NEWS.md
In lindbrook/cholera: Amend, Augment and Aid Analysis of John Snow's Cholera Map

amend ortho.proj and sim.ortho.proj.

fix colors in plot.walkingB(type = "area.polygons").

amend computation of neighborhood edges in walkingB(case.set = "observed").

fix order of graph edges in embedNodes() for neighborhoodDataB().

remove mode and algorithm in igraph: distances() and shortest_paths().

specify mode and algorithm in igraph: distances() and shortest_paths().

use x$case.set in plot.walking_path().

pass case.set to neighborhoodDataB() and return it in walkingPath().

use meter.to.yard in distanceTime().

add case 296 to segment "137-3" in caseRoadClassificationFix().

fix Falconberg Court and Mews isolate in walkingB(case.set = expected).

remove Workhouse exception and clean simulateFatalitiesB().

clean and comment unstackFatalitiesB().

fix numerical zoom in caseLocator().

fix negative zoom in segmentLocator(), streetNameLocator() and streetNumberLocator().

export "fixed" fatalities with unstackFatalitiesB().
move do.call()'s into auxiliary functions().

fix orthogonalProjectionFatalitiesB() for single/manual "within.radius".

add unstackFatalitiesB() prototype.

make fixFatalities() internal.

rename roadSegmentFix() to caseRoadClassificationFix().

amend balance between ortho and Eucl proximity in simulateFatalitiesB().

add simulateFatalitiesB() version of sim.ortho.proj.

adopt orthogonalProjectionFatalities() strategy in simulateFatalitiesB().

amend case 440 in ortho.proj: Euclidean distance to road endpoint.
use ortho.proj created by orthogonalProjectionFatalities().

add cases 56 and 286 to segment "160-3" in roadSegmentFix().

prioritize orthogonal over Euclidean in orthogonalProjectionFatalities().

set orthogonalProjectionFatalities(case.type = "fatality").

add a different St James Workhouse exception to simulateFatalitiesB().

add St James Workhouse exception to orthogonalProjectionFatalities().

change case 19 back to 18 on segment "290-1" in roadSegmentFix().

add simulateFatalitiesB() prototype.
amend computation of nr.seg in orthogonalProjectionFatalities().

add exception for roadSegmentFix() cases in orthogonalProjectionFatalities().

change case 18 to 19 on segment "290-1" in roadSegmentFix().

use stats::dist() in orthogonalProjectionFatalities().

add segment ID to title and temp fix for simulated case # in caseLocator().

amend/set orthogonalProjectionFatalities(radius = 2).

leverage dist() more in orthogonalProjectionFatalities().

add orthogonalProjectionFatalities() prototype.
reduce computation and amend criteria for Euclidean distance cases.

add edgesLength() to embedNodes.R.

fix edge distances in embedNodes() with all embeddings = FALSE.

amend/fix validateCase().

temp fix for landmarks in longTitle() and mapDataRange().

add/use cholera::meter.to.yard (1.093613).

start simulated orthogonal projection cases at 10,001.

add new simulateFatalities() prototype.
amend simulateFatalities() documentation.

amend sim.ortho.proj.

add regularCases().

add exception for Adam and Eve Court isolate in walkingB().

add/use pumpTokensB() prototype.
return 'pump.select' with walkingB().

add exception for Falconberg Court and Mews isolates in walkingB().

temp fix for "observed" and "expected" walkingNominal(case.set).

fix duplicate road segment endpoints (self-loops) in embedNodes().

return 'cores' with walkingB().

add code for 'area.points' and 'area.polygons' in plot.walkingB(case.set = "expected").
return 'case.pump' with walkingB(case.set = "expected").

limit computation of paths to case.set == "observed"; re-enable multi.core.

clean walkingB() code.

add walkingB() prototype.

add pump/street name to output of nearestPump(latlong = TRUE)$distance.

add addNeighborhoodWalkingLatlong() prototype.

amend/use index0().

remove unused code in travelingSalesman().

add/set nearestPumpLatlong(location = "nominal").

add/set nearestPumpNominal(location = "nominal").

add/set addNeighborhoodCases(latlong = FALSE).

use do.call() in nearestPump().
return data frame for nearestPumpNominal(metric = "euclidean").

use lapply() for peripheryCases() and travelingSalesman() in plot.walkingLatlong().

add/set addKernelDensity(latlong = FALSE).

add/amend methods for pumpCase().

amend classes for euclideanLatlong() and walkingLatlong().

