R Observatory: Metrics for fmt version 2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

fmt

2.0Package record

Variance Estimation of FMT Method (Fully Moderated T-Statistic)

0packages depend

2.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Lianbo YuCRAN page ↗

The FMT method computes posterior residual variances to be used in the denominator of a moderated t-statistic from a linear model analysis of gene expression data. It is an extension of the moderated t-statistic originally proposed by Smyth (2004) doi:10.2202/1544-6115.1027. LOESS local regression and empirical Bayesian method are used to estimate gene specific prior degrees of freedom and prior variance based on average gene intensity levels. The posterior residual variance in the denominator is a weighted average of prior and residual variance and the weights are prior degrees of freedom and residual variance degrees of freedom. The degrees of freedom of the moderated t-statistic is simply the sum of prior and residual variance degrees of freedom.

Install

R (CRAN)Ubuntu (r2u)

install.packages("fmt", 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-fmt

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 53 s · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 2
Examples that run: 100%1 run in a plain check
Exported functions with examples: 50%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #18,506 · ~8/day · ~229/mo

Releases R versions

Daily download trend is not available in this view yet.

30430 days

69290 days

2.7K1 year

Compare downloads with other packages →

Also on70 r2u

How downloads are counted

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Installing fmt adds 0 packages. 1 more not on CRAN is not measured.

Depends (2)

R >= 3.5.0limma

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

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)

Lianbo Yu

Author, Maintainer since 1.0 (2012)

Listed in earlier versions (1)

The Ohio State University

no longer listed · 1.0

Releases (2)

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
unarchivedReturned to CRAN
2022-09-05
2.0Latest
record
2022-09-05 · current release · diff ↗ ·
removed 1 export
pattern:.

added 2 exports
fmt, plotFMT
R
R 4.2.0 released · 2022-04-22
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
archivedRemoved from CRAN
2019-01-26
check problems were not corrected despite reminders
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10

Show 3 earlier eventsHide 3 earlier events

R
R 3.0.0 released · 2013-04-03
1.0
record
2012-08-30
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-08-30
Total releases: 2 / 14 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Download size: 3.2 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("fmt")

Format

Yu, L. (2022). fmt: Variance Estimation of FMT Method (Fully Moderated T-Statistic) (Version 2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.fmt

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 fmt version 2.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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