fastbeta

0.5.1

Fast Approximation of Time-Varying Infectious Disease Transmission Rates

0packages depend

2.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Mikael JaganFirst published 2023-08-289 releasesCRAN page ↗GitHub ↗

A fast method for approximating time-varying infectious disease transmission rates from disease incidence time series and other data, based on a discrete time approximation of an SEIR model, as analyzed in Jagan et al. (2020) doi:10.1371/journal.pcbi.1008124.

Install

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

install.packages("fastbeta", 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("davidearn/fastbeta")

Development version from davidearn/fastbeta. 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-fastbeta

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-fastbeta

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-fastbeta

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

Health

CRAN checks

13OK

Slowest check: 2.6 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.15

not tracked

Coverage

100%

Documentation · exports

None

Vignettes

README

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

2.5K

CRAN downloads in the past year

Rank #18,103 · ~7/day · ~208/mo

Releases R versions

Daily download trend is not available in this view yet.

29330 days

64790 days

2.5K1 year

Compare downloads with other packages →

Also on438 r2u20 autocran

Repository

GitHub ↗ davidearn/fastbeta

1Stars

0Forks

0Open issues

0Open PRs

0Releases

411Commits

411 commits · 0% stars, 30d

Stars over time

2025-08-26 · 12026-07-07 · 1

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.3

Imports (3)

grDevicesgraphicsstats

LinkingTo (0)

none

Suggests (4)

adaptivetau deSolvetoolsutils

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

Rd 1,566 (43%)R 1,381 (38%)C 671 (19%)

Code characteristics

Object systems

S32

Cyclomatic complexity: 11.0 median / 46 max
Documented parameters: 59%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

31 12 exported

Complexity

13.8 avg / 46 max

Call network

31 nodes / 17 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (2)

Maintainer (1)

Mikael Jagan

Author, Maintainer

Authors (1)

Mikael Jagan

Author, Maintainer

Contributors (1)

David Earn

Contributor

Release timeline

9 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.5.1Latest
2025-10-26 · current release · diff ↗
0.5.0
2025-10-15 · diff ↗
0.4.0
2025-04-28 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.3.2
2025-03-24 · diff ↗
0.3.1
2024-11-22 · diff ↗
0.3.0
2024-05-18 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.2.0
2023-12-12 · diff ↗
0.1.1
2023-11-28 · diff ↗
0.1.0
2023-08-28
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-08-28
Total releases: 9 / 3 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.3
Bundled data: 56 KB / 5 files
Download size: 104 KB
Installed size: not tracked yet
With dependencies: not tracked yet