# 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.
