Package 'arear'

Description

NHS trust admissions data from the legacy COVID API from 2021

Usage

apiTrusts

Format

A 72928 line data frame:

date

the ONS code for the ares

area_name

The name for the area

area_type

the type of area (LSOA, DZ or LGD)

area_code

the NHS ODS code

metric

hospital cases

metric_name

hospital cases

value

the count

Description

Get feature service information from an arcgis rest service

Usage

arcgisServiceInfo(url, ...)

Arguments

Value

a dataframe of available feature and map services

Examples

url = "https://services1.arcgis.com/ESMARspQHYMw9BZ9/ArcGIS/rest/services"
arcgisServiceInfo(url)

Description

Clear data from the passthrough cache for complex or long running operations

Usage

cache_clear(
  .cache = rappdirs::user_cache_dir(utils::packageName()),
  .prefix = ".*",
  interactive = TRUE
)

Arguments

Value

nothing. called for side effects

Description

This implements the label propagation algorithm described in our paper: R. J. Challen, G. J. Griffith, L. Lacasa, and K. Tsaneva-Atanasova, ‘Algorithmic hospital catchment area estimation using label propagation’, BMC Health Services Research, vol. 22, no. 1, p. 828, June 2022, doi: 10.1186/s12913-022-08127-7.

Usage

catchment(
  supplyShape,
  supplyIdVar = "code",
  supplyVar,
  supplyOutputVars = supplyShape %>% dplyr::groups(),
  demandShape,
  demandIdVar = "code",
  demandVar,
  growthConstant = 1.2,
  bridges = arear::ukconnections,
  outputMap = TRUE,
  ...
)

Arguments

Value

a

Description

This implements the label propagation algorithm described in our paper: R. J. Challen, G. J. Griffith, L. Lacasa, and K. Tsaneva-Atanasova, ‘Algorithmic hospital catchment area estimation using label propagation’, BMC Health Services Research, vol. 22, no. 1, p. 828, June 2022, doi: 10.1186/s12913-022-08127-7.

Usage

createCatchment(
  supplyShape,
  supplyIdVar = "code",
  supplyVar,
  supplyOutputVars = supplyShape %>% dplyr::groups(),
  demandShape,
  demandIdVar = "code",
  demandVar,
  growthConstant = 1.2,
  bridges = arear::ukconnections,
  outputMap = TRUE
)

Arguments

Value

a

Description

A network of neighbouring map regions including connections due to bridges airports or ferry links, defined in the bridges input.

Usage

createNeighbourNetwork(
  shape,
  idVar = "code",
  bridges = arear::ukconnections,
  queen = FALSE,
  ...
)

Arguments

Value

an edge list of ids with from and to columns

Examples

edges = createNeighbourNetwork(
  shape = arear::testdata$grid11x11,
  idVar = "id"
)

# in regular grid each cell has 4 neighbours except the edges and corners
# we loose 1 per edge

nrow(edges) == 11*11*4-4*11

queens = createNeighbourNetwork(
  shape = arear::testdata$grid11x11,
  idVar = "id",
  queen = TRUE
)

# each cell has 8 queen neighbours
# except edge pieces which have 3 less, and corners which have 5 less.
nrow(queens) == 11*11*8 - 4*9*3 - 4*5

Description

Download a geojson url, optionally simplifies and cache the result

Usage

downloadGeojson(geojsonUrl, simplify = FALSE, ...)

Arguments

Value

the 'sf' object for this geoJson

Examples

# The ONS UK country files:
if (interactive()) {
  svc = "https://services1.arcgis.com/ESMARspQHYMw9BZ9/ArcGIS/rest/services"
  fs = sprintf("%s/%s",svc,"Countries_December_2024_Boundaries_UK_BUC/FeatureServer")
  layer = sprintf("%s/%s",fs,"0")
  map = downloadGeojson(layer)
  map %>% dplyr::glimpse()
}

Description

This function downloads and caches a zipped shape file map, unpacks it, finds the correct shape file layer optionally simplifies it and converts it to 'sf'.

Usage

downloadMap(zipUrl, mapName = NULL, simplify = FALSE, ...)

Arguments

Value

a 'sf' object containing the map

Examples

## Not run: 
downloadMap(
  zipUrl="https://bit.ly/3A9TnR1"
)

## End(Not run)

Description

Get layer information from a feature service

Usage

featureServerInfo(url, ...)