add single core/Windows exception in nearestPumpLatlong().

copyedit "Kernel Density Plot" vignette.

amend Windows and/or cores = 1 exception in nearestPumpNominal().

amend QGIS URL and update latlong syntax in README.

set addKernelDensity(multi.core = FALSE).

add/set neighborhoodWalking(latlong = FALSE).
add walkingNominal() and walkingLatlong().
archive latlongNeighborhoodWalking().

use stop(call. = FALSE) in nearestPumpNominal().

return paths in nearestPump().

make unitMeter() internal.

update euclideanPath() argument in nearestPumpNominal().

fix pumpFatalities(metric = "euclidean") and use do.call().

fix pumpFatalities(latlong = FALSE).

fix pumpFatalities() and use nearestPump().

amend/set nearestPump(latlong = FALSE).
archive latlongNearestPump().
add nearestPumpNominal() and nearestPumpLatlong().

set type = "roads" in plot.walking() and plot.latlong_walking().

make latlongNeighborhoodData(), latlongNeighborhoodDataB() and latlongNeighborhoodWalking() internal.

move walkingTime() to walkingTime.R.

rename latlongVoronoi.R to walkingAuxiliaryFunctions.R
rename latlongVoronoi() to latlongVoronoiVertices().

archive latlongNeighborhoodVoronoi().
amend class name in pumpTokens() and voronoiLatlong()

make latlongVoronoi() internal.

archive latlongEuclideanPath().

archive latlongStreetNameLocator().

promote streetNumberLocatorB() to streetNumberLocator().

fix/enable vector of street names in streetNameLocator().

amend latlong.regular.cases and latlong.sim.ortho.proj.

amend latlongSimulateFatalities() prototype.

incorporate case.select in location: neighborhoodEuclidean(latlong = TRUE).

incorporate case.select in location: neighborhoodEuclidean(latlong = FALSE).

promote addEuclideanPathB() to addEuclideanPath().

promote addWalkingPathB() to addWalkingPath().

amend/update pumpPump().

clean walkingPath(), casePump() and caseCase().

promote/amend walkingPathB() to walkingPath().

promote streetNameLocatorB() to streetNameLocator().

add 'dstn.nm' argument to pumpPumpEucl().

amend data.summary in pumpPumpEucl().

clean code and amend output of euclideanPath().

use any() in casePumpEucl()
match caseCaseEucl() output in casePumpEucl().

amend caseCaseEucl(), esp. Squares.

use cholera::fatalities in validateCase().

amend casePump() Square ID/name fix.

add Square ID/name fix and clean code in casePump().

fix pump name destination in walkingPathB().

remove "outdated" landmark destination detection in walkingPathB().

amend error and warning messages in validateCase() and validatePump().

remove "outdated" landmark destination detection in euclideanPath().

remove square.intersections argument.

fix validateCase() for character cases/landmarks.

remove redundant code and update variable names in in walkingPathB().

fix pump selection in casePumpEucl().

enable casePumpEucl(latlong = TRUE).

compute missing distance 'd' in casePumpEucl().

fix negtive selection and remove location argument in caseCaseEucl().

enable negative selection in validateCase().

clean and clarify casePumpEucl(latlong = FALSE).

use geosphere::distGeo() for latlong in caseCaseEucl() and pumpPumpEucl().
fix for cases in same stack (type = "cases").
remove redundant code in euclideanPath(), caseCaseEucl() and pumpPumpEucl().
update syntax for caseCaseEucl() and pumpPumpEucl() in euclideanPath().

move longTitle(), mapDataRange() and validate.R functions to pathFunctions.R.

use anchor case filter for all locations in casePumpEucl().

amend variable names in euclideanPath().
separate milepost arrows from direct arrow in plot.euclidean_path().
include origin case when location %in% c("anchor", "orthogonal").

remove lndmrk test.
add dstn.nm argument to caseCase().
return origin and location in walkingPathB().
add x argument to longTitle().
add anchor case filters to casePump() and caseCase().

update validateCase() in walkingPathB().

fix anchor orign.nm casePumpEucl().

distinguish anchor and case in euclideanPath() and longTitle().

archive caseLandmarks() and prior validateCase() and validatePump().

fix validateCase() for character cases.

add/set euclideanPath(square.intersections = FALSE); amend location argument.
amend casePumpEucl().

fix typo in validateCase().

amend validateCase(); move it and validatePump() to validate.R.

add exception for landmarks in casePumpEucl().
check case.set and location arguments in euclideanPath().

