R Observatory: Metrics for EmpiricalCalibration version 3.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

EmpiricalCalibration

3.1.4Package record

Routines for Performing Empirical Calibration of Observational Study Estimates

6packages depend

11.4Kdownloads / year

84.6%test coverage

13/13flavors OK

Overview

About

Maintained by Martijn SchuemieCRAN page ↗GitHub ↗Website ↗Issues ↗

Routines for performing empirical calibration of observational study estimates. By using a set of negative control hypotheses we can estimate the empirical null distribution of a particular observational study setup. This empirical null distribution can be used to compute a calibrated p-value, which reflects the probability of observing an estimated effect size when the null hypothesis is true taking both random and systematic error into account. A similar approach can be used to calibrate confidence intervals, using both negative and positive controls. For more details, see Schuemie et al. (2013) doi:10.1002/sim.5925 and Schuemie et al. (2018) doi:10.1073/pnas.1708282114.

Changes in 3.1.4

Changes

1. Removing extreme estimates (relative risk < 0.01 or relative risk > 100) before fitting null distribution.

Bugfixes

1. Changed initial parameter values when fitting null distribution using asymptotics and MCMC, avoid errors in some edge cases.

From NEWS.md in the release

Install

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

install.packages("EmpiricalCalibration", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("OHDSI/EmpiricalCalibration")

Development version from OHDSI/EmpiricalCalibration. Installs pak first if it is not already available.

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-empiricalcalibration

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-EmpiricalCalibration

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-EmpiricalCalibration

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: 9.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
ERROR13 OK, 1 ERROR2026-03-30
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.1.4

READMEYes · 380 wordsVignettesYes · 3 · dynamicNEWSYes · 0% structured · mentions 3.1.4Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 34 (1 internal)includes a package overview page
Examples that run: 82%23 run in a plain check · 5 never run
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 93%
Help pages citing references: 21%

Vignettes (3)

How these are measured

Downloads

11.4K

CRAN downloads in the past year

Rank #3,700 · ~31/day · ~953/mo

Releases R versions

Daily download trend is not available in this view yet.

97630 days

2.7K90 days

11.4K1 year

Compare downloads with other packages →

Also on479 r2u5 autocran85 c2d4u

How downloads are counted

Repository

ohdsi/empiricalcalibration ↗Organization: OHDSI

10Stars

9Forks

3Open issues

0Open PRs

7Releases

270Commits

12Commit identities

hades

270 commits · Last activity 2025-02-14

Responsiveness

How these are sampled

PRs merged (all time): 80%
Median days to close, 50 most recently updated closed issues: 90
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2023-03-08 · 102026-07-07 · 10

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/ohdsi/empiricalcalibration on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Governance and community (1)

PR template

Docs source (2)

pkgdown

GitHub Pages site last deployed 2025-02-14

Coverage (1)

Coverage reporting

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing EmpiricalCalibration adds 19 packages (8 with compiled code, 16 MB of source tarballs). Heaviest: ggplot2 6.0 MB, Rcpp 1.8 MB, isoband 1.5 MB.

Depends (1)

R >= 3.5.0

Imports (5)

ggplot2 gridExtramethodsrlang Rcpp

LinkingTo (1)

Rcpp

Suggests (7)

knitr markdown rmarkdown testthat CyclopssurvivalSequential

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

6direct

0indirect

Imports 6

Depends, Imports or LinkingTo, most downloaded first

EvidenceSynthesis CohortMethod SelfControlledCaseSeries pda SelfControlledCohort debiasedTrialEmulation

How these are counted

Code & Tests

Datasets

People & History

People (2)

Martijn Schuemie

Author, Maintainer since 1.1.0 (2016)

Marc Suchard

Author

Releases (15)

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
3.1.4Latest
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2025-02-14 · current release · diff ↗
3.1.3
record
2024-09-30 · diff ↗
R
R 4.4.0 released · 2024-04-24
3.1.2
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2023-12-21 · diff ↗
R
R 4.3.0 released · 2023-04-21
3.1.1
record
2022-08-09 · diff ↗
3.1.0
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2022-07-01 · diff ↗ ·
added 2 exports
compareEase, computeCvPoissonRegression
R
R 4.2.0 released · 2022-04-22
3.0.0
record
2021-09-28 · diff ↗ ·
added 5 exports
calibrateLlr, computeCvBinomial, computeCvPoisson, fitNullNonNormalLl, simulateMaxSprtData
R
R 4.1.0 released · 2021-05-18
2.1.0
record
2021-03-04 · diff ↗ ·
added 1 export
computeExpectedAbsoluteSystematicError
R
R 4.0.0 released · 2020-04-24
2.0.2
record
2020-04-07 · diff ↗
2.0.1
record
2020-01-13 · diff ↗

Show 11 earlier eventsHide 11 earlier events

2.0.0
record
2019-07-08 · diff ↗ ·
added 1 export
convertNullToErrorModel
R
R 3.6.0 released · 2019-04-26
1.4.0
record
2018-11-24 · diff ↗ ·
added 1 export
plotCiCalibrationEffect
R
R 3.5.0 released · 2018-04-23
1.3.6
record
2017-11-07 · diff ↗ ·
added 1 export
plotExpectedType1Error
1.3.1
record
2017-05-16 · diff ↗ ·
added 4 exports
computeTraditionalCi, evaluateCiCalibration, plotCiCoverage, plotErrorModel
R
R 3.4.0 released · 2017-04-21
1.2.0
record
2016-08-16 · diff ↗ ·
removed 1 export
plotCoverage

added 1 export
plotCiCalibration
R
R 3.3.0 released · 2016-05-03
1.1.0
record
2016-02-15
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-02-15
Total releases: 15 / 10 yrs
License: Apache License 2.0 OSI
Minimum R: ≥ 3.5.0
Bundled data: 13 KB / 5 files
Download size: 1.4 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("EmpiricalCalibration")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1002/sim.5925, 10.1073/pnas.1708282114.

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 EmpiricalCalibration version 3.1.4 [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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