Arguments

Value

a dataframe of layers

Examples

svc = "https://services1.arcgis.com/ESMARspQHYMw9BZ9/ArcGIS/rest/services"
fs = sprintf("%s/%s",svc,"Countries_December_2024_Boundaries_UK_BUC/FeatureServer")
url = sprintf("%s/%s",fs,"0")
featureServerInfo(fs)

Description

Get field information from a feature service layer.

Usage

featureServerLayerInfo(url, ...)

Arguments

Value

a dataframe of field names for the selected layer

Examples

svc = "https://services1.arcgis.com/ESMARspQHYMw9BZ9/ArcGIS/rest/services"
fs = sprintf("%s/%s",svc,"Countries_December_2024_Boundaries_UK_BUC/FeatureServer")
layer = sprintf("%s/%s",fs,"0")
featureServerLayerInfo(layer)

Description

Allow basic filtering queries only at the moment. Will cache the results and handles multipart transfers.

Usage

featureServerLayerQuery(
  url,
  where = "1 = 1",
  select = "*",
  ...,
  limit = NULL,
  crs = 4326,
  queryParams = list()
)

Arguments

Value

a 'sf' of the query result

Examples

svc = "https://services1.arcgis.com/ESMARspQHYMw9BZ9/ArcGIS/rest/services"
fs = sprintf("%s/%s",svc,"Countries_December_2024_Boundaries_UK_BUC/FeatureServer")
layer = sprintf("%s/%s",fs,"0")

# default all 4 nations:
sf = featureServerLayerQuery(layer)
cat(sf$CTRY24CD)

# england only
sf2 = featureServerLayerQuery(layer, where="CTRY24CD LIKE 'E%'")
cat(sf2$CTRY24CD)

if (interactive()) {
  # Download the first 4000 LSOAs. There are lots of LSOAs and this
  # query has to be paginated. This also shows the limit feature
  # and the verbose output of the cache.
  lsoa = sprintf("%s/%s",svc,"LSOA_DEC_2021_EW_NC_v3/FeatureServer/0")
  withr::with_options(list(cache.verbose=TRUE), {
    sf_lsoa = featureServerLayerQuery(lsoa, limit = 4000)
  })

  cat(nrow(sf_lsoa))
}

Description

This assumes unique keys defined in input and output shapes through column grouping and outputs a mapping table between input and output groups. The input is related to the output by containment. I.e. the result will be where the input is wholly contained within the output shape

Usage

getContainedIn(
  inputShape,
  outputShape,
  inputVars = inputShape %>% dplyr::groups(),
  outputVars = outputShape %>% dplyr::groups(),
  suffix = c(".x", ".y")
)

Arguments

Value

- a mapping as a dataframe relating the 'inputVars' columns and 'outputVars' columns

Examples

# find the hospitals in a given area.
mapping = getContainedIn(
  inputShape = arear::surgecapacity,
  outputShape = arear::ukcovidmap(),
  inputVars = dplyr::vars(hospitalId),
  outputVars = dplyr::vars(code)
)

Description

get the intersection between to maps with ids. Caches the result in the working directory.

Usage

getIntersection(
  inputShape,
  outputShape,
  suffix = c(".x", ".y"),
  recalcArea = TRUE,
  ...
)

Arguments

Value

a sf object representing the intersection of the input and output shapes.

Description

If a map needs to be downloaded as a shapefile then it is stored temporarily. The location of this download directory can be set as option("arear.download.dir" = "~/.)

Usage

getMap(mapId = names(sources)[1], sources = arear::mapsources, ...)

Arguments

Value

a standard sf map

Examples

if (interactive()) {
  map = getMap("NHSER20")
  map %>% dplyr::glimpse()
}

Description

interpolate a variable from one set of shapes to another

Usage

interpolateByArea(
  inputDf,
  inputShape,
  by,
  interpolateVar,
  outputShape,
  inputVars = inputDf %>% dplyr::groups(),
  outputVars = outputShape %>% dplyr::groups(),
  aggregateFn = sum
)

Arguments

Value

a dataframe containing the grouping columns in 'inputVars' and 'outputVars', and the interpolated value of 'interpolateVar'

Description

List the standard maps available to download

Usage

listStandardMaps()

Value

a vector of map names

Examples

# example code
listStandardMaps()

Description

Data available under open government licence: http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/

Usage

londonShape

Format

A sf geometry with 1 row:

codeType

NHSER

code

E4000003 - the NHSER code for London

name

London

altCode

NA

area

the area

geometry

the outline

Description

A list of URLs to get maps, and metadata about the maps in the shapefiles and the column labelling.