add/set walkingPathB(case.set = "observed", location = "nominal").
use amended validateCase() in walkingPathB().

amend validateCase(case.set = "expected").

export case.set in euclideanPath().
clean plot.euclidean_path().
fix casePumpEucl(location = "orthogonal") with case.set == "observed".
fix casePumpEucl(case.set == "expected").

add geoCartesianSimulation() prototype.

enable euclideanPath(latlong = TRUE, location = "orthogonal").

add a stop() for validateCase(location) error.

add/set euclideanPath(case.set = "observed", location = "nominal").

add validateCase(case.set, location).

archive euclideanPathB().

amend latlong.regular.cases and latlong.sim.ortho.proj.

use regular.cases with latlongSimulateFatalities(recompute = FALSE).

restore regular.cases and sim.ortho.proj.

amend regular.cases and sim.ortho.proj.

promote caseLocatorB() to caseLocator().

enable negative numerical selection in validatePump().

add/set euclideanNominal(brute.force = FALSE).

add/set neighborhoodEuclidean(case.select = "address").

add/set addNeighborhoodCases(case.set = "observed", case.select = "address").

add neighborhoodVoronoi(latlong = TRUE, polygon.vertices = TRUE).

amend cell names for voronoiNominal(polygon.vertices = TRUE).

change "case.location" argument to 'location' with values "nominal" or "orthogonal" in neighborhoodVoronoi().

change "case.location" argument to 'location' with values "nominal" or "orthogonal" in neighborhoodEuclidean().

change "case.location" argument to 'location' with values "nominal" or "orthogonal" in addNeighborhoodEuclidean().

change "case.location" argument to 'location' with values "nominal" or "orthogonal" in addNeighborhoodCases().

change "case.location" argument to 'location' with values "nominal" or "orthogonal" in euclideanPath().

use neighborhoodVoronoi() as wrapper for voronoiNominal() and voronoiLatlong().
set "nominal" and "orthogonal" as arguments for case.location and pump.location.

use neighborhoodEuclidean() as wrapper for euclideanNominal() and euclideanLatlong().

add geoCartesianCoord().

add caseLocatorB() prototype.
include case when computing xlim and ylim.

add streetNumberLocatorB() prototype.

fix numerical zoom in streetNameLocatorB(latlong = FALSE).

add streetNameLocatorB() prototype.

archive latlongSegmentLocator().
promote segmentLocatorB() to segmentLocator().
add "nominal" distance subtitle.

temporarily allow sole selection of pump 2 (isolate) in selectPump().

add segmentLocatorB() prototype.

allow NULL segment.id in latlongSegmentLocator().

set/fix limit for positive zoom in segmentLocator().

allow NULL segment id in segmentLocator().

use latlongSegmentLocator() numeric zoom in segmentLocator().

show cases with numeric zoom in latlongSegmentLocator().

add numeric zoom in latlongSegmentLocator().

set/fix limit for positive zoom in geoCartesianStreetLocator().

set plot.walking(type = "area.points").

use amended meterLatLong().

embed origin, topleft and bottomright in meterLatLong().

add/set caseDistance(latlong = FALSE).

add/set addCase(latlong = FALSE).

add/set addIndexCase(latlong = FALSE).

amend pump icons in plot.latlong_walking(type = "area.polygons").

add latlongSegmentLocator() prototype.

amend syntax in roadSegments().

add/set segmentLength(latlong = FALSE).

amend pump graphics for "area.points" and "area.polygons" in plot.latlong_walking().

contextualize pumps for plot(latlongNeighborhoodWalking(case.set = "snow")).

add contextual pumps in plot.latlong_walking().

use pump IDs in latlongNearestPump().

enable pump.select argument for plot.latlong_walking(type = "streets").

enable pump.select argument in latlongNearestPump().

compute whole and split segments in plot.latlong_walking(type = "streets").

extract 'edges' for plot.latlong_walking(type = "streets").

add plot.latlong_walking(type = "streets").

return 'nearest.pump' in latlongNeighborhoodWalking().

return 'cores' in latlongNeighborhoodWalking().

add/set plot.latlong_walking(type = "area.points").
add plot.latlong_walking(type = "area.polygons").

remove dev.mode argument from latlongNearestPump().

add latlongNeighborhoodWalking(case.set = "expected") prototype.

add latlongNearestPump(case.set = "expected") prototype.

set snowNeighborhood(latlong = FALSE).
add St James Workhouse segment ("148-1") to whole.segs in snowNeighborhood().

