Package: cholera 0.9.1.9122

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

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

Authors:lindbrook [aut, cre]

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manual.pdf |manual.html✨
card.svg |card.png
cholera/json (API)
NEWS

# Install 'cholera' in R:
install.packages('cholera', repos = c('https://lindbrook.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lindbrook/cholera/issues

Datasets:

On CRAN:

Conda:

choleradata-visualizationdatasetsepidemiologyjohn-snowpublic-healthtriangulation-delaunayvoronoivoronoi-polygons

9.17 score 140 stars 88 scripts 380 downloads 52 exports 82 dependencies

Last updated from:76540addb1. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK254
source / vignettesOK237
linux-release-x86_64OK256
macos-release-arm64OK129
macos-oldrel-arm64OK128
windows-develOK223
windows-releaseOK190
windows-oldrelOK197
wasm-releaseOK140

Exports:addCaseaddDelaunayaddEuclideanPathaddFrameaddIndexCaseaddKernelDensityaddLandmarksaddLandmarkSquaresaddNeighborhoodCasesaddNeighborhoodEuclideanaddNeighborhoodSnowaddNeighborhoodWalkingaddPlaguePitaddPumpaddRoadsaddVoronoiaddWalkingPathaddWhiteheadcaseLocatorclassifierAuditeuclideanPathisoVerticesmapRangeneighborhoodEuclideanneighborhoodSnowneighborhoodVoronoineighborhoodWalkingoxfordWeatherpearsonResidualsprofile2Dprofile3DpumpCasepumpDatapumpFatalitiespumpLocatorroadSegmentssegmentHighlightsegmentLocatorsimulateFatalitiessnowColorssnowMapsohoGraphstreetHighlightstreetLengthstreetNameLocatorstreetNamesstreetNumberLocatortanakaContourPlottimeSeriesunstackFatalitiesvoronoiPolygonswalkingPath

Dependencies:askpassbase64encbslibcachemclassclassIntclicodetoolscpp11crosstalkcurlDBIdeldirdigeste1071elevatrevaluatefastmapfontawesomeforeachfsfurrrfuturegeosphereglobalsgluehighrHistDatahtmltoolshtmlwidgetshttrigraphisobanditeratorsjquerylibjsonliteKernSmoothknitrlatticelazyevallifecyclelistenvmagrittrmapisomaplegendMASSMatrixmemoisemimeopensslparallellypkgconfigpngpracmaprogressrproxypurrrR6rappdirsrasterRColorBrewerRcpprlangrmarkdowns2sasssfshapeslippymathspsystanakaterrathreejstinytexTSPunitsvctrsviridisLitewkxfunyaml

"Unstacking" Bars

lindbrook

Rendered fromunstacking.bars.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2025-03-14
Started: 2018-01-18

Duplicate and Missing Cases

lindbrook

Rendered fromduplicate.missing.cases.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2025-03-14
Started: 2016-09-10

Kernel Density Plot

lindbrook

Rendered fromkernel.density.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2025-03-14
Started: 2018-03-05

Parallelization

lindbrook

Rendered fromparallelization.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2025-03-14
Started: 2019-08-27

Roads

lindbrook

Rendered fromroads.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2025-03-14
Started: 2016-09-10

Time Series

lindbrook

Rendered fromtime.series.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2025-03-14
Started: 2016-09-10

voronoiPolygons(): Tiles, Triangles and Polygons

lindbrook

Rendered fromtiles.polygons.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2025-03-14
Started: 2018-12-23

