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


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Documentation for package ‘cholera’ version 0.9.1

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A B C E F I L M N O P R S T U V W

cholera-package cholera

-- A --

addCase Add observed case(s) to plot.
addDelaunay Add Delaunay triangles.
addEuclideanPath Add Euclidean path from case/landmark to nearest or selected pump. (prototype)
addIndexCase Highlight index case at 40 Broad Street.
addKernelDensity Add 2D kernel density contours.
addLandmarks Add landmarks to plot.
addLandmarkSquares Add Golden and Soho Squares to plot.
addNeighborhoodCases Add observed neighborhood cases.
addNeighborhoodEuclidean Add expected Euclidean pump neighborhoods.
addNeighborhoodSnow Adds Snow's graphical annotation of the Broad Street pump walking neighborhood.
addNeighborhoodWalking Add walking neighborhoods.
addPlaguePit Add plague pit (Marshall Street).
addPump Add selected pump(s) to plot.
addRoads Add all streets and roads to plot.
addVoronoi Add Voronoi cells.
addWalkingPath Add walking path from case/landmark to nearest or selected pump. (prototype)
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 --

caseLocator Locate case by numerical ID.
cholera cholera

-- E --

euclideanPath Compute Euclidean path coordinates from observed case/landmark to nearest/selected pump.

-- 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.
frame.data Map frame data c("x", "y") and c("lon", "lat").
frame.sample Partitioned map frame points (segment endpoints).
frame.segments Dodson and Tobler's "Map Frame" street data transformed into road segments.

-- I --

isoVertices Isochrone and isodistance vertices (prototype)

-- L --

landmark.squares Centers of city squares.
landmarks Landmark coordinates.
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).
latlong.regular.cases "Expected" cases (latlong).
latlong.sim.ortho.proj Road "address" of simulated (i.e., "expected") cases (latlong).

-- M --

mapRange Compute xlim and ylim of Snow's map.
meter.to.yard Meter to yard conversion factor.

-- N --

neighborhoodEuclidean Compute Euclidean path pump neighborhoods.
neighborhoodSnow Compute Snow's graphical annotation of Broad Street pump neighborhood.
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.

-- P --

pearsonResiduals Compute Pearson Residuals (prototype)
plague.pit Plague pit coordinates.
plot.euclidean Plot method for neighborhoodEuclidean().
plot.euclideanLatlong Plot method for euclideanLatlong()
plot.euclidean_path Plot the path of the Euclidean distance between cases and/or pumps.
plot.iso_vertices Plot method for isoVertices().
plot.profile_perspective Plot method for profilePerspective().
plot.snow Plot method for neighborhoodSnow().
plot.soho_graph Plot method for sohoGraph().
plot.time_series Plot aggregate time series data from Vestry report.
plot.voronoi_latlong Plot method for voronoiLatlong()
plot.voronoi_nominal Plot Voronoi neighborhoods.
plot.walking Plot method for neighborhoodWalking().
plot.walking_path Plot the walking path between selected cases and/or pumps.
print.euclidean Print method for neighborhoodEuclidean().
print.euclideanLatlong Print method for neighborhoodEuclidean(latlong = TRUE).
print.euclidean_path Print method for euclideanPath().
print.iso_vertices Print method for isoVertices().
print.time_series Print summary data for timeSeries().
print.voronoi_latlong Print method for voronoiLatlong().
print.voronoi_nominal Print method for voronoiNominal().
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.
roadSegments Reshape 'roads' data frame into 'road.segments' data frame.

-- S --

segmentHighlight Highlight segment by ID.
segmentLocator Plot/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 Project simulated fatalities onto road network
snow.neighborhood Snow neighborhood fatalities.
snowColors Create a set of colors for pump neighborhoods.
snowMap Plot John Snow's cholera map.
sohoGraph Compute network graph of roads and embed cases, landmarks and pumps (prototype).
streetHighlight Highlight road by name.
streetLength Compute length of selected street.
streetNameLocator Locate street(s) by name(s).
streetNames Street names (alphabetized).
streetNumberLocator Locate street by its numerical ID.
summary.euclidean Summary method for neighborhoodEuclidean().
summary.voronoi_nominal Summary method for voronoiNominal().

-- T --

tanakaContourPlot Tanaka contour plot.
timeSeries Aggregate time series fatality data from the Vestry report.

-- U --

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 walking path from case/landmark to nearest or selected pump.