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

## Documentation for package ‘cholera’ version 0.7.9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F I L M N O P R S T U V W

cholera-package | cholera: amend, augment and aid analysis of John Snow's cholera map

## -- A --

addCase | Add observed case(s) to plot.
addDelaunay | Add Delaunay triangles.
addEuclideanPath | Add the path for the Euclidean distance between cases and/or pumps.
addFrame | Add map border to plot.
addIndexCase | Highlight index case at 40 Broad Street.
addKernelDensity | Add 2D kernel density contours.
addLandmarks | Add landmarks to plot.
addMilePosts | Add distance or time based "mileposts" to an observed walking neighborhood plot.
addNeighborhoodCases | Add observed cases by neighborhood.
addNeighborhoodEuclidean | Add expected Euclidean pump neighborhoods.
addNeighborhoodWalking | Add expected walking neighborhoods.
addPlaguePit | Add plague pit (Marshall Street).
addPump | Add selected pump(s) to plot.
addRoads | Add all streets and roads to plot.
addSnow | Adds Snow's graphical annotation of the Broad Street pump walking neighborhood.
addVoronoi | Add Voronoi cells.
addWalkingPath | Add the shortest walking path between a selected cases or pumps.
addWhitehead | Add Rev. Henry Whitehead's Broad Street pump neighborhood.
anchor.case | Anchor or base case of each stack of fatalities.

## -- B --

border | Numeric IDs of line segments that create the map's border frame.

## -- C --

caseLocator | Locate case by numerical ID.
classifierAudit | Test if case is orthogonal to segment.

## -- D --

distanceTime | Convert distance to elapsed time.

## -- E --

euclideanPath | Compute path of the Euclidean distance between cases and/or pumps.

## -- F --

fatalities | Amended Dodson and Tobler's cholera data.
fatalities.address | "Unstacked" amended cholera data with address as unit of observation.
fatalities.unstacked | "Unstacked" amended cholera fatalities data with fatality as unit of observation.
fixFatalities | Fix errors in Dodson and Tobler's digitization of Snow's map.

## -- I --

isoLines | Plot isochrone and isodistance regions (prototype)
isoVertices | Isochrone and isodistance vertices (prototype)

## -- L --

landmark.squares | Centers of city squares.
landmarkData | Landmark data.
landmarks | Orthogonal projection of landmarks onto road network.

## -- M --

mapRange | Compute xlim and ylim of Snow's map.

## -- N --

nearestPump | Compute shortest distances or paths to selected pumps.
neighborhoodData | Compute network graph of roads, cases and pumps.
neighborhoodEuclidean | Compute Euclidean path pump neighborhoods.
neighborhoodVoronoi | Compute Voronoi pump neighborhoods.
neighborhoodWalking | Compute walking path pump neighborhoods.

## -- O --

ortho.proj | Orthogonal projection of observed cases onto road network.
ortho.proj.pump | Orthogonal projection of 13 original pumps.
ortho.proj.pump.vestry | Orthogonal projection of the 14 pumps from the Vestry Report.
orthogonalProjection | Compute coordinates of orthogonal projection from case to road segment.
oxford.weather | Oxford monthly weather data, January 1853 - December 2019.
oxfordWeather | Weather data recorded in Oxford (Met Office UK).

## -- P --

pearsonResiduals | Compute Pearson Residuals (prototype)
plague.pit | Plague pit coordinates.
plot.classifier_audit | Plot result of classifierAudit().
plot.euclidean | Plot method for neighborhoodEuclidean().
plot.euclidean_path | Plot the path of the Euclidean distance between cases and/or pumps.
plot.iso | Plot method for isoVertices().
plot.neighborhood_data | Plot method for neighborhoodData().
plot.oxfordWeather | Plot method for oxfordWeather().
plot.povertyLondon | Plot method for povertyLondon().
plot.profile_perspective | Plot method for profilePerspective().
plot.time_series | Plot aggregate time series data from Vestry report.
plot.voronoi | Plot Voronoi neighborhoods.
plot.walking | Plot method for neighborhoodWalking().
plot.walking_path | Plot the walking path between selected cases and/or pumps.
plot.winterTemperatures | Plot method for winterTemperatures().
povertyLondon | Poverty and Born in London.
print.classifier_audit | Return result of classifierAudit().
print.euclidean | Print method for neighborhoodEuclidean().
print.euclidean_path | Print method for euclideanPath().
print.iso | Print method for isoVertices().
print.time_series | Print summary data for timeSeries().
print.voronoi | Print method for neighborhoodVoronoi().
print.walking | Print method for neighborhoodWalking().
print.walking_path | Print method for walkingPath().
profile2D | 2D Profile .
profile3D | 3D Profile.
pumpCase | Extract numeric case IDs by pump neighborhood.
pumpData | Compute pump coordinates.
pumpLocator | Locate water pump by numerical ID.
pumps | Dodson and Tobler's pump data with street name.
pumps.vestry | Vestry report pump data.

## -- R --

regular.cases | "Expected" cases.
road.segments | Dodson and Tobler's street data transformed into road segments.
roads | Dodson and Tobler's street data with appended road names.
roadSegments | Reshape 'roads' data frame into 'road.segments' data frame.

## -- S --

segmentHighlight | Highlight segment by ID.
segmentLength | Compute length of road segment.
segmentLocator | Locate road segment by ID.
sim.ortho.proj | Road "address" of simulated (i.e., "expected") cases.
sim.pump.case | List of "simulated" fatalities grouped by walking-distance pump neighborhood.
sim.walking.distance | Walking distance to Broad Street Pump (#7).
simulateFatalities | Generate simulated fatalities.
simulateWalkingDistance | Compute walking distance for simulated cases.
snow.neighborhood | Snow neighborhood fatalities.
snowColors | Create a set of colors for pump neighborhoods.
snowMap | Plot John Snow's cholera map.
snowNeighborhood | Plotting data for Snow's graphical annotation of the Broad Street pump neighborhood.
streetHighlight | Highlight road by name.
streetLength | Compute length of selected street.
streetNameLocator | Locate road by name.
streetNames | Street names (alphabetized).
streetNumberLocator | Locate road by numerical ID.
subsetRoadsSamples | Sample for road segment endpoints.
summary.euclidean | Summary method for neighborhoodEuclidean().
summary.voronoi | Summary method for neighborhoodVoronoi().
summary.walking | Summary method for neighborhoodWalking().

## -- T --

timeSeries | Aggregate time series fatality data from the Vestry report.

## -- U --

unitMeter | Convert nominal map distance to meters or yards.
unstackFatalities | Unstack "stacks" in Snow's cholera map.

## -- V --

voronoiPolygons | Extract vertices of Delaunay triangles and Dirichelet (Voronoi) tiles.

## -- W --

walkingPath | Compute the shortest walking path between cases and/or pumps.
winterTemperatures | Average Winter Temperatures.
withinRadius | Test whether point "b" is within a given radius of point "a".