Package: cholera 0.8.0.9486

lindbrook

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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cholera.pdf |cholera.html✨
cholera/json (API)

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

Peer review:

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

Datasets:

On CRAN:

choleradata-visualizationdatasetsepidemiologyjohn-snowpublic-healthtriangulation-delaunayvoronoivoronoi-polygons

9.32 score 135 stars 95 scripts 395 downloads 60 exports 81 dependencies

Last updated 3 hours agofrom:0b658c6db2. Checks:OK: 1 NOTE: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 26 2024
R-4.5-winNOTENov 26 2024
R-4.5-linuxNOTENov 26 2024
R-4.4-winNOTENov 26 2024
R-4.4-macNOTENov 26 2024
R-4.3-winNOTENov 26 2024
R-4.3-macNOTENov 26 2024

Exports:addCaseaddDelaunayaddEuclideanPathaddFrameaddIndexCaseaddKernelDensityaddLandmarksaddLandmarkSquaresaddMilePostsaddNeighborhoodCasesaddNeighborhoodEuclideanaddNeighborhoodWalkingaddPlaguePitaddPumpaddRoadsaddSnowaddVoronoiaddWalkingPathaddWhiteheadcaseDistancecaseLocatoreuclideanPathfixFatalitieslandmarkDatamapRangenearestPumpneighborhoodDataneighborhoodDataBneighborhoodEuclideanneighborhoodVoronoineighborhoodWalkingoxfordWeatherpearsonResidualspovertyLondonprofile2Dprofile3DpumpCasepumpDatapumpFatalitiespumpLocatorroadSegmentssegmentHighlightsegmentLengthsegmentLocatorsimulateFatalitiessnowColorssnowMapsnowNeighborhoodstreetHighlightstreetLengthstreetNameLocatorstreetNamesstreetNumberLocatortanakaContourPlottimeSeriesunstackFatalitiesvoronoiPolygonswalkingBwalkingPathwinterTemperatures

Dependencies:askpassbase64encbslibcachemclassclassIntclicodetoolscpp11crosstalkcurlDBIdeldirdigeste1071elevatrevaluatefastmapfontawesomeforeachfsfurrrfuturegeosphereglobalsgluehighrHistDatahtmltoolshtmlwidgetshttrigraphisobanditeratorsjquerylibjsonliteKernSmoothknitrlatticelazyevallifecyclelistenvmagrittrmapisomaplegendMASSMatrixmemoisemimeopensslparallellypkgconfigpngpracmaprogressrproxypurrrR6rappdirsrasterRColorBrewerRcpprlangrmarkdowns2sasssfslippymathspsystanakaterrathreejstinytexTSPunitsvctrsviridisLitewkxfunyaml

"Unstacking" Bars

lindbrook

Rendered fromunstacking.bars.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2024-03-31
Started: 2018-01-18

Duplicate and Missing Cases

lindbrook

Rendered fromduplicate.missing.cases.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2024-03-31
Started: 2016-09-10

Kernel Density Plot

lindbrook

Rendered fromkernel.density.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2024-09-27
Started: 2018-03-05

Parallelization

lindbrook

Rendered fromparallelization.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2021-04-21
Started: 2019-08-27

Roads

lindbrook

Rendered fromroads.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2024-03-31
Started: 2016-09-10

Time Series

lindbrook

Rendered fromtime.series.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2019-02-10
Started: 2016-09-10

voronoiPolygons(): Tiles, Triangles and Polygons

lindbrook

Rendered fromtiles.polygons.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2021-10-08
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 distance or time based "mileposts" to an observed walking neighborhood plot.addMilePosts
Add observed neighborhood cases.addNeighborhoodCases
Add expected Euclidean pump neighborhoods.addNeighborhoodEuclidean
Add expected walking neighborhoods.addNeighborhoodWalking
Add plague pit (Marshall Street).addPlaguePit
Add selected pump(s) to plot.addPump
Add all streets and roads to plot.addRoads
Adds Snow's graphical annotation of the Broad Street pump walking neighborhood.addSnow
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
Compute distance between case fatalities (meters).caseDistance
Locate case by numerical ID.caseLocator
Compute Euclidean path coordinates from observed case/landmark to nearest/selected pump.euclideanPath
Amended Dodson and Tobler's cholera data.fatalities
"Unstacked" amended cholera data with address as unit of observation.fatalities.address
"Unstacked" amended cholera fatalities data with fatality as unit of observation.fatalities.unstacked
Fix errors in Dodson and Tobler's digitization of Snow's map.fixFatalities
Map frame data c("x", "y") and c("lon", "lat").frame.data
Partitioned map frame points (segment endpoints).frame.sample
Centers of city squares.landmark.squares
Centers of city squares.landmark.squaresB
Landmark data.landmarkData
Orthogonal projection of landmarks onto road network.landmarks
Landmark coordinates.landmarksB
Orthogonal projection of observed address (latlong) cases onto road network.latlong.ortho.addr
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
Compute shortest distances to selected pumps.nearestPump
Compute network graph of roads, cases and pumps.neighborhoodData
Compute network graph of roads, cases and pumps (prototype).neighborhoodDataB
Compute Euclidean path pump neighborhoods.neighborhoodEuclidean
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 - February 2024.oxford.weather
Weather data recorded in Oxford (Met Office UK).oxfordWeather
Compute Pearson Residuals (prototype)pearsonResiduals
Plague pit coordinates.plague.pit
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 neighborhoodData().plot.neighborhood_data
Plot method for oxfordWeather().plot.oxfordWeather
Plot method for povertyLondon().plot.povertyLondon
Plot method for profilePerspective().plot.profile_perspective
Plot aggregate time series data from Vestry report.plot.time_series
Plot Voronoi neighborhoods.plot.voronoi
Plot method for voronoiLatlong()plot.voronoiLatlong
Plot method for walkingNominal().plot.walking
Plot the walking path between selected cases and/or pumps.plot.walking_path
Plot method for walkingB().plot.walkingB
Plot method for walkingLatlong().plot.walkingLatlong
Plot method for winterTemperatures().plot.winterTemperatures
Poverty and Born in London.povertyLondon
Print method for neighborhoodEuclidean().print.euclidean
Print method for euclideanPath().print.euclidean_path
Print summary data for timeSeries().print.time_series
Print method for voronoiNominal().print.voronoi
Print method for voronoiLatlong().print.voronoiLatlong
Print method for walkingNominal().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
Compute length of road segment.segmentLength
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 networksimulateFatalities
Snow neighborhood fatalities.snow.neighborhood
Create a set of colors for pump neighborhoods.snowColors
Plot John Snow's cholera map.snowMap
Plotting data for Snow's graphical annotation of the Broad Street pump neighborhood.snowNeighborhood
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 voronoiNominal().summary.voronoi
Summary method for walkingNominal().summary.walking
Tanaka contour plot.tanakaContourPlot
Aggregate time series fatality data from the 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 pump neighborhoods.walkingB
Compute walking path from case/landmark to nearest or selected pump.walkingPath
Average Winter Temperatures.winterTemperatures