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

## Documentation for package ‘cholera’ version 0.7.0

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

## Help Pages

cholera-package | cholera: amend, augment and aid analysis of John Snow's cholera map
addCase | Add observed case(s).
addDelauny | Add Delauny 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.
border | Numeric IDs of line segments that create the map's border frame.
caseLocator | Locate case by numerical ID.
classifierAudit | Test if case is orthogonal to segment.
distanceTime | Convert distance to elapsed time.
euclideanPath | Compute path of the Euclidean distance between cases and/or pumps.
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.
landmark.squares | Centers of city squares.
landmarkData | Landmark data.
landmarks | Orthogonal projection of landmarks onto road network.
mapRange | Compute xlim and ylim of Snow's map.
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.
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.
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.neighborhood_data | Plot method for neighborhoodData().
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.
print.classifier_audit | Return result of classifierAudit().
print.euclidean | Print method for neighborhoodEuclidean().
print.euclidean_path | Print method for euclideanPath().
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.
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.
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.
streetNumberLocator | Locate road by numerical ID.
summary.euclidean | Summary method for neighborhoodEuclidean().
summary.voronoi | Summary method for neighborhoodVoronoi().
summary.walking | Summary method for neighborhoodWalking().
timeSeries | Aggregate time series fatality data from the Vestry report.
unitMeter | Convert nominal map distance to meters or yards.
unstackFatalities | Unstack "stacks" in Snow's cholera map.
voronoiPolygons | Extract vertices of Delauny triangles and Dirichelet (Voronoi) tiles.
walkingPath | Compute the shortest walking path between cases and/or pumps.
withinRadius | Test whether point "b" is within a given radius of point "a".