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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 0.8.0

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 0.7.9

Note

• an interim release to address code changes in ‘deldir’ v1.0-2.

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 0.7.5

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 0.7.0

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 0.6.5

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.

cholera 0.6.0

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()

cholera 0.5.1

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 0.5.0

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: addCase(), addKernelDensity(), addMilePosts(), addNeighborhood(); neighborhoodEuclidean(), neighborhoodWalking()

• “walking.speed” argument added to: addMilePosts(), nearestPump(), addEuclideanPath(), euclideanDistance(), euclideanPath(), addWalkingPath(), walkingDistance() and 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

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

New S3 Functions

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

Vignette Changes

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

cholera 0.4.0

Data Changes

• ortho.proj.pump and ortho.proj.pump.vestry now include node ID.

• roads and road.segments amend street names: “Unknown-B” to “Tent Court” (Edmund Cooper’s map); “Unknown-D” to “St James’s Market” (https://maps.nls.uk); “Unknown-E” to “Market Street (II)” (https://maps.nls.uk).

Function Changes

• addKernelDensity(): uses “pump.subset” and “pump.select” arguments.
• addLandmarks(): add landmarks from Edmund Cooper’s map.
• classifierAudit() can return coordinates of address.
• nearestPump() now incorporates nearestPath().
• neighborhoodWalking(): segment and sub-segment implementation.
• pumpData() returns node ID.
• timeSeries() includes day of the week.
• walkingDistance(): add “simulated” expected cases.

New Functions

• addNeighborhood()

New S3 Implementations

• plot.walking(): type = “area.points” and type = “area-polygons”; type = “area-polygons” via pearlString() replaces alphahull::ashape().
• print.walking() uses expectedCount().

Vignette Changes

• add “Kernel Density Plot”.
• update “Pump Neighborhoods” with discussion of area plots.

cholera 0.3.0

Data Changes

• ortho.proj reclassify case 483: Pulteney Court (I) (“242-1”) -> Little Windmill Street (“326-2”).
• ortho.proj reclassify reclassify cases 369, 434, 11, 53, 193: Poland Street (“194-1”) -> St James Workhouse (“148-1”).

Function Changes

• addSnow(): “area”, “street” and “boundary” graphical annotation.
• caseLocator() highlight home road segment.
• neighborhoodWalking(): “case-set” argument: “observed”, “expected” and “snow”.
• neighborhoodWalking(): updated implementation and improved performance.
• neighborhoodWalking(): pre-computed configurations from version 0.2.1 removed.
• segmentLocator(), streetNameLocator() and streetNumberLocator(): highlight segment or street cases; option to plot all cases, anchor cases or no cases.

New S3 Implementations

• timeSeries()
• walkingDistance(): incorporates and deprecates walkingPath().

New Functions

• addIndexCase()
• nearestPath()
• nearestPump()
• nodeData()
• segmentLength()
• snowNeighborhood()
• streetLength()
• unitMeter()

New S3 Functions

• classifierAudit()
• euclideanDistance()

cholera 0.2.1

• Initial CRAN release.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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