude" ], "rows": 56, "table": true, "tojson": true }, { "name": "zipcodes", "title": "Zipcode Location Dataset", "object": "zipcodes", "class": [ "data.table", "data.frame" ], "fields": [ "id", "zip_code", "state", "state_name", "county", "region", "region_id", "region_name", "pop", "modified", "latitude", "longitude" ], "rows": 41684, "table": true, "tojson": true } ], "_help": [ { "page": "add_location_counts", "title": "Add location counts to cluster location list", "topics": [ "add_location_counts" ] }, { "page": "add_spline_threshold", "title": "Use spline lookup to restrict `ObservedExpectedGrid` to potential clusters", "topics": [ "add_spline_threshold" ] }, { "page": "check_vars", "title": "check for variables in frame", "topics": [ "check_vars" ] }, { "page": "compress_clusters", "title": "Compress a cluster_alert_table", "topics": [ "compress_clusters" ] }, { "page": "compress_clusters_fast", "title": "Fast version of compress clusters", "topics": [ "compress_clusters_fast" ] }, { "page": "counties", "title": "County Location Dataset", "topics": [ "counties" ] }, { "page": "county_distance_matrix", "title": "Get distance matrix for counties within a state", "topics": [ "county_distance_matrix" ] }, { "page": "create_custom_dist_list", "title": "Create a sparse distance list from custom location data", "topics": [ "create_custom_dist_list" ] }, { "page": "create_dist_list", "title": "Generalized distance list as sparse list", "topics": [ "create_dist_list" ] }, { "page": "custom_distance_matrix", "title": "Build a Distance Matrix from a Custom Data Frame", "topics": [ "custom_distance_matrix" ] }, { "page": "example_count_data", "title": "Example Count Dataset", "topics": [ "example_count_data" ] }, { "page": "find_clusters", "title": "Find clusters", "topics": [ "find_clusters" ] }, { "page": "find_clusters_by_df", "title": "Wrapper: Find clusters by data frame only", "topics": [ "find_clusters_by_df" ] }, { "page": "gen_nearby_case_info", "title": "Return baseline and test period case grids restricting by distance", "topics": [ "gen_nearby_case_info" ] }, { "page": "generate_case_grids", "title": "Get test period and baseline period case counts", "topics": [ "generate_case_grids" ] }, { "page": "generate_heatmap", "title": "Generate heatmap of data", "topics": [ "generate_heatmap" ] }, { "page": "generate_heatmap_data", "title": "Get heat map data from a set of location, date, count data", "topics": [ "generate_heatmap_data" ] }, { "page": "generate_observed_expected", "title": "Generate the observed and expected information", "topics": [ "generate_observed_expected" ] }, { "page": "generate_summary_table", "title": "Summary count-by-location-and-date data, given baseline and test interval lengths, and an end-date for the test interval", "topics": [ "generate_summary_table" ] }, { "page": "generate_time_series_data", "title": "Generate time series data", "topics": [ "generate_time_series_data" ] }, { "page": "generate_time_series_plot", "title": "Generate timeseries plot data", "topics": [ "generate_time_series_plot" ] }, { "page": "get_baseline_dates", "title": "Generate baseline dates vector", "topics": [ "get_baseline_dates" ] }, { "page": "get_nearby_locations", "title": "Get nearby locations", "topics": [ "get_nearby_locations" ] }, { "page": "get_test_dates", "title": "Generate test dates vector", "topics": [ "get_test_dates" ] }, { "page": "identify_states", "title": "Identify states from location frame", "topics": [ "identify_states" ] }, { "page": "inject_counts", "title": "Add data counts for parameterized injected clusters", "topics": [ "inject_counts" ] }, { "page": "map_clusters", "title": "Map Clusters", "topics": [ "map_clusters" ] }, { "page": "prepare_map_data", "title": "Prepare cluster result and shape file for mapping", "topics": [ "prepare_map_data" ] }, { "page": "reduce_clusters_to_min", "title": "Filter clusters on minimum overall count", "topics": [ "reduce_clusters_to_min" ] }, { "page": "spline_001", "title": "Spline Lookup Table - 0.001", "topics": [ "spline_001" ] }, { "page": "spline_005", "title": "Spline Lookup Table - 0.005", "topics": [ "spline_005" ] }, { "page": "spline_01", "title": "Spline Lookup Table - 0.01", "topics": [ "spline_01" ] }, { "page": "spline_05", "title": "Spline Lookup Table - 0.05", "topics": [ "spline_05" ] }, { "page": "state_distance_matrix", "title": "Get distance matrix for states in the US", "topics": [ "state_distance_matrix" ] }, { "page": "states", "title": "State Location Dataset", "topics": [ "states" ] }, { "page": "tract_distance_matrix", "title": "Build a Tract Distance Matrix for a State", "topics": [ "tract_distance_matrix" ] }, { "page": 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