FES 1.0

This is the first official CRAN release of FES, the reference R implementation of Fisher exact scanning for dependency.

Package interface

• Converted the original scripts into an installable, documented R package.

• Renamed the public analysis function from fisherScan() to the concise package-level interface fes().

• Standardized the public spelling of the Sidak correction in the returned Sidak component and the plot.sidak argument.

• Replaced the fixed Figures/ output switch with output.dir, so files are written only to a directory explicitly supplied by the user.

• Added opt-in window-level results and structure plots so FES can locate and characterize dependencies in addition to testing for their presence.

Statistical and computational improvements

• Restored the intended active-resolution count in the global p-value calculation; a historical sum() call with no argument always returned zero.

• Added input validation, numerically stable Sidak corrections, bounded p-values, and safe handling of resolutions with no testable windows.

Visualization and examples

• Improved plotting and corrected the window-level Sidak adjustment used in plots. Scan panels now use colorblind-friendly shared scales, informative annotations, observation overlays, and high-contrast significance outlines.

• Added visual demos covering the original example, nonlinear dependence, localized dependence, dependency maps, local direction changes, and evidence across scanning resolutions.

• Added demos showing how FES learns local direction changes, circular structure, and alternating association patterns.

• Structure maps now default to a single automatically selected partition stratum, avoiding hard-to-read overlaps across resolution levels. Explicit stratum selection and an opt-in cross-resolution overlay remain available.

Quality and release infrastructure

• Added automated tests, package citation metadata, and continuous integration.