R Observatory: Metrics for REffectivePred version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

REffectivePred

1.0.1Package record

Pandemic Prediction Model in an SIRS Framework

0packages depend

5.7Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Razvan RomanescuCRAN page ↗

A suite of methods to fit and predict case count data using a compartmental SIRS (Susceptible – Infectious – Recovered – Susceptible) model, based on an assumed specification of the effective reproduction number. The significance of this approach is that it relates epidemic progression to the average number of contacts of infected individuals, which decays as a function of the total susceptible fraction remaining in the population. The main functions are pred.curve(), which computes the epidemic curve for a set of parameters, and estimate.mle(), which finds the best fitting curve to observed data. The easiest way to pass arguments to the functions is via a config file, which contains input settings required for prediction, and the package offers two methods, navigate_to_config() which points the user to the configuration file, and re_predict() for starting the fit-predict process. The main model was published in Razvan G. Romanescu et al. doi:10.1016/j.epidem.2023.100708.

Install

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

install.packages("REffectivePred", 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-reffectivepred

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-REffectivePred

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-REffectivePred

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

2NOTE11OK

Check messages

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘re_predict.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 120.5 min · r-release-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-09-08
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-07
NOTE12 OK, 1 NOTE2026-07-11
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 16 (1 internal)
Examples that run: 100%4 run in a plain check
Exported functions with examples: 29%
Documented parameters: 92%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

5.7K

CRAN downloads in the past year

Rank #12,564 · ~16/day · ~475/mo

Releases R versions

Daily download trend is not available in this view yet.

29730 days

89190 days

5.7K1 year

Compare downloads with other packages →

Also on66 r2u2 autocran

How downloads are counted

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing REffectivePred adds 3 packages (2 with compiled code, 863 KB of source tarballs). Heaviest: zoo 675 KB, yaml 106 KB, config 82 KB.

Depends (0)

none

Imports (5)

yaml config zoogrDevicesutils

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 (4)

Razvan Romanescu

Author, Maintainer since 1.0.0 (2024)

Md Ashiqul Haque

Author

Songdi Hu

Author

Olivier Tremblay-Savard

Author

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
1.0.1Latest
record
2024-11-12 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.0
record
2024-02-02
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-02-02
Total releases: 2 / 2 yrs
License: GPL (>= 2) OSI
Download size: 35 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("REffectivePred")

Format

Romanescu, R., Haque, M. A., Hu, S., & Tremblay-Savard, O. (2024). REffectivePred: Pandemic Prediction Model in an SIRS Framework (Version 1.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.REffectivePred

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 REffectivePred version 1.0.1 [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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