R Observatory: Metrics for CIfinder version 2.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CIfinder

2.0.0

Estimate the Confidence Intervals for Predictive Values

0packages depend

2.4Kdownloads / year

24.3%test coverage

11/13checks pass

Overview

About

Maintained by Dadong ZhangFirst published 2023-06-154 releasesCRAN page ↗

Computes confidence intervals for the positive predictive value (PPV) and negative predictive value (NPV) based on varied scenarios. In situations where the proportion of diseased subjects does not correspond to the disease prevalence (e.g. case-control studies), this package provides two types of solutions: 1) five methods for estimating confidence intervals for PPV and NPV via ratio of two binomial proportions including Gart & Nam (1988), Walter (1975), MOVER-J (Laud, 2017), Fieller (1954), and Bootstrap (Efron, 1979); 2) three direct methods that compute the confidence intervals including Pepe (2003), Zhou (2007), and Delta. In prospective studies where the proportion of diseased subjects is an unbiased estimate of the disease prevalence, this package provides several methods for calculating the confidence intervals for PPV and NPV including Clopper-Pearson, Wald, Wilson, Agresti-Coull, and Beta. See the Details and References sections in the corresponding functions.

Install

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

install.packages("CIfinder", 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-cifinder

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-CIfinder

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-CIfinder

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 1.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.03

24.3%

Coverage · measured lines

100%

Documentation · exports

5

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 604 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 50%

Downloads

2.4K

CRAN downloads in the past year

Rank #18,332 · ~7/day · ~202/mo

Releases R versions

Daily download trend is not available in this view yet.

16730 days

59790 days

2.4K1 year

Compare downloads with other packages →

Also on114 r2u8 autocran

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (5)

ratescistatsbootRdpack kableExtra

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (5)

Dadong Zhang Jingye Wang <jwang16@illumina.com> Johan Surtihadi <jsurtihadi@illumina.com>

no longer listed · 1.0.0

Johan Surtihadi

no longer listed · 1.0.1 to 2.0.0

Jingye Wang

no longer listed · 1.0.1 to 2.0.0

Dadong Zhang

no longer listed · 1.0.1 to 2.0.0

Suqin Cai

no longer listed · 2.0.0

Package Timeline

4 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
2.0.0Latest
2024-04-12 · current release · diff ↗
1.0.2
2023-10-30 · diff ↗
1.0.1
2023-08-16 · diff ↗
1.0.0
2023-06-15
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-06-15
Total releases: 4 / 3 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.6.0
Download size: 78 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CIfinder")

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 CIfinder version 2.0.0 [Data set]. HJJB, LLC. Data release v2026-08-11. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-11, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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