Configure SaTScan for a Bernoulli purely spatial scan

Defines the analysis parameters required by SaTScan's GUI to conduct a Bernoulli-based purely spatial scan, either to detect clusters of high rates of acute malnutrition or both high and low rates.

User input is limited to specifying the analysis area filename, the destination directory for the parameters file, the SaTScan version in use, and the type of clusters to be detected. All other parameters are pre-defined by this function.

Usage

ww_configure_satscan(
  filename = character(),
  params_dir = character(),
  satscan_version = character(),
  .scan_for = c("high-rates", "high-low-rates")
)

Arguments

filename: A quoted string identifying the analysis area.
params_dir: A quoted string of the folder or directory where the parameters file (produced by this function) should be saved. This can be the same directory as that specified in ww_wrangle_data().
satscan_version: A quoted string indicating the version of SaTScan installed on the user's computer. Internally, this value is checked against the latest available version. If it is older, a warning is issued with a link to SaTScan’s website. Although the analysis is not interrupted, it is recommended to use the latest version.
.scan_for: A quoted string indicating the type of clusters to scan for. To scan for high-rate clusters only, set .scan_for = "high-rates". To scan for both high and low rates, set .scan_for = "high-low-rates".

Details

For more information on Bernoulli purely spatial scans, refer to the SaTScan technical documentation available at: https://www.satscan.org/techdoc.html.

References

Kulldorff, M. (2022) SaTScan user guide for version 10.1. Available at: https://www.satscan.org/.

Examples

## Given a temporary directory ----
tmp <- withr::local_tempdir()
directory <- file.path(tmp, "input-files")

## Wrangle data with `{mwana}` ----
x <- anthro |>
  dplyr::rename(longitude = x, latitude = y) |>
  mwana::mw_wrangle_wfhz(
    sex = sex,
    .recode_sex = TRUE,
    weight = weight,
    height = height
  ) |>
  mwana::define_wasting(
    zscores = wfhz,
    .by = "zscores",
    edema = oedema
  )
#> ================================================================================

## Apply the function ----
ww_wrangle_data(
  .data = x,
  filename = "Locality",
  dir = directory,
  .gam_based = "wfhz"
)
#> [1] "/tmp/RtmpYB1d5u/file1d637b2ecd4e/input-files/Locality"

library(rsatscan) # important to make `{wowi}` access `{rsatscan}`-specific eviroment
#> rsatscan only does anything useful if you have SaTScan
#> See http://www.satscan.org/ for free access

#### Configure SaTScan ----
do.call(
  what = ww_configure_satscan,
  args = list(
    filename = "Locality",
    params_dir = directory,
    satscan_version = "10.3.2",
    .scan_for = "high-low-rates"
  )
)

## Show file's content ----
file.show(file.path(tmp, "input-files/Locality.prm"))