cholera 0.9.1

Georeferenced Data and Functions

• provisional support for (georeferenced) longitude and latitude for data and
  functions (for functions, set latlong = TRUE).

Data Changes

• add longitude and latitude to plague.pit data.
• add frame.segments
• amend road.segments with latlong data.
• use amended road.segments (w/ latlong) in various functions.

Documentation Changes

• restore .jpg and .png to README.
• restore NEWS.md to source file and amend markdown.

Function Changes

• rename neighborhoodData() to sohoGraph().
• add/set drop.isolates = FALSE in embedNodes() and neighborhoodData().
• add latlongPlaguePit() and plaguePitPDF().
• add/set addPlaguePit(latlong = FALSE).
• add rotatePoint(dataset = "plague.pit").
• vectorize addFrame(), addRoads() and landmarkPerimeter().
• add/set embedNodes(drop.isolates = TRUE).
• export isoVertices().
• add/set plot.iso_vertices(add = FALSE).
• rename isoLines() to isoPoints() and add/set isoPoints(add = FALSE).
• amend/simplify latlongOrthoAddress().
• archive latlongEmbed().
• rename squareCenter() in addLandmarks() to squareCenterB().
• amend pump 2 (Adam and Eve) warnings in casePump() and pumpPump().

Function Fixes

• correct class for sohoGraph() output.
• use cholera::roads$id rather than indices to fix latlongFrame().
• add variable check to latlongLandmarks() and landmarksPDF().
• fix typo in name of quadrantCoordinates().
• fix/amend pump 2 (Adam and Eve) warnings in casePump() and pumpPump().

cholera 0.9.0

Georeferenced Data and Functions

Provisional support for (georeferenced) longitude and latitude for practically all data and functions (for functions, set latlong = TRUE).

Data Changes

• add and document missing Clifford Street segment; cliffordStreet().
• add/use cholera::meter.to.yard (1.093613).
• use "&" as longitude-latitude coordinates delimiter.
• set address of Model Lodging Houses to Hopkins Street
• set Lion Brewery address to Broad Street.
• add Marlborough Street Magistrates Court.
• add appendixB().
• archive oxford.weather.

Data Fixes

• add exception for pump 8 polygon for neighborhoodWalking(6:9, case.set =
  "expected").
• add Adam and Eve Court pump exception to neighborhoodWalking().
• add exception for single pump for pump.select in neighborhoodWalking().
• amend caseCase() for duplicate nodes: case 369 and St James Workhouse 1019.
• add case 296 to segment "137-3" in caseRoadClassificationFix().
• add cases 56 and 286 to segment "160-3" in caseRoadClassificationFix().
• amend case 440 in ortho.proj: use Euclidean distance to road endpoint.
• fix duplicate road segment endpoints (self-loops) in embedNodes().

Function Changes and Fixes

• faster implementation of neighborhoodWalking() and plot.walking(). See
  "Parallelization" vignette.
• parallelization off by default (multi.core = FALSE). See "Parallelization"
  vignette.
• allow negative values in plot methods zoom argument to "zoom out".
• change polygon.type from "perimeter" to "border".
• pair add*() with plot.*(add = FALSE).
• rename and amend snowNeighborhood() to neighborhoodSnow().
• move various auxiliary function files to various utils-*.R.
• archive addMilePosts(), oxfordWeather(), povertyLondon() and
  winterTemperatures().
• amend balance between orthogonal and Euclidean proximity in
  simulateFatalities().
• prioritize orthogonal over Euclidean in orthogonalProjectionFatalities().
• fix/enable vector of street names in streetNameLocator().
• migrate from sp::spDistsN1() to geosphere::distGeo().

Documentation

• update "Parallelization" vignette.
• use Internet Archive URLs for Frerichs's UCLA website links.
• note Dodson and Tobler data and code on Internet Archive's Wayback Machine.
• move vignettes online to GitHub repository.

cholera v0.8.0

New Functions

• caseDistance().
• pumpFatalities().

New Data

• latlong.ortho.addr, latlong.ortho.pump and latlong.ortho.pump.vestry.
• frame.data.

Fixes

• fix addVoronoi(color).
• fix nearestPump(metric = "euclidean", vestry = TRUE).
• fix/change unitMeter(distance.unit = "native").
• use aes_string() in profile2D().

Data Changes

• use Poland Street as street address for St James Workhouse.
• re-compute ortho.proj with amended unstackFatalities().
• roadSegmentFix() places cases 440 and 145 on road segment "259-1".

