R Observatory: Metrics for epiCo version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

epiCo

1.0.1Package record

Statistical and Viz Tools for Vector-Borne Diseases in Colombia

0packages depend

2.8Kdownloads / year

92.1%test coverage

13/13flavors OK

Overview

About

Maintained by Juan D. UmañaCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides statistical and visualization tools for the analysis of demographic indicators, and spatio-temporal behavior and characterization of outbreaks of vector-borne diseases (VBDs) in Colombia. It implements travel times estimated in Bravo-Vega C., Santos-Vega M., & Cordovez J.M. (2022), and the endemic channel method (Bortman, M. (1999) https://iris.paho.org/handle/10665.2/8562).

Changes in 1.0.1

Break changes

epiCo now displays the plots in English or Spanish automatically according to the local system configuration

New features

endemic_channel plot can display less than 52 current observations
age_risk now accepts ages over 100 years old

Internal changes

Replace RColorBrewer by base R equivalent
Deleted unexpected errors from tests
Add geometric_sd tests
expect_message() display an error when there are unused arguments

Minor changes

Fix misleading error message in geometric_mean function

Show all changes in 1.0.1Hide the rest of the changes in 1.0.1

Documentation

CRAN Installation instructions
DOI information
Fix color specification in Endemic Channel vignette

Bug fixes

endemic_channel function now accepts the input of NULL or NA values
Fix bug on ‘weighted’ method in geometric_mean function
Fix bug on ‘positive’ method in geometric_mean function
Fix bug on ‘positive’ method in geometric_sd function

From NEWS.md in the release

Install

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

install.packages("epiCo", 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("epiverse-trace/epiCo")

Development version from epiverse-trace/epiCo. 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-epico

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-epiCo

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-epiCo

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: 3.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMEYes · 550 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 1.0.1Citation fileNoWebsiteYes · pkgdown

Help pages: 22 (8 internal)includes a package overview page
Examples that run: 100%11 run in a plain check
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #13,074 · ~8/day · ~235/mo

Releases R versions

Daily download trend is not available in this view yet.

38330 days

86490 days

2.8K1 year

Compare downloads with other packages →

Also on129 r2u8 autocran

How downloads are counted

Repository

epiverse-trace/epico ↗Organization: epiverse-trace

12Stars

1Forks

7Open issues

3Open PRs

2Releases

250Commits

6Commit identities

rdemographicsr-packagespatio-temporal-analysisdecision-supportoutbreak-analysiscolombiavector-borne-diseases

250 commits · Last activity 2025-04-29 · 0% stars, 30d · Default branch at 1.0.1.9000, ahead of CRAN 1.0.1 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 89%
Median days to close, 50 most recently updated closed issues: 33
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-07-01 · 132026-08-11 · 12

How these are measured

PracticesBeta

15 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/epiverse-trace/epico on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (4)

Code of conduct (inherited from epiverse-trace)Contributing guide (inherited from epiverse-trace)Issue templatesPR template

Docs source (3)

pkgdown

GitHub Pages site last deployed 2025-01-08 · The repository has a site deploy workflow

pkgdown site last built 2025-01-08, before release 1.0.1 (2025-01-15)

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 3 practices

CRAN release process (1)

cran-comments.md

Research and citation (1)

CITATION.cff

Lint, format, editor (3)

lintrLint workflowRStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing epiCo adds 97 packages (59 with compiled code, 104 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.0.0

Imports (15)

dplyr ggplot2 ggraphgrDevicesigraph incidence leaflet lubridate magrittr rlang scales spdepstatstreemapifyutils

LinkingTo (0)

none

Suggests (6)

checkmate covr knitr rmarkdown spelling testthat (>= 3.0.0)

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)

Juan D. Umaña

Juan Montenegro-Torres

Author

Julian Otero

Author

Hugo Gruson

Contributor

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
unarchivedReturned to CRAN
2025-01-15
1.0.1Latest
record
2025-01-15 · current release · diff ↗
archivedRemoved from CRAN
2025-01-10
issues were not corrected in time
1.0.0
record
2024-06-28
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-06-28
Total releases: 2 / 2 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Bundled data: 408 KB / 3 files
Download size: 3.8 MB

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("epiCo")

Format

Umaña, J. D., Gruson, H., Montenegro-Torres, J., & Otero, J. (2025). epiCo: Statistical and Viz Tools for Vector-Borne Diseases in Colombia (Version 1.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.epiCo

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

The repository also keeps a CITATION.cff.

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 epiCo version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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