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

Documentation for package ‘cholera’ version 0.9.1

Help Pages

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.