R Observatory: Metrics for cholera version 0.9.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

cholera

0.9.1Package record

Amend, Augment and Aid Analysis of John Snow's Cholera Map

0packages depend

4.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Peter LiCRAN page ↗GitHub ↗Issues ↗

Amends errors, augments data and aids analysis of John Snow's map of the 1854 London cholera outbreak.

Changes in 0.9.1

Georeferenced Data and Functions

provisional support for (georeferenced) longitude and latitude for data and functions (for functions, set latlong = TRUE).

Data Changes

add longitude and latitude to plague.pit data.
add frame.segments
amend road.segments with latlong data.
use amended road.segments (w/ latlong) in various functions.

Documentation Changes

restore .jpg and .png to README.
restore NEWS.md to source file and amend markdown.

Function Changes

Show all changes in 0.9.1Hide the rest of the changes in 0.9.1

rename neighborhoodData() to sohoGraph().
add/set drop.isolates = FALSE in embedNodes() and neighborhoodData().
add latlongPlaguePit() and plaguePitPDF().
add/set addPlaguePit(latlong = FALSE).
add rotatePoint(dataset = "plague.pit").
vectorize addFrame(), addRoads() and landmarkPerimeter().
add/set embedNodes(drop.isolates = TRUE).
export isoVertices().
add/set plot.iso_vertices(add = FALSE).
rename isoLines() to isoPoints() and add/set isoPoints(add = FALSE).
amend/simplify latlongOrthoAddress().
archive latlongEmbed().
rename squareCenter() in addLandmarks() to squareCenterB().
amend pump 2 (Adam and Eve) warnings in casePump() and pumpPump().

Function Fixes

correct class for sohoGraph() output.
use cholera::roads$id rather than indices to fix latlongFrame().
add variable check to latlongLandmarks() and landmarksPDF().
fix typo in name of quadrantCoordinates().
fix/amend pump 2 (Adam and Eve) warnings in casePump() and pumpPump().

From NEWS.md in the release

Install

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

install.packages("cholera", 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("lindbrook/cholera")

Development version from lindbrook/cholera. 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-cholera

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-cholera

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-cholera

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: 6.9 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 0.9.1

READMEYes · 1,595 wordsVignettesYes · 7 · staticNEWSYes · 100% structured · mentions 0.9.1Citation fileNo

Help pages: 106includes a package overview page
Examples that run: 45%17 run in a plain check · 21 never run
Exported functions with examples: 61%
Documented parameters: 100%
Return-value docs: 59%
Help pages citing references: 0%

Vignettes (7)

"Unstacking" Bars HTML
Duplicate and Missing Cases HTML
Kernel Density Plot HTML
Parallelization HTML
Roads HTML
Time Series HTML
voronoiPolygons(): Tiles, Triangles and Polygons HTML

How these are measured

Downloads

4.9K

CRAN downloads in the past year

Rank #6,495 · ~13/day · ~409/mo

Releases R versions

Daily download trend is not available in this view yet.

48230 days

1.3K90 days

4.9K1 year

Compare downloads with other packages →

Also on222 r2u13 autocran55 c2d4u

How downloads are counted

Repository

lindbrook/cholera ↗Account: lindbrook

142Stars

16Forks

0Open issues

0Open PRs

13Releases

5,271Commits

1Commit identities

rcholerajohn-snowpublic-healthepidemiologydata-visualizationdatasetsvoronoi

5,271 commits · Last activity 2026-10-21 · +0.7% stars, 30d · Default branch at 0.9.1.9182, ahead of CRAN 0.9.1 (checked 2026-10-21) · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 15
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-05 · 1362026-10-24 · 142

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/lindbrook/cholera on 2026-10-21.

Governance and community (1)

Contributing guide

Docs source (2)

README.Rmd

GitHub Pages site last deployed 2019-01-05

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing cholera adds 75 packages (41 with compiled code, 72 MB of source tarballs). Heaviest: sf 9.3 MB, HistData 8.8 MB, bslib 5.6 MB.