promote/rename snowNeighborhoodB() to snowNeighborhood().

add/set addSnow(latlong = FALSE).

amend road segments and sub-segments in snowNeighborhoodB(latlong = TRUE).

use snowNeighborhoodB() in addSnow().

amend/update latlong.regular.cases and latlong.sim.ortho.proj.

make geoCartesianStreetLocator(zoom) logical or numeric.

define more nearest segments by euclidean rather than othogonal distance in latlongSimulateFatalities().

add/set geoCartesianStreetLocator(street.col = "gray").

add/set geoCartesianStreetLocator(zoom.padding = 0).

add St James Workhouse segment ("148-1") to whole.segs in snowNeighborhoodB().

use vector of streets for zoom in latlongStreetNameLocator().

add street name spell-check and draw streets with lines() in geoCartesianStreetLocator().

add internal geoCartesianStreetLocator().

add snowNeighborhoodB() prototype.

add exception for single pump selection in latlong_pathData().

use computed distance to identify pump isolate(s) in latlong_pathData().
clean latlongNeighborhoodWalking().

amend computation of obs.edges in plot.latlong_walking().

add latlongNearestPump(case.set = "snow").

amend list structure of shortest path in latlongNearestPump().

replace identifyEdgesB() with auditEdge() in addNeighborhoodWalking().

replace identifyEdgesB() with auditEdge() in plot.latlong_walking().

fix typo in classifyCase() for snowNeighborhood().

add latlongNeighborhoodWalking(case.set = "snow").

add snowMap() to plot.neighborhoodWalking() for case.set = "snow".

amend/restore profile2D() 'ggplot2' code.

move interpolation code for "tmin" NA to plot.oxfordWeather().

add/set plot.oxfordWeather(unit.observation = "month").

archive profile2D() 'ggplot2' code.

add addLandmarkSquares().

move post.info and amend subtitle in euclideanPathB() and walkingPathB().

clean addEuclideanPathB() and addWalkingPathB().

add addEuclideanPathB() prototype.

remove long.title argument from addWalkingPathB(); clean code.

use Internet Archive links for Frerichs's UCLA website links.

fix Dodson and Tobler URL for winbuilder.

note Dodson and Tobler data and code on Internet Archive's Wayback Machine.

amend/update oxford.weather.
amend temperaturePlot().
amend rainPlot().
archive monthEndDate().
clean plot.oxfordWeather().

add/set plot.oxfordWeather(end.year = NULL); amend graph elements.

add addWalkingPathB() prototype.

use cholera::landmarksB in addLandmarks().

fix mapDataRange() for Square labels with euclideanPathB().

fix multiple origins (e.g., Squares) in euclideanPathB().
amend argument name in sqCases().
filter orgn and dstn in caseCaseEucl() for anchors and landmarks.
fix multiple numeric origins in caseCaseEucl().

add euclideanPathB() prototype.
amend distance computation and function output.
add plot.euclidean_path_B() prototype.
add latlongEuclideanPosts() and latlongCartesian().
amend plot.euclidean_path_B() prototype.

drop selectPump() in casePump() and pumpPump() in walkingPathB().

copyedit function documentation; format code.

amend fix for Square cases with NULL origin/destination in caseCase().
add amended sqCases().

remove redundant code in plot.walking_path_B().
fix duplicate Square origin label in plot.walking_path_B().

add validateCase() and validatePump(); archive sqCases().
amend variables and code in casePump(), caseCase() and pumpPump().
amend variables in plot.walking_path_B(), longTitle() and mapDataRange().
use validateCase() and validatePump(); amend variables in walkingPathB().

fix Square cases with NULL origin/destination in caseCase().

add/use sqCases() and drop/archive validateDestinationCases() in caseCase().

use caseLandmarks() in validateDestinationCases().

exclude other Square destination cases with a Square origin.

fix landmark destination test in walkingPathB().

exclude landmark destinations when origin is landmark (prototype).

fix check for compound Square postfixes (e.g., "Soho Square-S1").

add/use caseLandmarks() for Square entry/exit names.

fix numerical landmarks (esp. Squares) in walkingPathB().

amend/add walkingPathB(destination = NULL, include.landmarks = TRUE).

add caseCase(include.landmarks). .

filter origin cases from destination in caseCase() for walkingPathB(destination = NULL).

check 'type' in walkingPathB().

don't plot destination case when type = "case-pump" in plot.walking_path_B().

enable origin = NULL for caseCase().
enable origin = NULL for pumpPump().
enable origin = NULL for walkingPathB().

update/copyedit 'cholera-package' and use "_PACKAGE".

temporarily round distance and time to tenth's place in plot.walking_path_B().

remove roadSegmentFix(), simulateWalkingDistance() and subsetRoadsSamples() from NAMESPACE.

remove isoLines() and isoVertices() from NAMESPACE.