Usage

mapsources

Format

A list with:

source

the human readable location of the map

url

the web location of the downloadable map shapefile

mapName

the name of the map contained in the shapefile (which can contain multiple maps)

codeCol

the name of the shapefile column containing the code of the area

nameCol

the name of the shapefile column containing the name of the area

altCodeCol

the name of the shapefile column containing the an alternative code for the area

simplify

should the map be simplified when loaded?

license

license terms

Description

A map theme to remove extraneous clutter

Usage

mapTheme()

Examples

ggplot2::ggplot(arear::testdata$gridDemand)+
  ggplot2::geom_sf(ggplot2::aes(fill=demand))+
  mapTheme()

Description

This can be used to pick out specific highlighted regions based on a filter, label it on a map using a short code, and provide a tabular lookup of label to full name.

Usage

plotLabelledMap(
  data,
  mapping,
  ...,
  labelMapping,
  labelStyle = list(),
  labelSort = NULL,
  labels = 6,
  labelSize = 6,
  tableSize = 6,
  labelInset = c("both", "inset", "main")
)

Arguments

Value

a list containing 4 items. Plot and legend may be added together to form a ggplot patchwork. e.g. 'p = plotLabelledMap(...)' then 'p$plot+ggplot2::scale_fill_viridis_c()+ggplot2::facet_wrap(dplyr::vars(...))+p$legend+patchwork::plot_annotation(taglevels="A")' to actually show the map.

plot

a ggplot object showing a chloropleth (usually) which is defined by the main mapping aesthetics, with an overlaid labelling layer defined by the 'labelMapping' label aesthetic. This does not include fill or colour scales so you will probably want 'plot+ggplot2::scale_fill_viridis_c()' or something similar to define the fill

. If the input data is grouped this plot will be facetted by group.

legend

a ggplot patchwork containing the lookup table from labels to other data (as determined by the 'labelMapping' aesthetics)

labelDf

the filtered dataframe of the labels appearing in the labelling layer. The .x and .y columns are added which show where the label is placed on the main map. the .label and .name show the labels and names respectively

labeller

A function that returns a layer of the labels, formatted in same way as the main map. the labeller function takes optional xVar and yVar parameter which are columns in the sf object. These define the x and y aesthetics of the labeller and default to the same position as the main map. The labeller function can be used to add a labels layer to a different map, or to a different graph. This might be useful if you want to combine cartograms with points of interest and have them consistently labelled.

Examples

# create some test data:
tmp = dplyr::bind_rows(lapply(1:4,
  function(i) testdata$diamond11x11 %>%
    dplyr::mutate(set = sprintf("set %d",i), value = runif(x)
))) %>% dplyr::group_by(set) %>%
  dplyr::mutate(name = sprintf("%s-%s", letters[x+6], letters[y+6]))

ggplot2::ggplot(tmp)+ggplot2::geom_sf(ggplot2::aes(fill = value))+
  ggplot2::facet_wrap(~set)

p = plotLabelledMap(
  data = tmp,
  mapping = ggplot2::aes(fill = value),
  labelMapping = ggplot2::aes(label=name,percent=sprintf("%1.1f%%",value*100)),
  labels = 2
)

p$plot+p$legend

Description

Create a new map with a pop-out panel to show areas where there is a high density of people for example. Defaults work well for London on an England only map.

Usage

popoutArea(
  shape,
  popoutShape = arear::londonShape,
  popoutPosition = c("NE", "NW", "SE", "SW"),
  popoutScale = 3,
  nudgeX = 0.25,
  nudgeY = 0.25
)

Arguments

Value

A new map with the content intersecting the popout area duplicated, expanded and placed in the specified corner.