Function Changes

• add exception for observed v. expected in neighborhoodData() via embedSites().
• add/set addCase(pch = 1, cex = 1, point.lwd = 2).
• add addCase(case %in% c("all", "anchor"), col = col).
• add/set addFrame(col = "black").
• add/set latlong = FALSE in addFrame() and addRoads().
• add/set plot.euclidean(add.title = TRUE).
• add/set plot.walking_path(stacked = TRUE).
• add/set segmentLocator(cex.text = 0.67).
• add/set streetHighlight(col = "red", lwd = 3).
• add/set walkingPath(null.origin.landmark = FALSE).
• add/use duplicateNode() in neighborhoodData() via embedSites().
• amend addVoronoi().
• amend error/exception handling in walkingPath().
• amend unstackFatalities() and use roadSegmentFix().
• fix/amend milePosts() for distance and time.

Longitude and Latitude Prototypes

• add/set snowMap(latlong = FALSE).
• add/set addPump(latlong = FALSE).
• add/ser roadSegments(latlong = FALSE).
• add/set voronoiPolygons(latlong = FALSE).
• latlongNeighborhoodVoronoi().
• latlongNeighborhoodWalking().
• latlongWalkingPath().

Documentation

• note on "computing Voronoi diagrams with geographic data".

Archived/Deprecated Functions

• roadHighlight().

cholera v0.7.9

New Function

• add streetNames().

Data Change

• amend oxford.weather data to include entire data set.

Fixes

• amend code for 'deldir' v1.0-2: addDelaunay().
• fix addSnow().
• fix pumpTokens() for plot.walking(type = "roads").

Function Changes

• add/set addPump(cex = 1).
• add/set segmentHighlight(col = "red").
• add/set plot.oxfordWeather(month = "september").
• amend plot.oxfordWeather(statistic = "rain").
• change addDelauny() to addDelaunay().
• change type = "road" to "roads" in plot.walking().
• "gray" out unobserved and unselected pumps in pumpTokens().

cholera v0.7.5

New Data

• oxford.weather

New Functions

• isoLines()
• isoVertices()
• oxfordWeather()
• povertyLondon()
• segmentHighlight()
• winterTemperatures()

Function Changes

• add addCase(case = NULL).
• add and set neighborhoodVoronoi(case.location = "address").
• add and set neighborhoodVoronoi(pump.location = "nominal").
• add subtitles for selected pumps in plot.euclidean().

Fixes

• fix unneeded warnings in addEuclideanPath().
• fix typo, from Silver Street to Cross Street, for meter benchmark in roads
  vignette.

Vignettes

• add discussion of Euclidean and Voronoi "expected" neighborhoods.

cholera v0.7.0

New Feature

• support for parallel computation on Windows.

Fixes

• fix computation of core in neighborhoodWalking().
• fix nearestPump(metric = "euclidean", case.set = ("observed", "expected")).

Function Changes

• rename and amend simWalkingDistance() to simulateWalkingDistance().
• deprecate case.set argument in addNeighborhoodCases().
• add nearestPump(metric = "walking", case.set = "expected").
• amend expectedCount() for summary.walking().
• add unstackAuxiliaryFunctions.R

Vignettes

• add Parallelization vignette.

cholera v0.6.5

Fixes

• fix plot.walking_path() timeposts.
• fix plot.walking_path(observed = FALSE).
• fix St James Workhouse for walkingPath(type = "cases").
• fix St James Workhouse for euclideanPath(type = "cases").
• fix city squares for plot.euclidean_path().
• fix computed time in nearestPump() and amend sim.walking.distance.

New Data

• add sim.walking.distance.

Function Changes

• add nearestPump(metric = "euclidean").
• add distance.unit argument to addWhitehead().
• add pch and point.size arguments to addNeighborhoodCases().
• add pos argument to addCase().
• add output argument to voronoiPolygons().
• add summary.euclidean(), summary.voronoi() and summary.walking().
• add multi.core argument to simWalkingDistance().
• add case.location to addEuclideanPath().
• add 'case' argument to pumpCase().
• amend travelingSalesman() argument in addSnow().
• amend print.euclidean(), print.voronoi() and print.walking().
• amend argument 'case' to 'data' in addKernelDensity().
• amend plot.walking() titles.
• deprecate pearlString() in favor of travelingSalesman().
• deprecate statistic argument in neighborhoodVoronoi().
• enable col argument in addRoads().
• enable 'address' and 'nominal' cases in plot.voronoi().
• exclude landmarks from case.set - "expected".
• rename deldirVertices() back to voronoiPolygons().

Vignettes

• rename "deldirPolygons()" to "voronoiPolygons()".
• remove Pump Neighborhoods vignette.

