R Observatory: Metrics for NAM version 1.8.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

NAM

1.8.0Package record

Nested Association Mapping

1packages dependsuggested by 1

5.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Alencar XavierCRAN page ↗

Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) doi:10.1093/bioinformatics/btv448. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.

Install

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

install.packages("NAM", 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-nam

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-NAM

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-NAM

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: 3.5 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-02
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.8.0

READMENoVignettesYes · 2 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 14includes a package overview page
Examples that run: 9%1 run in a plain check · 10 never run
Exported functions with examples: 85%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 57%

Also includes 4 demo scripts (run with demo())

Vignettes (2)

Background for Meta-analysis HTML
Introduction to NAM HTML

How these are measured

Downloads

5.2K

CRAN downloads in the past year

Rank #5,504 · ~14/day · ~436/mo

Releases R versions

Daily download trend is not available in this view yet.

69430 days

1.5K90 days

5.2K1 year

Compare downloads with other packages →

Also on388 r2u5 autocran2.9K conda_forge182 bioconda132 c2d4u

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing NAM adds 1 package (1 with compiled code, 1.8 MB of source tarballs). Heaviest: Rcpp 1.8 MB.

Depends (1)

R >= 3.2.0

Imports (1)

Rcpp

LinkingTo (1)

Rcpp

Suggests (3)

knitr rmarkdown bWGR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

SoyNAM

Suggests, most downloaded first

MoBPS

How these are counted

Code & Tests

Datasets

People & History

People (4)

Alencar Xavier

Author, Maintainer since 1.0 (2015)

William Muir

Author

Katy Rainey

Author

Shizhong Xu

Author

Listed in earlier versions (3)

Show 3 peopleHide 3 people

Tiago Pimenta

no longer listed · 1.0 to 1.4

Qishan Wang

no longer listed · 1.0 to 1.4

Shizhong Xu.

no longer listed · 1.0.2.1 to 1.7.3

Releases (38)

Pick two releases to compare their code metrics.

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R 4.6.0 released · 2026-04-24
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2026-01-24 · current release · diff ↗
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R 4.5.0 released · 2025-04-11
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R 4.4.0 released · 2024-04-24
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R 4.3.0 released · 2023-04-21
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R 4.2.0 released · 2022-04-22
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R 4.1.0 released · 2021-05-18
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R 4.0.0 released · 2020-04-24
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R 3.6.0 released · 2019-04-26
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R 3.5.0 released · 2018-04-23
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R 3.3.0 released · 2016-05-03
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R 3.2.0 released · 2015-04-16
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2015-01-04
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R 3.1.0 released · 2014-04-10

Package metadata

First published: 2015-01-04
Total releases: 38 / 11 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.2.0
Bundled data: 1,013 KB / 3 files
Download size: 1.1 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("NAM")

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

It points to 10.1093/bioinformatics/btv448.

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 NAM version 1.8.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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