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

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Documentation for package ‘cholera’ version 0.7.9

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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 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 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. 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".