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

## Documentation for package ‘cholera’ version 0.9.1

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

## Help Pages

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

cholera-package | cholera

## -- A --

addCase | Add observed case(s) to plot.
addDelaunay | Add Delaunay triangles.
addEuclideanPath | Add Euclidean path from case/landmark to nearest or selected pump. (prototype)
addIndexCase | Highlight index case at 40 Broad Street.
addKernelDensity | Add 2D kernel density contours.
addLandmarks | Add landmarks to plot.
addLandmarkSquares | Add Golden and Soho Squares to plot.
addNeighborhoodCases | Add observed neighborhood cases.
addNeighborhoodEuclidean | Add expected Euclidean pump neighborhoods.
addNeighborhoodSnow | Adds Snow's graphical annotation of the Broad Street pump walking neighborhood.
addNeighborhoodWalking | Add walking neighborhoods.
addPlaguePit | Add plague pit (Marshall Street).
addPump | Add selected pump(s) to plot.
addRoads | Add all streets and roads to plot.
addVoronoi | Add Voronoi cells.
addWalkingPath | Add walking path from case/landmark to nearest or selected pump. (prototype)
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.
cholera | cholera

## -- E --

euclideanPath | Compute Euclidean path coordinates from observed case/landmark to nearest/selected pump.

## -- 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.
frame.data | Map frame data c("x", "y") and c("lon", "lat").
frame.sample | Partitioned map frame points (segment endpoints).
frame.segments | Dodson and Tobler's "Map Frame" street data transformed into road segments.

## -- I --

isoVertices | Isochrone and isodistance vertices (prototype)

## -- L --

landmark.squares | Centers of city squares.
landmarks | Landmark coordinates.
latlong.ortho.addr | Orthogonal projection of observed address (latlong) cases onto road network.
latlong.ortho.pump | Orthogonal projection of 13 original pumps (latlong).
latlong.ortho.pump.vestry | Orthogonal projection of the 14 pumps from the Vestry Report (latlong).
latlong.regular.cases | "Expected" cases (latlong).
latlong.sim.ortho.proj | Road "address" of simulated (i.e., "expected") cases (latlong).

## -- M --

mapRange | Compute xlim and ylim of Snow's map.
meter.to.yard | Meter to yard conversion factor.

## -- N --

neighborhoodEuclidean | Compute Euclidean path pump neighborhoods.
neighborhoodSnow | Compute Snow's graphical annotation of Broad Street pump neighborhood.
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.

## -- P --

pearsonResiduals | Compute Pearson Residuals (prototype)
plague.pit | Plague pit coordinates.
plot.euclidean | Plot method for neighborhoodEuclidean().
plot.euclideanLatlong | Plot method for euclideanLatlong()
plot.euclidean_path | Plot the path of the Euclidean distance between cases and/or pumps.
plot.iso_vertices | Plot method for isoVertices().
plot.profile_perspective | Plot method for profilePerspective().
plot.snow | Plot method for neighborhoodSnow().
plot.soho_graph | Plot method for sohoGraph().
plot.time_series | Plot aggregate time series data from Vestry report.
plot.voronoi_latlong | Plot method for voronoiLatlong()
plot.voronoi_nominal | Plot Voronoi neighborhoods.
plot.walking | Plot method for neighborhoodWalking().
plot.walking_path | Plot the walking path between selected cases and/or pumps.
print.euclidean | Print method for neighborhoodEuclidean().
print.euclideanLatlong | Print method for neighborhoodEuclidean(latlong = TRUE).
print.euclidean_path | Print method for euclideanPath().
print.iso_vertices | Print method for isoVertices().
print.time_series | Print summary data for timeSeries().
print.voronoi_latlong | Print method for voronoiLatlong().
print.voronoi_nominal | Print method for voronoiNominal().
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.
pumpFatalities | Compute fatalities by pump.
pumpLocator | Locate water pump by numerical ID.
pumps | Dodson and Tobler's pump data with street name.
pumps.vestry | Vestry report pump data.

## -- R --

rd.sample | Sample of road intersections (segment endpoints).
rectangle.filter | Rectangular filter 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.

## -- S --

segmentHighlight | Highlight segment by ID.
segmentLocator | Plot/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 | Project simulated fatalities onto road network
snow.neighborhood | Snow neighborhood fatalities.
snowColors | Create a set of colors for pump neighborhoods.
snowMap | Plot John Snow's cholera map.
sohoGraph | Compute network graph of roads and embed cases, landmarks and pumps (prototype).
streetHighlight | Highlight road by name.
streetLength | Compute length of selected street.
streetNameLocator | Locate street(s) by name(s).
streetNames | Street names (alphabetized).
streetNumberLocator | Locate street by its numerical ID.
summary.euclidean | Summary method for neighborhoodEuclidean().
summary.voronoi_nominal | Summary method for voronoiNominal().

## -- T --

tanakaContourPlot | Tanaka contour plot.
timeSeries | Aggregate time series fatality data from the Vestry report.

## -- U --

unstackFatalities | Unstack "stacks" in Snow's cholera map.

## -- V --

voronoi.polygons | Coordinates of Voronoi polygon vertices for original map.
voronoi.polygons.vestry | Coordinates of Voronoi polygon vertices for Vestry Report map.
voronoiPolygons | Extract vertices of Delaunay triangles and Dirichelet (Voronoi) tiles.

## -- W --

walkingPath | Compute walking path from case/landmark to nearest or selected pump.