DESCRIPTION

• remove 'scales" from Imports.

v0.6.0

Fixes

• fix title in euclideanPath(type = "case-pump").
• fix destination label for walkingPath(destination = NULL).

Data Changes

• add Earl of Aberdeen residence (Argyll House).
• nominal and orthogonal coordinates for landmarks.

Function Changes

• addNeighborhood() -> addNeighborhoodWalking()

Function Changes - new arguments

• addSnow(type = "perimeter", line.width = 2)
• neighborhoodData(embed = TRUE, embed.landmarks = TRUE)
• neighborhoodEuclidean(case.set = "expected")
• plot.voronoi(voronoi.cells = TRUE, delauny.triangles = FALSE)
• snowMap(...)
• streetNameLocator(add.subtitle = TRUE, token = id)
• streetNumberLocator(add.subtitle = TRUE, token = id)

Function Changes - polygon.method argument

• addNeighborhoodEuclidean(polygon.method = "traveling.salesman")
• plot.euclidean(polygon.method = "traveling.salesman")
• addNeighborhoodWalking(polygon.method = "pearl.string")
• plot.walking(polygon.method = "pearl.string")

Function Change - landmarks as origin and/or destination (treated as cases)

• euclideanPath()
• walkingPath()
• find nearest case or landmark, given pump (i.e., reverse lookup)

Function Changes - case.location argument: "address" or "nominal"

• addVoronoi(case.location = "nominal")
• euclideanPath(case.location = "nominal")
• neighborhoodEuclidean(case.location = "nominal")
• addNeighborhoodEuclidean(case.location = "nominal")

New Functions

• addCase()
• addDelauny()
• addNeighborhoodCases()
• deldirVertices()
• orthogonalProjection()
• profile2D()
• profile3D()
• streetHighlight()

New Exported Functions

• fixFatalities()
• landmarkData()

New S3 Function

• pearsonResiduals()
• plot.neighborhood_data()

New Vignette

• "deldirVertices(): Tiles, Triangles and Polygons"

Deprecated Functions

• euclideanDistance()
• walkingDistance()

v0.5.1

Fixes

• backward compatibility (R 3.4.4) related to base::isFALSE() & bug fix.
• fix for multiple results in walkingDistance() and walkingPath().

Function Changes

• enable ellipses (...) in plot.time_series() (#1).
• enable ellipses and negative selection in addPump().
• consolidate addEuclideanPath(), euclideanDistance(), euclideanPath(),
  walkingDistance() and walkingPath()

New Functions

• addBorder()
• addRoads()
• mapRange()

cholera v0.5.0

Data Changes

• regular.cases and sim.ortho.proj:
  increase number of observations from 5K to 20K.

Function Changes

• "alpha.level" argument to control path transparency
  addEuclideanPath() and addWalkingPath()

• distance and time based "mileposts"
  addEuclideanPath() and addWalkingPath().
  plot.euclidean_path() and plot.walking_path().
  addMilePosts().

• "pump.subset" and "pump.select" arguments
  addCases(), addKernelDensity(), addMilePosts(), addNeighborhood(),
  neighborhoodEuclidean(), neighborhoodWalking()

• "walking.speed" argument added to:
  addMilePosts(), nearestPump(),
  addEuclideanPath(), euclideanDistance(), euclideanPath(),
  addWalkingPath(), walkingDistance(), walkingPath()

• euclideanDistance() no longer S3.
  generic S3 functionality moved to euclideanPath().

• multiCore() moved to multiCore.R.

• neighborhoodVoronoi()
  plot.voronoi() adds "euclidean.paths" argument for star graph.

• neighborhoodWalking()
  "area.polygons" related functions for plot_walking() moved to pearlString.R.

• simulateFatalities():
  default is now 20K observations.
  use proximate in addition to orthogonal distances to find "addresses".

• snowMap() new arguments:
  "add.cases", "add.pumps", "add.roads".

• unitMeter() default unit of measurement is now "meter".

• walkingAuxillaryFunctions.R:
  location of walking related helper functions.

• walkingDistance() no longer S3.
  generic S3 functionality moved to walkingPath().

New Functions

• addCases()
• addEuclideanPath()
• addMilePosts()
• addNeighborhood()
• addWalkingPath()()
• distanceTime()

New S3 Implementations

• euclideanPath()
• walkingPath()
• neighborhoodEuclidean()

Vignette Changes

• Lab Notes available online and on GitHub:
  "duplicate.missing.cases.notes"
  "pump.neighborhoods.notes"
  "unstacking.bars.notes"