Examples

tmp = popoutArea(
  arear::testdata$diamond11x11 %>% dplyr::mutate(value = x+y),
  arear::testdata$offsetBox,
  popoutPosition = "NE",
  popoutScale = 1.25
)

ggplot2::ggplot(tmp)+
  ggplot2::geom_sf(ggplot2::aes(fill=value))+
  ggplot2::scale_fill_gradient2()+
  ggplot2::geom_sf(data = arear::testdata$offsetBox, alpha=0)

Description

Preview a map with POI using leaflet

Usage

preview(
  shape,
  shapeLabelGlue = "{name}",
  shapePopupGlue = "{code}",
  poi = NULL,
  poiLabelGlue = "{name}",
  poiPopupGlue = "{code}"
)

Arguments

Value

htmlwidget

Description

Save a 'sf' as a shapefile to disk

Usage

saveShapefile(shape, mapId, dir = getwd(), overwrite = FALSE)

Arguments

Value

a the filename of the zipped shapefile

Examples

if (interactive()) {
  svc = "https://services1.arcgis.com/ESMARspQHYMw9BZ9/ArcGIS/rest/services"
  fs = sprintf("%s/%s",svc,"Countries_December_2024_Boundaries_UK_BUC/FeatureServer")
  layer = sprintf("%s/%s",fs,"0")
  map = downloadGeojson(layer)
  map %>% dplyr::glimpse()
  map2 = map %>% standardiseMap(codeCol = CTRY24CD, nameCol = CTRY24NM)
  map2 %>% dplyr::glimpse()
  saveShapefile(map2, "ctry24", dir = tempdir())
}

Description

This function renames a 'sf' with a minimal set of attributes with consistent naming with 'code', 'name' and 'codeType' columns and an optional 'altCode' column. Renames all columns to be lower case, and makes sure the 'area' column is calculated. It also loses any 'Z' or 'M' layers.

Usage

standardiseMap(
  sf,
  codeCol = "code",
  nameCol = "name",
  altCodeCol = NULL,
  codeType = NA_character_,
  ...
)

Arguments

Value

a standardised map with exactly the following columns: 'code', 'codeType', 'name', 'altCode', 'geometry' and 'area'

Examples

# example code
if (interactive()) {
  svc = "https://services1.arcgis.com/ESMARspQHYMw9BZ9/ArcGIS/rest/services"
  fs = sprintf("%s/%s",svc,"Countries_December_2024_Boundaries_UK_BUC/FeatureServer")
  layer = sprintf("%s/%s",fs,"0")
  map = downloadGeojson(layer)
  map %>% dplyr::glimpse()
  map2 = map %>% standardiseMap(codeCol = CTRY24CD, nameCol = CTRY24NM)
  map2 %>% dplyr::glimpse()
}

Description

Locations of UK general medical hospitals in mid march 2020 with estimates of beds available and maximal surge capacity HDU beds. This was manually assembled and curated from various sources in mid march 2020 as the NHS geared up to provide additional capacity to cope with the surge in COVID cases. It is not an up to date picture of NHS capacity. It does not include mental health or community hospitals. The surge capacity seems to have been calculated quite differently in Scotland.

Usage

surgecapacity

Format

A sf geometry with:

nation

England, Wales, etc...

hospitalId

An id for the hospital

sector

NHS or independent

hospitalName

the hospital name

pcds

the UK postcode of the hospital

trustId

the NHS trust or local health board of the hospital

trustName

the NHS trust or local health board name

tier1

indicator of the role of the hospital as an acure provider

hduBeds

the number of hdu beds the hospital could have provided at maximum surge in March 2020

acuteBeds

the number of acute beds the hospital could have provided at maximum surge in March 2020

Description

A list of regular lattice SF polygons used for testing purposes

Usage

testdata

Format

A list with:

grid5x5

5x5 grid centred on 0,0

grid11x11

11x11 grid centred on 0,0

diamond5x5

5x5 diagonal grid centred on 0,0

diamond11x11

11x11 diagonal grid centred on 0,0

gridDemand

an 11x11 grid with a demand parameter

gridSupply

a 3 point supply

gridSupply2

another 3 point supply with only 2 ids

gridSupplyViolateConstraint

a 4 point supply with 2 points in the same grid square

gridSupplyDegenerate

a 5 point supply with 2 points in the same grid square amd a different 2 points with the same id

Description

Small area single digit estimates are aggregated to include only over 18s, and combining gender

Usage

uk2019adultpopulation

Format

A 41740 line data frame:

code

the ONS code for the ares

name

The name for the area

codeType

the type of area (LSOA, DZ or LGD)

population

the size of the population

Details

Data available under open government licence: http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/

Source

England and Wales

https://www.ons.gov.uk/peoplepopulationandcommunity/populationandmigration/populationestimates/datasets/lowersuperoutputareamidyearpopulationestimates

Scotland

https://www.nrscotland.gov.uk/statistics-and-data/statistics/statistics-by-theme/population/population-estimates/2011-based-special-area-population-estimates/small-area-population-estimates/time-series#2018

Northern Ireland

https://www.opendatani.gov.uk/dataset/3333626e-b96e-4b90-82fb-474c6c03b868/resource/64bd8dc4-935f-4bdd-9232-90ff33f24732/

Description

These estimates are appropriate for the majority of the pandemic, and are the highest geographical resolution estimates by single year of age that I could find.

