R Observatory: Metrics for PredictABEL version 1.2-4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PredictABEL

1.2-4Package record

Assessment of Risk Prediction Models

0packages depend

13.3Kdownloads / year

–test coverage

9/13flavors OK

Overview

About

Maintained by Suman KunduCRAN page ↗

We included functions to assess the performance of risk models. The package contains functions for the various measures that are used in empirical studies, including univariate and multivariate odds ratios (OR) of the predictors, the c-statistic (or area under the receiver operating characteristic (ROC) curve (AUC)), Hosmer-Lemeshow goodness of fit test, reclassification table, net reclassification improvement (NRI) and integrated discrimination improvement (IDI). Also included are functions to create plots, such as risk distributions, ROC curves, calibration plot, discrimination box plot and predictiveness curves. In addition to functions to assess the performance of risk models, the package includes functions to obtain weighted and unweighted risk scores as well as predicted risks using logistic regression analysis. These logistic regression functions are specifically written for models that include genetic variables, but they can also be applied to models that are based on non-genetic risk factors only. Finally, the package includes function to construct a simulated dataset with genotypes, genetic risks, and disease status for a hypothetical population, which is used for the evaluation of genetic risk models.

Install

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

install.packages("PredictABEL", 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-predictabel

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-PredictABEL

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-PredictABEL

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

4NOTE9OK

Check messages

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

Maintainer: ‘Suman Kundu <suman_math@yahoo.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Suman",
                      family = "Kundu",
                      role = c("aut", "cre"),
                      email = "suman_math@yahoo.com"),
               person(given = c("Yurii", "S."),
                      family = "Aulchenko",
                      role = "aut"),
               person(given = c("A.", "Cecile", "J.W."),
                      family = "Janssens",
                      role = "aut"))
as necessary.

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespace in Imports field not imported from:
  ‘lazyeval’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 2.3 min · r-oldrel-windows-x86_64

Status changes

NOTE9 OK, 4 NOTE2026-06-09
ERROR9 OK, 3 NOTE, 1 ERROR2026-06-08
NOTE10 OK, 4 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2-4

READMENoVignettesNoNEWSYes · 100% structuredCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 16includes a package overview page
Examples that run: 100%15 run in a plain check
Exported functions with examples: 93%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 56%

How these are measured

Downloads

13.3K

CRAN downloads in the past year

Rank #3,674 · ~36/day · ~1.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

86930 days

2.7K90 days

13.3K1 year

Compare downloads with other packages →

Also on72 r2u2 autocran

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing PredictABEL adds 59 packages (32 with compiled code, 61 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 2.12.0

Imports (5)

Hmisc ROCR PBSmodelling lazyevalmethods

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

Datasets

People & History

People (from the free-text Author field) (3)

Suman Kundu

Yurii S. Aulchenko

A. Cecile J.W. Janssens

Maintainer since 1.1 (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
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
1.2-4Latest
record
2020-03-09 · current release · diff ↗
unarchivedReturned to CRAN
2020-02-25
1.2-3
record
2020-02-25 · diff ↗
archivedRemoved from CRAN
2020-02-19
check problems were not corrected despite reminders
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
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16

Show 10 earlier eventsHide 10 earlier events

1.2-2
record
2014-12-21 · diff ↗
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
1.2-1
record
2012-07-27 · diff ↗ ·
added 1 export
pattern:.
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
1.2
record
2011-10-19 · diff ↗
R
R 2.13.0 released · 2011-04-13
1.1
record
2011-02-10
R
R 2.12.0 released · 2010-10-15

Package metadata

First published: 2011-02-10
Total releases: 6 / 15 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.12.0
Bundled data: 96 KB / 1 file
Download size: 83 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PredictABEL")

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 PredictABEL version 1.2-4 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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