Set RoxygenNote to "7.3.1".

amend "Clifford Street missing segment" note.
remove cliffordStreet() from NAMESPACE.

fix multi-edge destination nodes in caseCase().

draft landmarksB note.

plot origin Square names in plot.walking_path_B().
amend longTitle(type = "pumps").

enable multiple origins and use walking path type functions.

add pumpPump() prototype.

add caseCase() prototype.

add casePump() prototype.

change @docType "package" to "_PACKAGE" in cholera.R for 'roxygen2' 7.3.0.

add pumpCase.default() to NAMESPACE for 'roxygen2' 7.3.0.

add pearsonResiduals() methods to NAMESPACE for 'roxygen2' 7.3.0.

remove multi.core argument from walkingPathB().
set RoxygenNote to "7.3.0".

allow multiple landmarks in mapDataRange().

fix labels for origin landmark Squares.

amend mapDataRange().

add/use mapDataRange() in walkingPathB().

fix latlong coordinates for modelLodgingHouses().
update landmarksB.

add type exception for landmark destinations in walkingPathB().

change numeric zoom to a factor >= 0 in plot.walking_path_B().

increase default padding for plot.walking_path_B().

remove multi.core in neighborhoodDataB() for latlongNearestPump() and walkingPathB().

copyedit Clifford Street missing segment description in README.

use walkingPathB() in README.

remove parallel code from neighborhoodDataB().

remove parallel implementation of embedNodes().

fix zoom for non-landmarks and tweak zoom padding for latlong = TRUE.

move segmentIntersection() to landmarkDataB.R.

rename geodesicMeters() to geoCartesian().

fix coordinates in stLukesChurch().
update landmarksB.

change geodesic to geo.cartesian in segmentTrigonometryAddress().

clean modelLodgingHouses().

accommodate landmark labels in plot.walking_path_B().

restore nodeData().
fix typo for landmarksB documentation

provisionally use landmarksB and landmark.squaresB.

fix squareCenterB() output variable names.

add landmarksB and landmark.squaresB data frames.

drop .proj suffix from coordinate names in Squares() and squareCenterB().

rename coordinates in functions in landmarkDataB().

implement parallel version of landmarkDataB().

change geodesics to geo.cartesian in landmarkB functions.

amend pantheonBazaar() and stLukesChurch().

use "&" as coordinate delimeter in pasteCoordsB().
add/set squareExitsB(latlong = FALSE).
amend squareCenterB() latlong variables.
amend nominal and latlong coordinates in Squares().

amend nominal and latlong coordinates in stJamesWorkhouse().

amend nominal and latlong coordinates in stLukesChurch().

add segmentGeoCartesian().

add amended roadSegmentData().

rename roadSegmentData() to roadSegEndpt().

amend nominal and latlong coordinates in johnSnow().

amend nominal and latlong coordinates in pantheonBazaar().

amend nominal and latlong coordinates in karlMarx().

amend nominal and latlong coordinates in magistratesCourt().
fix output of magistratesCourt().

amend nominal and latlong coordinates in lionBrewery().

amend nominal and latlong coordinates in cravenChapel().
add coordsCartesian() and projCartesian().

amend exception for single coordinates in meterLatLong().

fix exception for single coordinates in meterLatLong().

set address to Hopkins Street; use proportion method in modelLodgingHouses().

add exception for single coordinates (1 row) in meterLatLong().

amend nominal and latlong coordinates in modelLodgingHouses().

rename/amend assignLandmarkAddress() to projectLandmarkAddress().

amend nominal and latlong coordinates in argyllHouse().

add/set roadSegmentData(latlong = FALSE).

add/set segmentTrigonometryAddress(latlong = FALSE).

add landmarkPDF().

amend landmarkSquares() and Squares(label.coord = TRUE).

alphabetize landmarks and fix case IDs.

set exit order in Squares().

amend assignLandmarkAddress() and renumber landmark case IDs.

use landmarkDataB() in nodeData().

revert to other endpoint in stJamesWorkhouse().

set case IDs for Golden and Soho Square to 20021:20022 in landmarkSquares().

