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

Documentation for package ‘cholera’ version 0.8.0

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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 --

caseDistance	Compute distance between case fatalities.
caseLocator	Locate case by numerical ID.

-- 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.
frame.data	Map frame data c("x", "y") and c("lon", "lat").
frame.sample	Partitioned map frame points (segment endpoints).

-- I --

isoLines

Plot isochrone and isodistance regions (prototype)

-- L --

landmark.squares	Centers of city squares.
landmarkData	Landmark data.
landmarks	Orthogonal projection of landmarks onto road network.
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).
latlongAddress	Compute latitude and longitude of case "addresses" (prototype).
latlongFatalities	Compute latitude and longitude of non-address fatalities (prototype).
latlongLandmarks	Compute Georeferenced Latitude and Longitude (prototype).
latlongNearestPump	Compute shortest georeferenced distances (and walking paths) to selected pumps (prototype).
latlongNeighborhoodData	Compute network graph of roads, cases and pumps.
latlongNeighborhoodVoronoi	Compute Voronoi pump neighborhoods (lat-long prototype).
latlongNeighborhoodWalking	Compute walking path pump neighborhoods.
latlongPumps	Compute Georeferenced Latitude and Longitude (prototype).
latlongRoads	Compute latitude and longitude for unique road segment endpoints (prototype).
latlongVoronoi	Compute Georeferenced Latitude and Longitude of vertices of Voronoi polygons.
latlongWalkingPath	Plot walking path to nearest pump (prototype).

-- 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.
oxford.weather	Oxford monthly weather data, January 1853 - December 2019.
oxfordWeather	Weather data recorded in Oxford (Met Office UK).

-- P --

plague.pit	Plague pit coordinates.
plot.euclidean	Plot method for neighborhoodEuclidean().
plot.euclidean_path	Plot the path of the Euclidean distance between cases and/or pumps.
plot.latlongNeighborhoodVoronoi	Plot method for latlongNeighborhoodVoronoi()
plot.latlong_neighborhood_data	Plot method for latlongNeighborhoodData().
plot.latlong_walking	Plot method for latlongNeighborhoodWalking().
plot.latlong_walking_path	Plot the walking path between selected cases and/or pumps.
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.euclidean	Print method for neighborhoodEuclidean().
print.euclidean_path	Print method for euclideanPath().
print.iso	Print method for isoVertices().
print.latlongNeighborhoodVoronoi	Print method for latlongNeighborhoodVoronoi().
print.latlong_walking_path	Print method for latlongWalkingPath().
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.
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.
roadSegmentFix	Bar orientation classification errors.
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 --

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 the shortest walking path between cases and/or pumps.
winterTemperatures	Average Winter Temperatures.