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

## Documentation for package ‘cholera’ version 0.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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).