add/amend functions and clean code in landmarkDataB().

amend modelLodgingHouses().

add landmarkSquares().

make pump.select first argument in addNeighborhoodWalking().

amend addCase(case %in% c("anchor", "fatality", "orthogonal")).

enable addSnow().

add/use Squares().

amend coordinates in squareCenterB() and squareExitsB().

provisionally restore tanakaContourPlot().

clean code for Squares in landmarkDataB().

add more functions to landmarkDataB().

add/use roadSegmentData().

amend provisional landmarkDataB().

add segmentTrignometryAddress().

add addressProportion().

add squareCenterB().

add cravenChapel().

add notes about model lodging houses.

add assignLandmarkAddress().

add importFrom deldir tile.list in voronoiPolygons().

add stLukes().

add lionBrewery().

fix magistratesCourt().

clean landmarkDataB().

amend magistratesCourt().

add roadTheta() and trignometricDelta().

use isTRUE()/isFALSE() in walkingPathB().

add Marlborough Street Magistrates Court and landmark street location/address.
add/use magistratesCourt().

clean DESCRIPTION Imports.

check for internet connection in tanakaContourPlot().

provisionally restore tanakaContourPlot().

use importFrom for functions with limited package use.

clean up use of double colon operator.

clean DESCRIPTION Imports.

use importFrom for 'sp' functions.

use landmark addresses (lon.proj and lat.proj) in embedNodes().

set Lion Brewery address (lon.proj and lat.proj) to Broad Street.

move final "last mile" arrow and path info in plot.walking_path_B().

fix Golden Square in latlongLandmarks(); amend 'landmarks'.

use separate zoom padding for latlong = TRUE/FALSE in walkingPathB().

set path color to "blue" for walkingPathB(path %in% c("cases", "pumps")).

use separate cutpoints, latlong = TRUE/FALSE, for zero length arrows with walkingPathB().

archive latlongWalkingPath().

add plot and print methods for walkingPathB().

return "edges" and set class to "walking_path_B" for walkingPathB().

fix walking.time computation and use "xy" as path coordinates in walkingPathB(latlong = FALSE).

add walkingPathB().

amend graphical elements and syntax in plot.latlong_walking_path().

amend syntax for plot.latlong_walking_path(long.title = TRUE).

fix validateDestinationCases() for multiple landmark names.

add/set plot.latlong_walking_path(long.title = TRUE).

return "pmp" with latlongWalkingPath().

add plot(latlongWalkingPath(type = "case-pump")) prototype.

simplify computation of "ego.node" in latlongWalkingPath(destination = NULL).

consolidate path data computation latlongWalkingPath().

consolidate "data.summary" output in latlongWalkingPath().

compute "d" for latlongWalkingPath(origin = grep("Square", origin), destination = NULL, type = "case-pump").

add additional message(s) and exclusion(s) of origin in destination for latlongWalkingPath().
add message about pump 2 isolate in latlongWalkingPath(destination = NULL, type = "pumps").

allow landmark and pump names in latlongWalkingPath().

allow multiple Squares in validateDestinationCases().

fix pump names (street names) in selectPump().

add type = "cases" and type = "pumps" to latlongWalkingPath().
allow landmark and pump names in latlongWalkingPath().

allow pump names (street names) in selectPump().
fix selectPump() using all(pump.num < 0).

allow negative selection in validateDestinationCases().
remove redundant num.chk.

add exception for all(destination.chk) == TRUE in validateDestinationCases().

add validateDestinationCases() prototype.

archive nominalNeighborhoodData().

add/set latlongNeighborhoodWalking(case.set = "observed", weighted = TRUE).
parallelize computation of paths in plot.latlong_walking()

use neighborhoodDataB() in latlongWalkingPath().

use neighborhoodDataB() in latlongNearestPump().

separate cases, landmarks and pumps in embedNodes().

use latlong road segment endpoint for cases 286 & 369 in latlongOrthoAddress().
amend cases 286 & 369 in latlong.ortho.addr data frame.

amend The Pantheon latlong coordinates in landmarks data frame.

amend Golden and Soho Square(s) latlong coordinates in landmarks data frame.

use georeferenced segment coordinates for Squares in latlongLandmarks().
use landmarkDataB() in landmarksPDF() and latlongLandmarks(); exclude Squares.

add code for latlongWalkingPath(weighted = FALSE).

archive latlongEmbedB() and nominalEmbed().
add neighborhoodDataB().

