Eagle

2.5

Multiple Locus Association Mapping on a Genome-Wide Scale

0packages depend

4.4Kdownloads / year

–test coverage

6/13checks pass

Overview

About

Maintained by Andrew GeorgeFirst published 2017-08-2820 releasesCRAN page ↗

An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred and outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. For users unfamiliar with R, to perform an analysis, run 'OpenGUI()'. This opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.

Install

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

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

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

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-eagle

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-Eagle

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-Eagle

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

7NOTE6OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-release-windows-x86_64

Slowest check: 7.6 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-06-09
6 OK · 7 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
6 OK · 6 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-22
5 OK · 9 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
5 OK · 8 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
3 OK · 11 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 44%
Documented parameters: 100%
Return-value docs: 67%
References docs: 0%

Downloads

4.4K

CRAN downloads in the past year

Rank #10,615 · ~12/day · ~367/mo

Releases R versions

Daily download trend is not available in this view yet.

31130 days

1K90 days

4.4K1 year

Compare downloads with other packages →

Also on403 r2u41 autocran

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (6)

R >= 4.0shinyFiles shinyBS ggplot2 ggthemes plotly

Imports (10)

R.utils mmap shiny shinythemes shinyjs fontawesomestatsutilsparalleldata.table

LinkingTo (2)

RcppEigen Rcpp

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 4,689 (46%)C++ 4,321 (42%)Rd 1,140 (11%)C 72 (1%)

Code characteristics

Cyclomatic complexity: 2.0 median / 46 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

125 9 exported

Complexity

5.7 avg / 46 max

Call network

125 nodes / 125 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (10)

Maintainer (1)

Andrew George

Author, Maintainer

Authors (1)

Andrew George

Author, Maintainer

Contributors (9)

Contributor

Contributor

Contributor

Contributor

Contributor

Contributor

Contributor

Contributor

Show 1 more contributors

Noah Zaitlen

Contributor

Package Timeline

20 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
2.5Latest
2021-11-30 · current release · diff ↗
2.4.5
2021-06-10 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.4.4
2021-04-22 · diff ↗
2.4.3
2021-01-12 · diff ↗
2.4.2
2020-12-06 · diff ↗
2.4.1
2020-10-19 · diff ↗
2.4
2020-08-26 · diff ↗
2.3
2020-07-22 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.2
2020-03-03 · diff ↗

Show 14 earlier events

2.1.1
2019-11-17 · diff ↗
2.1.0
2019-11-14 · diff ↗
2.0.0
2019-11-07 · diff ↗
1.5.2
2019-08-22 · diff ↗
1.5.1
2019-05-24 · diff ↗
1.5.0
2019-05-17 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.4.0
2019-04-23 · diff ↗
1.3.0
2019-01-31 · diff ↗
1.2.0
2018-12-17 · diff ↗
1.1.0
2018-08-22 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.2
2017-08-28
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-08-28
Total releases: 20 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0
Download size: 1.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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