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Releases: lindbrook/cholera

cholera v0.8.0

01 Mar 15:06
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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

11 Oct 21:57
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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

22 Apr 15:14
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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

28 Aug 17:25
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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

11 Jun 17:30
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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

17 Mar 18:04
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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

17 Mar 17:58
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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

16 Jul 19:46
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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"

cholera v0.4.0

01 Apr 16:04
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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 v0.3.0

27 Jan 00:18
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Data Changes

  • ortho.proj:
    • reclassify case 483:
      • Pulteney Court (I) ("242-1") -> Little Windmill Street ("326-2").
    • 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".
    • updated implementation and improved performance.
    • 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()