add latlongNeighborhoodDataB() prototype.

add embedNodes() prototype.

add orthogonal longitude and latitude to landmarks data frame.

add landmarkDataB().

use vars in nominalEmbed() and latlongEmbedB().

add latlongEmbedB() prototype - based on nominalEmbed().

temporarily revert "case" to "anchor" for nodes created by nominalEmbed().

add/set nominalEmbed(embed.pumps = TRUE).

add/set nominalNeighborhoodData(embed.pumps = TRUE).

add nominalNeighborhoodData() and nominalEmbed() prototypes.

compute geographic distance for edges and output road.data in latlongNeighborhoodData().

compute edges$id2 and output road.data in latlongEmbed().

add/set embed.addr = TRUE in latlongEmbed() and latlongNeighborhoodData().

use selectPump() in latlongNearestPump(metric = "walking").

restrict Adam and Eve Court exception to latlongNearestPump(case.set = "expected").

use walkingTime() in latlongNearestPump().

add/set latlongNearestPump(case.set = "observed") and parallelize.
amend exception for Adam and Eve Court.

add/set latlongEmbed(case.set = "observed") and parallelize.

add/set latlongNeighborhoodData(case.set = "observed").

change neighborhoodData(observed = TRUE) to neighborhoodData(case.set = "observed").

use snowMap() and addRoads() in plot.walking().
drop msg argument in neighborhoodWalking().

clean plot.latlongEuclidean(type).

remove redundant addRoads() in plot.euclidean().

enable neighborhoodEuclidean(case.location = "orthogonal"); remove msg argument.

add/set plot.latlongVoronoi(delaunay.voronoi = "voronoi").

add/set plot.voronoi(delaunay.voronoi = "voronoi").

amend latlongNeighborhoodEuclidean() for amended latlongVoronoi().

add/set addDelaunay(latlong = FALSE, line.width = 1).

compute Voronoi cells and Delaunay triangles in latlongVoronoi().
amend addVoronoi() for amended latlongVoronoi().

use snowMap() in plot.voronoi().

change latlongNeighborhoodVoronoi()'s class to "latlongVoronoi".
use pumpTokens(); loop over pump names in plotLatlongVoronoiCases().

add exceptions for "voronoi" and "latlongVoronoi" classes in pumpTokens().

use pump.id for selection and pump.select for title in latlongNeighborhoodVoronoi().

add plots for latlongNeighborhoodEuclidean(case.set = "expected").

add/set latlong = FALSE to pearlStringRadius(), peripheryCases() and travelingSalesman().

add/set pumpTokens(latlong = FALSE) and amend display of unselected pumps.

assign pump names to list elements in latlongVoronoi().
fix latlongVoronoi(pump.select).

amend color selection in neighborhoodVoronoi().

use pump.id instead of pumpID in neighborhoodWalking().

amend and simplify pumpTokens().

change latlongNeighborhoodEuclidean() class to "latlongEuclidean".

use separate auxilliary plot functions in plot.euclidean().

add zone, rd.name.short and rd.name.check variables (columns) to appendixB().

add appendixB().

add/set latlongNeighborhoodEuclidean(case.set = "observed").

add latlong coordinates for latlong.regular.cases.

add/set latlongSimulateFatalities(recompute = FALSE).

use case.location %in% c("address", "orthogonal") in addNeighborhoodCases().
use case.location %in% c("address", "orthogonal") in addNeighborhoodEuclidean().
set case.set = "expected" in euclideanPath() in addNeighborhoodEuclidean().
use case.location %in% c("address", "orthogonal") in neighborhoodEuclidean().
update parLapply() for amended addEuclideanPath().

amend addEuclideanPath(case.location, case.set, mileposts, milepost.unit, milepost.interval).

fix plot.latlong_euclidean_path(milepost.interval).

use case.location %in% c("address", "orthogonal") and case.set %in% c("observed", "expected").

amend pumpTokens() for negative selection.

use "&" as coordinate delimeter in ortho.proj.pump and ortho.proj.pump.vestry.

fix euclideanPath() and addEuclideanPath() for revised quandrantCoordinates().

temporarily archive tanakaContourPlot() for 'sp' evolution.

add latlongNeighborhoodEuclidean().

add title to plot.latlongNeighborhoodVoronoi().

use plotLatlongVoronoiCases().

use "address" or "orthogonal" for case.location and pump.location.

