R Observatory: Metrics for CFO version 2.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CFO

2.2.0Package record

CFO-Type Designs in Phase I/II Clinical Trials

0packages depend

6.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Jialu FangCRAN page ↗Website ↗

In phase I clinical trials, the primary objective is to ascertain the maximum tolerated dose (MTD) corresponding to a specified target toxicity rate. The subsequent phase II trials are designed to examine the potential efficacy of the drug based on the MTD obtained from the phase I trials, with the aim of identifying the optimal biological dose (OBD). The 'CFO' package facilitates the implementation of dose-finding trials by utilizing calibration-free odds type (CFO-type) designs. Specifically, it encompasses the calibration-free odds (CFO) (Jin and Yin (2022) doi:10.1177/09622802221079353), randomized CFO (rCFO), precision CFO (pCFO), two-dimensional CFO (2dCFO) (Wang et al. (2023) doi:10.3389/fonc.2023.1294258), time-to-event CFO (TITE-CFO) (Jin and Yin (2023) doi:10.1002/pst.2304), fractional CFO (fCFO), accumulative CFO (aCFO), TITE-aCFO, and f-aCFO (Fang and Yin (2024) <doi: 10.1002/sim.10127>). It supports phase I/II trials for the CFO design and only phase I trials for the other CFO-type designs. The ‘CFO' package accommodates diverse CFO-type designs, allowing users to tailor the approach based on factors such as dose information inclusion, handling of late-onset toxicity, and the nature of the target drug (single-drug or drug-combination). The functionalities embedded in 'CFO' package include the determination of the dose level for the next cohort, the selection of the MTD for a real trial, and the execution of single or multiple simulations to obtain operating characteristics. Moreover, these functions are equipped with early stopping and dose elimination rules to address safety considerations. Users have the flexibility to choose different distributions, thresholds, and cohort sizes among others for their specific needs. The output of the 'CFO' package can be summary statistics as well as various plots for better visualization. An interactive web application for CFO is available at the provided URL.

Install

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

install.packages("CFO", 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-cfo

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-CFO

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-CFO

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: 3.6 min · r-oldrel-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 2.2.0

READMENoVignettesNoNEWSNoCitation fileNoWebsiteYes

Help pages: 21
Examples that run: 100%21 run in a plain check
Exported functions with examples: 100%
Documented parameters: 79%
Return-value docs: 100%
Help pages citing references: 86%

How these are measured

Downloads

6.3K

CRAN downloads in the past year

Rank #8,412 · ~17/day · ~528/mo

Releases R versions

Daily download trend is not available in this view yet.

40430 days

1.1K90 days

6.3K1 year

Compare downloads with other packages →

Also on86 r2u11 autocran

How downloads are counted

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing CFO adds 27 packages (13 with compiled code, 16 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, farver 1.2 MB.

Depends (0)

none

Imports (7)

survivaldplyr ggplot2 Iso pbapply RColorBrewer scales

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 (4)

Jialu Fang

Author, Maintainer since 1.0.0 (2024)

Wenliang Wang

Author

Guosheng Yin

Author

Ninghao Zhang

Author · added in 2.0.0

Releases (9)

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
2.2.0Latest
record
2024-11-15 · current release · diff ↗ ·
added 1 export
pCFO.next
2.1.0
record
2024-10-16 · diff ↗ ·
added 3 exports
CFOeff.selectobd, gammatable, rCFO.next
2.0.0
record
2024-09-11 · diff ↗ ·
added 3 exports
CFOeff.next, CFOeff.oc, CFOeff.simu
1.3.1
record
2024-06-26 · diff ↗
1.3.0
record
2024-06-22 · diff ↗
1.2.1
record
2024-06-06 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1.1
record
2024-04-05 · diff ↗
1.1.0
record
2024-03-05 · diff ↗
1.0.0
record
2024-02-26
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-02-26
Total releases: 9 / 2 yrs
License: GPL-2 OSI
Download size: 67 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CFO")

Format

Fang, J., Wang, W., Yin, G., & Zhang, N. (2024). CFO: CFO-Type Designs in Phase I/II Clinical Trials (Version 2.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.CFO

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 CFO version 2.2.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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