R Observatory: Metrics for fdrci version 2.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

fdrci

2.4Package record

Permutation-Based FDR Point and Confidence Interval Estimation

0packages depend

3.3Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Joshua MillsteinCRAN page ↗

FDR functions for permutation-based estimators, including pi0 as well as FDR confidence intervals. The confidence intervals account for dependencies between tests by the incorporation of an overdispersion parameter, which is estimated from the permuted data. Also included are options for an analog parametric approach.

Install

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

install.packages("fdrci", 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-fdrci

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-fdrci

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-fdrci

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Joshua Millstein <joshua.millstein@usc.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 1.7 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.4

READMEYes · 79 wordsVignettesYes · 1 · staticNEWSNoCitation fileYes · computed when R runs itWebsitenot declared in DESCRIPTION

Help pages: 6includes a package overview page
Examples that run: 100%5 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 100%

Vignettes (1)

fdrci: FDR selection and adjustment - HGSOC HTML

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #13,690 · ~9/day · ~275/mo

Releases R versions

Daily download trend is not available in this view yet.

32330 days

85690 days

3.3K1 year

Compare downloads with other packages →

Also on67 r2u5 autocran

How downloads are counted

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing fdrci adds 17 packages (7 with compiled code, 14 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, farver 1.2 MB.

Depends (0)

none

Imports (2)

ggplot2stats

LinkingTo (0)

none

Suggests (5)

rmarkdown knitr GEOquery dplyr foreach

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)

Joshua Millstein

Author, Maintainer since 1.0 (2011)

Releases (6)

Pick two releases to compare their code metrics.

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
2.4Latest
record
2022-10-18 · current release · diff ↗
2.3
record
2022-06-08 · diff ↗ ·
added 1 export
meff.jm
R
R 4.2.0 released · 2022-04-22
2.2
record
2021-06-11 · diff ↗ ·
removed 1 export
pattern:.

added 4 exports
FDRplot, MV_q, fdrTbl, fdr_od
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
2.1
record
2016-11-15 · diff ↗
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16

Show 5 earlier eventsHide 5 earlier events

R
R 3.1.0 released · 2014-04-10
2.0
record
2013-10-05 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.0
record
2012-10-29
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-10-29
Total releases: 6 / 14 yrs
License: Artistic-2.0 OSI
Download size: 361 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("fdrci")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 fdrci version 2.4 [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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