add/set latlongNeighborhoodVoronoi(case.location = "anchor", pump.location = "nominal")

set neighborhoodVoronoi(case.location %in% c("address", "anchor")).
fix pumpTokens() for negative selection in plot.voronoi().
use only address(es) or anchor(s) for plot.voronoi(euclidean.paths = TRUE).

remove add.case argument from plot.latlongNeighborhoodVoronoi().

migrate from sp::spDistsN1() to geosphere::distGeo() in plotLatlongEuclideanPaths().

add latlong.sim.ortho.proj and latlong.regular.cases.

add latlongSimulateFatalities() and latlongRegularCartesianCases().

set case.location = c("address" "fatality"); use ortho.proj with case.location = "address".

use plotLatlongEuclideanPaths() in latlongNeighborhoodVoronoi().

set col = "gray" for roads in plot.voronoi().

use serialization format version 3 for fatalities, fatalities.address and fatalities.unstacked.

use "&" as coordinate delimeter in embedSites(), nodeData() and numericNodeCoordinates().

add/use embedSites(ortho.pump).

amend latlong.ortho.addr using amended latlongOrthoAddress().

choose nearest road segment endpoint for manual reclassification cases that fail bisection test in latlongOrthoAddress().

amend latlong.ortho.addr for GCP v.02.

add/set latlongOrthoAddress(radius = 60).

amend fatalities.unstacked for GCP v.02; add fatalitiesUnstack().

amend fatalities and fatalities.address for GCP v.02.

use milePosts() in plot.walking_path().

rename drawPathB() and milePosts() to drawPathLatLong() and milePostsLatLong(); contextualize subtitle.

add/set plot.walking_path(mileposts = TRUE).

set/use quandrantCoordinatesB() as default quandrantCoordinates().

plot case and pump addresses in plot.latlong_walking_path().

change "pump.id" to "id" in latlongEmbed() and latlongNearestPump().

amend subtitle in latlongEuclideanPath().

enable latlongEuclideanPath(case.location).
amend eucl.data and format code.
make mileposts conditional on path distancce.

change "pump.id" to "id" in latlongOrthoPump().

add latlongEuclideanPath().
add milepost graphic to latlongEuclideanPath().

update latlong.ortho.addr, latlong.ortho.pump and latlong.ortho.pump.vestry (GCP v.02).

amend/update latlongOrthoAddress() for GCPs v.02.

add note about missing Clifford Street segment.

add/set segmentHighlight(latlong = FALSE, rotate.label = FALSE).

add missing Clifford Street segment; use GCPs v.02.

add cliffordStreet().

use specific street IDs in unitMeter().

add/set streetHighlight(latlong = FALSE).

add latlongOrthoLandmarks() prototype.

remove from NAMESPACE latlong functions that document data.

remove orthogonal code from latlongLandmarks().

remove unused functions from latlongCoordinates().

use streetLength(latlong = TRUE) and clean code in latlongStreetNameLocator().

fix distanceTime(distance.unit = "native").

add/set streetLength(latlong = FALSE).

add/set snowMap(add.axes_box = FALSE).

reset (delete) lon-lat for recomputation in latlongFrame() and latlongRoads().
remove ::: operators and un-export latlongRoads().

use "&" as coordinate delimeter in latlongRoads().
amend classification error diagnostic in latlongRoads().

fix addRoads() in snowMap(add.tanaka = FALSE).

add tanakaContourPlot().

add latlongStreetNameLocator().

enable snowMap(add.landmarks = TRUE).
add/set addLandmarks(latlong = FALSE).
add/set addLandmarks(text.col = "black").
add Golden Square and Soho Square to addLandmarks(latlong = TRUE).
add point only for St Luke's Church in addLandmarks(latlong = FALSE).
add point and pos = 4 label for St Luke's Church in addLandmarks(latlong = TRUE).
enable addLandmarks(highlight.perimeter = TRUE, latlong = TRUE).
add Adam and Eve Court and Falconberg Court and Mews to addLandmarks(latlong = TRUE).

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().

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().

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.

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.

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.

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()

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()

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(), 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" "unstacking.bars.notes"

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.

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()

Initial CRAN release.

lindbrook/cholera documentation built on Jan. 13, 2025, 3:49 p.m.

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Note that we can't provide technical support on individual packages. You should contact the package authors for that.

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

NEWS.md In lindbrook/cholera: Amend, Augment and Aid Analysis of John Snow's Cholera Map

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

NEWS.md
In lindbrook/cholera: Amend, Augment and Aid Analysis of John Snow's Cholera Map