R Observatory: Metrics for FES version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

FES

1.0Package record

Fisher Exact Scanning for Dependency

0packages depend

586downloads / year

93.1%test coverage

13/13flavors OK

Overview

About

Maintained by Li MaCRAN page ↗GitHub ↗Issues ↗

Implements Fisher exact scanning (FES), a multiscale test of dependence for continuous or discrete bivariate data. The method scans nested binary partitions using Fisher's exact tests and combines evidence across windows and resolutions with Sidak, Bonferroni, and meta-analysis corrections. The methodology is described in Ma and Mao (2019) doi:10.1080/01621459.2017.1397522.

Changes in 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.

Show all changes in 1.0Hide the rest of the changes in 1.0

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.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("FES", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("mastatlab/fes")

Development version from mastatlab/fes. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-fes

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-FES

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-FES

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 59 s · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-07-23

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0

READMEYes · 374 wordsVignettesNoNEWSYes · 67% structured · mentions 1.0Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 3 (1 internal)includes a package overview page
Examples that run: 100%1 run in a plain check
Exported functions with examples: 100%
Documented parameters: 73%
Return-value docs: 100%
Help pages citing references: 67%

Also includes 6 demo scripts (run with demo())

How these are measured

Downloads

586

CRAN downloads in the past year

Rank #22,932 · ~2/day · ~49/mo

Releases R versions

Daily download trend is not available in this view yet.

21230 days

56890 days

5861 year

Compare downloads with other packages →

Also on15 r2u2 autocran

How downloads are counted

Repository

mastatlab/fes ↗Organization: MaStatLab

1Stars

0Forks

0Open issues

0Open PRs

0Releases

13Commits

3Commit identities

License file reads as GPL-3.0 · 13 commits · Last activity 2026-07-14

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/mastatlab/fes on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing FES adds no packages beyond those that come with R.

Depends (1)

R >= 3.6.0

Imports (4)

graphicsgrDevicesmethodsstats

LinkingTo (0)

none

Suggests (2)

BayesFactor testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Li Ma

Releases (1)

1.0Latest
record
2026-07-22 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-07-22
Total releases: 1 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.6.0
Download size: 19 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("FES")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1080/01621459.2017.1397522.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for FES version 1.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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