R Observatory: Metrics for MicroMoB version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MicroMoB

0.1.2Package record

Discrete Time Simulation of Mosquito-Borne Pathogen Transmission

0packages depend

3.6Kdownloads / year

84.7%test coverage

13/13flavors OK

Overview

About

Maintained by Sean L. WuCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides a framework based on S3 dispatch for constructing models of mosquito-borne pathogen transmission which are constructed from submodels of various components (i.e. immature and adult mosquitoes, human populations). A consistent mathematical expression for the distribution of bites on hosts means that different models (stochastic, deterministic, etc.) can be coherently incorporated and updated over a discrete time step.

Changes in 0.1.2

skip plumber API tests on CRAN due to occasional failures out of developer

control.

From NEWS.md in the release

Install

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

install.packages("MicroMoB", 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("dd-harp/MicroMoB")

Development version from dd-harp/MicroMoB. 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-micromob

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-MicroMoB

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-MicroMoB

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: 10.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.2

READMEYes · 438 wordsVignettesYes · 9 · dynamicNEWSYes · 100% structured · mentions 0.1.2Citation fileNoWebsiteYes · pkgdown

Help pages: 146includes a package overview page
Examples that run: 100%11 run in a plain check
Exported functions with examples: 14%
Documented parameters: 100%
Return-value docs: 96%
Help pages citing references: 0%

Vignettes (9)

Micro-MoB (Microsimulation for mosquito-borne pathogens) HTML
Advanced topics HTML
Beverton-Holt aquatic model HTML
Blood feeding HTML
Contributing HTML
Queueing model for human superinfection HTML
Ross-Macdonald mosquito model HTML
Ross-Macdonald transmission model HTML
Simple behavioral state mosquito model HTML

How these are measured

Downloads

3.6K

CRAN downloads in the past year

Rank #12,967 · ~10/day · ~296/mo

Releases R versions

Daily download trend is not available in this view yet.

32230 days

87190 days

3.6K1 year

Compare downloads with other packages →

Also on376 r2u7 autocran

How downloads are counted

Repository

dd-harp/micromob ↗Organization: dd-harp

2Stars

0Forks

4Open issues

0Open PRs

6Releases

299Commits

2Commit identities

299 commits · Last activity 2024-05-31

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2022-03-03 · 12026-07-07 · 2

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/dd-harp/micromob on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (1)

Code of conduct

Docs source (3)

pkgdown

GitHub Pages site last deployed 2024-05-31 · The repository has a site deploy workflow

pkgdown site last built 2024-05-31

Coverage (2)

Coverage reporting.covrignore

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing MicroMoB adds 2 packages (1 with compiled code, 1.0 MB of source tarballs). Heaviest: jsonlite 1.0 MB, abind 21 KB.

Depends (0)

none

Imports (2)

abind jsonlite

LinkingTo (0)

none

Suggests (10)

knitr rmarkdown testthat ggplot2 data.table callr httr readr withr plumber

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (3)

Sean L. Wu

Author, Maintainer since 0.0.9 (2022)

David L. Smith

Author

Sophie Libkind

Contributor

Releases (5)

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
0.1.2Latest
record
2023-01-17 · current release · diff ↗ ·
added 22 exports
get_K_aqua_BH, get_eip_mosquito_RM, get_f_mosquito_RM, get_kappa_mosquito_RM, get_lambda_aqua_trace, get_molt_aqua_BH, get_nu_mosquito_RM, get_p_mosquito_RM, get_psi_mosquito_RM, get_q_mosquito_RM, get_surv_aqua_BH, set_K_aqua_BH, set_eip_mosquito_RM, set_f_mosquito_RM, set_kappa_mosquito_RM, set_lambda_aqua_trace, set_molt_aqua_BH, set_nu_mosquito_RM, set_p_mosquito_RM, set_psi_mosquito_RM, set_q_mosquito_RM, set_surv_aqua_BH
0.1.0
record
2022-07-01 · diff ↗ ·
added 6 exports
api_config_global, compute_bloodmeal_simple, get_tmax, get_tnow, observe_pfpr, setup_humans_SIP
R
R 4.2.0 released · 2022-04-22
0.0.12
record
2022-03-17 · diff ↗
0.0.11
record
2022-03-09 · diff ↗ ·
added 12 exports
get_config_alternative_trace, get_config_aqua_BH, get_config_aqua_trace, get_config_humans_MOI, get_config_humans_SIR, get_config_humans_SIS, get_config_mosquito_RM, get_config_mosquito_trace, get_config_visitor_trace, output_aqua, output_mosquitoes, setup_mosquito_BQ
0.0.9
record
2022-02-01
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-02-01
Total releases: 5 / 4 yrs
License: MIT + file LICENSE OSI
Download size: 4.6 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MicroMoB")

Format

Wu, S. L., Libkind, S., & Smith, D. L. (2023). MicroMoB: Discrete Time Simulation of Mosquito-Borne Pathogen Transmission (Version 0.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.MicroMoB

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 MicroMoB version 0.1.2 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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