Usage

uk2019demographics()

Value

a dataframe with age, gender, codeType, code, name and count

Description

Shape file related to the mid year 2019 small area estimates for England, Wales, Scotland, and Northern Ireland. see [uk2019demographics()]

Usage

uk2019demographicsmap()

Details

There are 10 regions (mostly in Scotland) where the demographics estimates don't align with this map. This is a small number of people.

Data available under open government licence: http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/

Value

A 41730 line data frame:

code

the ONS code for the ares

name

The name for the area

codeType

the type of area (LSOA, DZ or LGD)

altCode

NA

Source

England and Wales

https://geoportal.statistics.gov.uk/datasets/lower-layer-super-output-areas-december-2011-boundaries-ew-bgc

Scotland

https://data.gov.uk/dataset/ab9f1f20-3b7f-4efa-9bd2-239acf63b540/data-zone-boundaries-2011

Northern Ireland

https://data.gov.uk/dataset/05f72866-b72b-476a-b6f3-57bd4a768674/osni-open-data-largescale-boundaries-local-government-districts-2012

Description

Small area single digit estimates are aggregated to include only over 65s, and combining gender.

Usage

uk2019retiredpopulation

Format

A 41730 line data frame:

code

the ONS code for the ares

name

The name for the area

codeType

the type of area (LSOA, DZ or LGD)

population

the size of the population

Details

Data available under open government licence: http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/

Source

England and Wales

https://www.ons.gov.uk/peoplepopulationandcommunity/populationandmigration/populationestimates/datasets/lowersuperoutputareamidyearpopulationestimates

Scotland

https://www.nrscotland.gov.uk/statistics-and-data/statistics/statistics-by-theme/population/population-estimates/2011-based-special-area-population-estimates/small-area-population-estimates/time-series#2018

Northern Ireland

https://www.opendatani.gov.uk/dataset/3333626e-b96e-4b90-82fb-474c6c03b868/resource/64bd8dc4-935f-4bdd-9232-90ff33f24732/

Description

geographical location of bridges / ferries UK connections. picked from https://developers.google.com/maps/documentation/javascript/examples/event-click-latlng#maps_event_click_latlng-html

Usage

ukconnections

Format

A dataframe with:

name

the connection

start.lat

the latitude of one end

start.long

the longditude of one end

end.lat

the latitude of the other end

end.long

the longditude of the other end

Description

Shape file related to the detailed level for PHE coronavirus statistical reporting in England, Wales, Scotland, and Northern Ireland on the coronavirus.gov.uk tracker. The legacy is the level at which detailed data was reported in the first wave, prior to the API and was aggregated by https://github.com/tomwhite/covid-19-uk-data

Usage

ukcovidmap(legacy = FALSE)

Arguments

Details

This map matches the data reported by the PHE coronavirus api when it is downloading lower tier local authority regions e.g. via https://api.coronavirus.data.gov.uk/v2/data?areaType=ltla&metric=newCasesBySpecimenDate&format=csv The API has now been discontinued.

There are 2 regions here for which no data is reported in this API - the city of London & the Isles of Scilly.

Data available under open government licence: http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/

Value

A 382 line data frame (or a 335 line data frame for legacy):

code

the ONS code for the ares

name

The name for the area

codeType

the type of area (LAD19)

altCode

NA

Source

England, Wales, Scotland & NI - LAD19

https://geoportal.statistics.gov.uk/datasets/local-authority-districts-december-2019-boundaries-uk-buc

England & Wales - LAD19

https://geoportal.statistics.gov.uk/datasets/local-authority-districts-december-2019-boundaries-uk-buc

Scotland - CA19

https://www.spatialdata.gov.scot/geonetwork/srv/eng/catalog.search#/metadata/1cd57ea6-8d6e-412b-a9dd-d1c89a80ad62

Northern Ireland -LGD12

https://data.gov.uk/dataset/05f72866-b72b-476a-b6f3-57bd4a768674/osni-open-data-largescale-boundaries-local-government-districts-2012