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


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Documentation for package ‘cholera’ version 0.2.1

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cholera-package cholera: amend, augment and aid analysis of John Snow's cholera data
addKernelDensity Add 2D kernel density contours to a plot.
addLandmarks Add landmarks.
addPlaguePit Add plague pit (Marshall Street).
addSnow Adds Snow's Annotation of the Broad Street pump walking neighborhood.
addVoronoi Add Voronoi cells.
addWhitehead Add 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.
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 apparent coding error in Dodson and Tobler's digitization of Snow's map.
neighborhoodVoronoi Compute Voronoi neighborhoods.
neighborhoodWalking Compute walking path 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.
plague.pit Plague pit coordinates.
plot.time.series Plot aggregate time series data from Vestry report.
plot.voronoi Plot Voronoi neighborhoods.
plot.walking Plot observed and simulated walking neighborhoods.
pump.case List of the observed fatality "addresses" grouped by pump neighborhood.
pumpCase Extract numeric case IDs by 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 dataframe into road.segments dataframe.
segmentLocator Locate road segment by its character ID.
sim.ortho.proj Orthogonal projection of simulated "expected" cases onto road network.
sim.pump.case List of "simulated" fatalities grouped by pump neighborhood.
simulateFatalities Generate simulated fatalities and their orthogonal projections.
snow.neighborhood Snow neighborhood fatalities.
snowColors Create a uniform set of colors for pump neighborhoods.
snowMap Plot John Snow's cholera map.
streetNameLocator Locate road by name.
streetNumberLocator Locate road by its numerical ID.
summary.voronoi Compute summary statistics for Voronoi neighborhoods.
summary.walking Compute summary statistics for walking path neighborhoods.
timeSeries Aggregate time series fatality data from the Vestry report.
unstackFatalities Unstack "stacks" in Snow's cholera map.
walkingDistance Compute the walking distance between a case and the nearest (selected) pump.
walkingPath Plot the walking path from a case to the nearest selected pump(s).