Readme and manuals

Help Manual

Help pageTopics
choleracholera-package cholera
Add observed case(s) to plot.addCase
Add Delaunay triangles.addDelaunay
Add Euclidean path from case/landmark to nearest or selected pump. (prototype)addEuclideanPath
Add map border to plot.addFrame
Highlight index case at 40 Broad Street.addIndexCase
Add 2D kernel density contours.addKernelDensity
Add landmarks to plot.addLandmarks
Add Golden and Soho Squares to plot.addLandmarkSquares
Add observed neighborhood cases.addNeighborhoodCases
Add expected Euclidean pump neighborhoods.addNeighborhoodEuclidean
Adds Snow's graphical annotation of the Broad Street pump walking neighborhood.addNeighborhoodSnow
Add walking neighborhoods.addNeighborhoodWalking
Add plague pit (Marshall Street).addPlaguePit
Add selected pump(s) to plot.addPump
Add all streets and roads to plot.addRoads
Add Voronoi cells.addVoronoi
Add walking path from case/landmark to nearest or selected pump. (prototype)addWalkingPath
Add Rev. Henry Whitehead's Broad Street pump neighborhood.addWhitehead
Anchor or base case of each stack of fatalities.anchor.case
Numeric IDs of line segments that create the map's border frame.border
Locate case by numerical ID.caseLocator
Test if case is orthogonal to segment.classifierAudit
Compute Euclidean path coordinates from observed case/landmark to nearest/selected pump.euclideanPath
Amended Dodson and Tobler's cholera data.fatalities
"Unstacked" fatalities data with "anchor" case as the unit of observation.fatalities.anchor
Amended fatalities data with all cases in a stack sharing the coordinates of the "anchor" case.fatalities.unstacked
Map frame data c("x", "y") and c("lon", "lat").frame.data
Partitioned map frame points (segment endpoints).frame.sample
Dodson and Tobler's "Map Frame" street data transformed into road segments.frame.segments
Isochrone and isodistance vertices (prototype)isoVertices
Centers of city squares.landmark.squares
Landmark coordinates.landmarks
Orthogonal projection of observed address (latlong) cases onto road network.latlong.ortho.anchor
Orthogonal projection of 13 original pumps (latlong).latlong.ortho.pump
Orthogonal projection of the 14 pumps from the Vestry Report (latlong).latlong.ortho.pump.vestry
"Expected" cases (latlong).latlong.regular.cases
Road "address" of simulated (i.e., "expected") cases (latlong).latlong.sim.ortho.proj
Compute xlim and ylim of Snow's map.mapRange
Meter to yard conversion factor.meter.to.yard
Compute Euclidean path pump neighborhoods.neighborhoodEuclidean
Compute Snow's graphical annotation of Broad Street pump neighborhood.neighborhoodSnow
Compute Voronoi pump neighborhoods.neighborhoodVoronoi
Compute walking path pump neighborhoods.neighborhoodWalking
Orthogonal projection of observed cases onto road network.ortho.proj
Orthogonal projection of 13 original pumps.ortho.proj.pump
Orthogonal projection of the 14 pumps from the Vestry Report.ortho.proj.pump.vestry
Oxford monthly weather data, January 1853 - December 2019.oxford.weather
Weather data recorded in Oxford (Met Office UK).oxfordWeather
Compute Pearson Residuals (prototype)pearsonResiduals
Plague pit coordinates.plague.pit
Plague pit coordinates.plague.pit.segments
Plot result of classifierAudit().plot.classifier_audit
Plot method for neighborhoodEuclidean().plot.euclidean
Plot the path of the Euclidean distance between cases and/or pumps.plot.euclidean_path
Plot method for euclideanLatlong()plot.euclideanLatlong
Plot method for isoVertices().plot.iso_vertices
Plot method for oxfordWeather().plot.oxfordWeather
Plot method for profilePerspective().plot.profile_perspective
Plot method for neighborhoodSnow().plot.snow
Plot method for sohoGraph().plot.soho_graph
Plot time series data, with date of removal of pump handle (Vestry report).plot.time_series
Plot method for voronoiLatlong()plot.voronoi_latlong
Plot Voronoi neighborhoods.plot.voronoi_nominal
Plot method for neighborhoodWalking().plot.walking
Plot the walking path between selected cases and/or pumps.plot.walking_path
Return result of classifierAudit().print.classifier_audit
Print method for neighborhoodEuclidean().print.euclidean
Print method for euclideanPath().print.euclidean_path
Print method for neighborhoodEuclidean(latlong = TRUE).print.euclideanLatlong
Print method for isoVertices().print.iso_vertices
Print method for neighborhoodSnow().print.snow
Print summary data for timeSeries().print.time_series
Print method for voronoiLatlong().print.voronoi_latlong
Print method for voronoiNominal().print.voronoi_nominal
Print method for neighborhoodWalking().print.walking
Print method for walkingPath().print.walking_path
2D Profile .profile2D
3D Profile.profile3D
Extract numeric case IDs by pump neighborhood.pumpCase
Compute pump coordinates.pumpData
Compute fatalities by pump.pumpFatalities
Locate water pump by numerical ID.pumpLocator
Dodson and Tobler's pump data with street name.pumps
Vestry report pump data.pumps.vestry
Sample of road intersections (segment endpoints).rd.sample
Rectangular filter data.rectangle.filter
"Expected" cases.regular.cases
Dodson and Tobler's street data transformed into road segments.road.segments
Dodson and Tobler's street data with appended road names.roads
Reshape 'roads' data frame into 'road.segments' data frame.roadSegments
Highlight segment by ID.segmentHighlight
Plot/Locate road segment by ID.segmentLocator
Road "address" of simulated (i.e., "expected") cases.sim.ortho.proj
List of "simulated" fatalities grouped by walking-distance pump neighborhood.sim.pump.case
Walking distance to Broad Street Pump (#7).sim.walking.distance
Project simulated fatalities onto road network.simulateFatalities
Snow neighborhood fatalities.snow.neighborhood
Create a set of colors for pump neighborhoods.snowColors
Plot John Snow's cholera map.snowMap
Compute network graph of roads and embed cases, landmarks and pumps (prototype).sohoGraph
Highlight road by name.streetHighlight
Compute length of selected street.streetLength
Locate street(s) by name(s).streetNameLocator
Street names (alphabetized).streetNames
Locate street by its numerical ID.streetNumberLocator
Summary method for neighborhoodEuclidean().summary.euclidean
Summary method for neighborhoodEuclidean(latlong = TRUE).summary.euclideanLatlong
Summary method for neighborhoodSnow().summary.snow
Summary method for voronoiNominal().summary.voronoi_nominal
Tanaka contour plot.tanakaContourPlot
John Snow and Committee data from Vestry report.timeSeries
Unstack "stacks" in Snow's cholera map.unstackFatalities
Coordinates of Voronoi polygon vertices for original map.voronoi.polygons
Coordinates of Voronoi polygon vertices for Vestry Report map.voronoi.polygons.vestry
Extract vertices of Delaunay triangles and Dirichelet (Voronoi) tiles.voronoiPolygons
Compute walking path from case/landmark to nearest or selected pump.walkingPath