epidscan

A Modern R Interface for Spatio-Temporal Scan Statistics.

epidscan brings modern data science workflows to epidemiological cluster detection. Currently powering SaTScan™, it is designed to be a flexible, type-safe, and stateless interface for spatial and space-time analysis.

Design Principles

• Stateless: No global side-effects.
• Type-Safe: ss_tbl classes ensure your data is analysis-ready before you run a single line of code.
• Spatial-Native: Built-in support for sf simple features.

Installation

# Install from GitHub
pak::pak("Songyosr/epidscan")

Requirements: SaTScan™ must be installed on your system.

Quick Start

Here is a complete space-time analysis of the New Mexico lung cancer dataset (included in the package).

library(epidscan)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(broom)

# 1. Prepare Data
# Load included datasets
data("NMlung_cas", "NMlung_pop", "NMlung_geo")

# Create validated inputs
cas <- ss_cas(NMlung_cas, loc_id = "county", cases = "cases", time = "date", time_precision = "month", covars = c("age_group", "sex"))
pop <- ss_pop(NMlung_pop, loc_id = "county", population = "population", time = "year", time_precision = "year", covars = c("age_group", "sex"))
geo <- ss_geo(NMlung_geo, loc_id = "county", coord1 = "x_km", coord2 = "y_km", coord_type = "cartesian")

# 2. Run Analysis
# Set path to SaTScan (adjust for your system)
# Note: This path is specific to macOS; adjust for Windows/Linux
# set_satscan_path("/Applications/SaTScan.app/Contents/app/satscan")
set_satscan_path("/Applications/SaTScan.app/Contents/app/satscan")
#> SatScan path set to: /Applications/SaTScan.app/Contents/app/satscan

# Configure with prm_options (Object-Oriented Parameter Management)
# This creates a reproducible parameter object that can be inspected and reused.
my_prm <- prm_options(
  AnalysisType = 3, # Retrospective Space-Time
  ModelType = 0, # Poisson
  MonteCarloReps = 999
)

# Run the analysis
result <- satscanr(
  cas, pop, geo,
  prm = my_prm,
  verbose = FALSE
)

# 3. Explore Results
# Tidy summary of detected clusters
summary(result)
#> SaTScan Results Summary
#> =======================
#> 
#> == SaTScan Analysis Summary ==================================
#> Model: Discrete Poisson [High Rates]
#> Scan:  Retrospective Space-Time
#> Time:  1973/01/01 to 1991/12/31 (Month)
#> Space: Circular (Max: 50% pop)
#> Sims:  999 Monte Carlo Reps
#> ==============================================================
#> 
#> Overview:
#>   Clusters detected:  6 (2 significant at p < 0.05)
#>   Locations analyzed: 37 (17 in clusters)
#>   Relative risk:      0.30 - 1.36
#> 
#> Most Likely Cluster:
#>   Cluster ID:         1
#>   P-value:            0.000000
#>   Observed:           714
#>   Expected:           502.0
#> 
#> Cluster Statistics:
#>   statistic        min        q1 median       mean        q3     max
#> 1   p_value 6.7257e-13 0.2020006  0.866  0.6128335   0.94275   0.996
#> 2 radius_km 0.0000e+00 0.0000000 58.860 64.3225655 121.00681 146.113
#> 
#> 
#> (Raw SaTScan text available. Use print(result, raw = TRUE) to view)

# Analysis-level metrics
tidy(result)
#> # A tibble: 6 × 13
#>   cluster center_id     x     y  p_value   llr observed expected obs_exp_ratio
#>     <int> <chr>     <dbl> <dbl>    <dbl> <dbl>    <dbl>    <dbl>         <dbl>
#> 1       1 Chaves      418   156 6.73e-13 42.1       714   502.            1.42
#> 2       2 Socorro     199   222 7.71e- 7 25.7      2474  2177.            1.14
#> 3       3 Lea         528   103 8.08e- 1  8.60       10     1.88          5.32
#> 4       4 Chaves      418   156 9.24e- 1  8.11      467   387.            1.21
#> 5       5 Sierra      166   127 9.49e- 1  7.91       10     2.05          4.88
#> 6       6 SanJuan      96   531 9.96e- 1  6.88       10     2.34          4.28
#> # ℹ 4 more variables: radius_km <dbl>, population <dbl>, start_date <date>,
#> #   end_date <date>

# Visualization
# map_clusters(result, simple = TRUE) # Interactive map (view locally)

For a detailed walkthrough, implementation details, and advanced configuration, see the Getting Started vignette.

Available Input Types

Function	File Type	Purpose	status
ss_cas()	.cas	Case counts	✓
ss_pop()	.pop	Population denominators	✓
ss_geo()	.geo	Spatial coordinates	✓
ss_ctl()	.ctl	Controls (Bernoulli)	✓
ss_grd()	.grd	Custom scan centers	✓
ss_nwk()	.nwk	Network edges	Under Dev
ss_nbr()	.nbr	Neighbor rankings	Under Dev
ss_met()	.met	Meta-locations	Under Dev

Documentation

• Getting Started
• Parameter Reference
• Report Issues

Citation

Please cite the original SaTScan software and methodology:

Kulldorff M. (1997). A spatial scan statistic. Communications in Statistics: Theory and Methods, 26:1481-1496.

Kulldorff M. and Information Management Services Inc. (2018). SaTScan™ User Guide. www.satscan.org.

To cite this R package:

citation("epidscan")

License

MIT © Songyos Rajborirug