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

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Documentation for package ‘cholera’ version 0.4.0

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cholera-package cholera: amend, augment and aid analysis of John Snow's cholera map
addIndexCase Highlight index case at 40 Broad Street.
addKernelDensity Add 2D kernel density contours.
addLandmarks Add landmarks.
addNeighborhood Add expected neighborhood polygons
addPlaguePit Add plague pit (Marshall Street).
addPump Add water pump by numerical ID.
addSnow Adds Snow's graphical annotation of the Broad Street pump walking neighborhood.
addVoronoi Add Voronoi cells.
addWhitehead Add Rev. Henry 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.
classifierAudit Test if case is orthogonal to segment.
euclideanDistance Compute the Euclidean distance between cases and/or pumps.
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 errors in Dodson and Tobler's digitization of Snow's map.
nearestPump Compute shortest walking distances or paths.
neighborhoodData Compute network graph of roads, cases and pumps.
neighborhoodVoronoi Compute Voronoi pump neighborhoods.
neighborhoodWalking Compute walking path pump 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.classifier_audit Plot result of classifierAudit().
plot.euclidean_distance Plot the Euclidean distance between cases and/or pumps.
plot.time_series Plot aggregate time series data from Vestry report.
plot.voronoi Plot Voronoi neighborhoods.
plot.walking Plot method for neighborhoodWalking().
plot.walking_distance Plot the walking distance between cases and/or pumps.
print.classifier_audit Return result of classifierAudit().
print.euclidean_distance Summary of euclideanDistance().
print.time_series Print summary data for timeSeries().
print.voronoi Print method for neighborhoodVoronoi().
print.walking Print method for neighborhoodWalking().
print.walking_distance Print method for walkingDistance().
pumpCase 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.
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.
segmentLength Compute length of road segment.
segmentLocator Locate road segment by ID.
sim.ortho.proj Orthogonal projection of simulated "expected" cases onto road network.
sim.pump.case List of "simulated" fatalities grouped by walking-distance pump neighborhood.
simulateFatalities Generate simulated fatalities and their orthogonal projections.
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.
streetLength Compute length of selected street.
streetNameLocator Locate road by name.
streetNumberLocator Locate road by numerical ID.
timeSeries Aggregate time series fatality data from the Vestry report.
unitMeter Convert nominal map distance to yards or meters.
unstackFatalities Unstack "stacks" in Snow's cholera map.
walkingDistance Compute the shortest walking distance between cases and/or pumps.