Depends (1)

R >= 3.5

Imports (16)

curl deldir elevatr geosphere HistData (>= 0.7-8)igraphKernSmoothpracma RColorBrewer rlang sp tanaka terra threejs TSP viridisLite

LinkingTo (0)

none

Suggests (3)

ggplot2 knitr rmarkdown

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 (1)

Peter Li

Author, Maintainer since 0.2.1 (2017)

Releases (13)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.9.1Latest
record
2025-05-01 · current release · diff ↗ ·
removed 1 export
neighborhoodData

added 2 exports
isoVertices, sohoGraph
R
R 4.5.0 released · 2025-04-11
0.9.0
record
2025-03-14 · diff ↗ ·
removed 28 exports
addFrame, addMilePosts, addSnow, caseDistance, fixFatalities, isoLines, landmarkData, latlongAddress, latlongFatalities, latlongLandmarks, latlongNearestPump, latlongNeighborhoodData, latlongNeighborhoodVoronoi, latlongNeighborhoodWalking, latlongPumps, latlongRoads, latlongVoronoi, latlongWalkingPath, nearestPump, oxfordWeather, povertyLondon, roadSegmentFix, segmentLength, simulateWalkingDistance, snowNeighborhood, subsetRoadsSamples, unitMeter, winterTemperatures

added 5 exports
addLandmarkSquares, addNeighborhoodSnow, neighborhoodSnow, pearsonResiduals, tanakaContourPlot
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.8.0
record
2023-03-01 · diff ↗ ·
removed 6 exports
classifierAudit, distanceTime, isoVertices, orthogonalProjection, pearsonResiduals, withinRadius

added 14 exports
caseDistance, latlongAddress, latlongFatalities, latlongLandmarks, latlongNearestPump, latlongNeighborhoodData, latlongNeighborhoodVoronoi, latlongNeighborhoodWalking, latlongPumps, latlongRoads, latlongVoronoi, latlongWalkingPath, pumpFatalities, roadSegmentFix
R
R 4.2.0 released · 2022-04-22
0.7.9
record
2021-10-11 · diff ↗ ·
removed 1 export
addDelauny

added 3 exports
addDelaunay, streetNames, subsetRoadsSamples
R
R 4.1.0 released · 2021-05-18
0.7.5
record
2021-04-22 · diff ↗ ·
added 6 exports
isoLines, isoVertices, oxfordWeather, povertyLondon, segmentHighlight, winterTemperatures
R
R 4.0.0 released · 2020-04-24
0.7.0
record
2019-08-28 · diff ↗ ·
removed 1 export
simWalkingDistance

added 2 exports
simulateWalkingDistance, withinRadius
0.6.5
record
2019-06-11 · diff ↗ ·
removed 1 export
deldirVertices

added 2 exports
simWalkingDistance, voronoiPolygons
R
R 3.6.0 released · 2019-04-26
0.6.0
record
2019-03-08 · diff ↗ ·
removed 5 exports
addBorder, addCases, addNeighborhood, euclideanDistance, walkingDistance

added 13 exports
addCase, addDelauny, addFrame, addNeighborhoodCases, addNeighborhoodEuclidean, addNeighborhoodWalking, deldirVertices, landmarkData, orthogonalProjection, pearsonResiduals, profile2D, profile3D, streetHighlight

Show 7 earlier eventsHide 7 earlier events

0.5.1
record
2018-08-15 · diff ↗ ·
added 3 exports
addBorder, addRoads, mapRange
0.5.0
record
2018-07-16 · diff ↗ ·
added 8 exports
addCases, addEuclideanPath, addMilePosts, addWalkingPath, distanceTime, euclideanPath, neighborhoodEuclidean, walkingPath
R
R 3.5.0 released · 2018-04-23
0.4.0
record
2018-04-01 · diff ↗ ·
removed 2 exports
nearestPath, nodeData

added 3 exports
addNeighborhood, addPump, neighborhoodData
0.3.0
record
2018-01-26 · diff ↗ ·
removed 1 export
walkingPath

added 10 exports
addIndexCase, classifierAudit, euclideanDistance, nearestPath, nearestPump, nodeData, segmentLength, snowNeighborhood, streetLength, unitMeter
0.2.1
record
2017-08-10
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-08-10
Total releases: 13 / 9 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5
Bundled data: 1.8 MB / 33 files
Download size: 3.9 MB

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("cholera")

Format

Peter Li. (2025). cholera: Amend, Augment and Aid Analysis of John Snow's Cholera Map (Version 0.9.1) [Computer software]. https://doi.org/10.32614/CRAN.package.cholera

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 cholera version 0.9.1 [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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