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Spatially interpolated dynamic and static maps

Source: R/interpMap.R
interpolate-map.Rd

These functions create interpolated surfaces out of data at individual monitoring sites. This can be useful to 'fill in the gaps' to estimate pollution concentrations where no monitoring is occurring, or better identify geographical patterns in pollution data. krigingMap() creates a smooth spatially interpolated surface using either inverse distance weighting or point kriging. voronoiMap() creates a surface of 'closest observation' polygons. The kriging formula is currently always pollutant ~ 1; krigingMap() does not currently support more complex models.

Usage

krigingMap(
  data,
  pollutant = NULL,
  statistic = "mean",
  percentile = 95,
  newdata = NULL,
  method = c("idw", "kriging"),
  breaks = NULL,
  labels = NULL,
  limits = NULL,
  latitude = NULL,
  longitude = NULL,
  crs = 4326,
  provider = "OpenStreetMap",
  cols = "turbo",
  alpha = 0.8,
  show.markers = TRUE,
  marker.border = "white",
  legend = TRUE,
  legend.position = NULL,
  legend.title = NULL,
  legend.title.autotext = TRUE,
  static = FALSE,
  vgm = gstat::vgm(psill = 1, model = "Exp", range = 50000, nugget = 1),
  args.idw = list(),
  args.variogram = list(),
  args.fit.variogram = list(),
  args.krige = list()
)

voronoiMap(
  data,
  pollutant = NULL,
  statistic = "mean",
  percentile = 95,
  newdata = NULL,
  breaks = NULL,
  labels = NULL,
  limits = NULL,
  latitude = NULL,
  longitude = NULL,
  crs = 4326,
  provider = "OpenStreetMap",
  cols = "turbo",
  alpha = 0.8,
  show.markers = TRUE,
  marker.border = "white",
  voronoi.border = "white",
  legend = TRUE,
  legend.position = NULL,
  legend.title = NULL,
  legend.title.autotext = TRUE,
  static = FALSE,
  args.voronoi = list()
)

Arguments

data

Input data table with pollutant and geo-spatial information.

required | scope: dynamic & static

A data frame. The data frame must contain at least one numeric column to interpolate, plus a decimal latitude and longitude (or X/Y coordinate used in conjunction with crs).

pollutant

Pollutant name.

required | scope: dynamic & static

The column name of the pollutant to plot. Multiple pollutants are prohibited by this function.

statistic

Statistic for aggregating pollutant data.

default: "mean" | scope: dynamic & static

Pollutant data will be aggregated by latitude & longitude; statistic controls how this is achieved. Possible statistics include:

  • "mean": the arithmetic mean (using mean())

  • "median": the median (middle) value (using stats::median())

  • "max": the maximum value (using max())

  • "min": the maximum value (using min())

  • "sd": the standard deviation (using stats::sd())

  • "percentile": a percentile value, defined using the percentile argument (using stats::quantile())

percentile

The percentile when `statistic = "percentile"

default: 95 | scope: dynamic & static

The percentile level used when statistic = "percentile". The default is 95, representing 95%. Should be between 0 and 100.

newdata

A spatial dataset of prediction locations.

default: NULL | scope: dynamic & static

By default, a bounding box of all latitudes and longitudes are used for prediction, but this is often not useful or aesthetically pleasing. newdata should be a spatial data frame (constructed with sf::st_as_sf()). This may be a country or authority boundary relevant to the data input.

method

Spatial interpolation method.

default: "idw" | scope: dynamic & static

The spatial interpolation method to use for krigingMap(). "idw" uses inverse distance weighting (IDW) which is simpler and faster. "kriging" uses full point kriging which is typically more accurate, but is also more complex and computationally intensive.

labels, breaks

Discretise the map color scale.

default: NULL | scope: dynamic & static

By default, a continuous colour scale is used. If breaks are provided, the colour scale will be discretised using cut(). labels can also be provided to customise how each factor level is labelled.

limits

Specifier for the plot colour scale bounds.

default: NULL | scope: dynamic & static

A numeric vector in the form c(lower, upper) used to define the colour scale. For example, limits = c(0, 100) would force the plot limits to span 0-100. If NULL, appropriate limits will be selected based on the range in data[[pollutant]].

latitude, longitude

The decimal latitude(Y)/longitude(X).

default: NULL | scope: dynamic & static

Column names representing the decimal latitude and longitude (or other Y/X coordinate if using a different crs). If not provided, will be automatically inferred from data by looking for a column named "lat"/"latitude" or "lon"/"lng"/"long"/"longitude" (case-insensitively).

crs

The coordinate reference system (CRS).

default: 4326 | scope: dynamic & static

The coordinate reference system (CRS) of the data, passed to sf::st_crs(). By default this is EPSG:4326, the CRS associated with the commonly used latitude and longitude coordinates. Different coordinate systems can be specified using crs (e.g., crs = 27700 for the British National Grid). Note that non-lat/lng coordinate systems will be re-projected to EPSG:4326 for plotting on the map.

provider

The basemap(s) to be used.

default: "OpenStreetMap" | scope: dynamic & static

The base map(s) to be used for the map. If not provided, will default to "OpenStreetMap"/"osm" for both dynamic and static maps.

  • Dynamic: Any number of leaflet::providers. See http://leaflet-extras.github.io/leaflet-providers/preview/ for a list of all base maps that can be used. If multiple base maps are provided, they can be toggled between using a "layer control" interface. By default, the interface will use the provider names as labels, but users can define their own using a named vector (e.g., c("Default" = "OpenStreetMap", "Satellite" = "Esri.WorldImagery"))

  • Static: One of rosm::osm.types().

There is some overlap in static and dynamic providers. For example, {ggspatial} uses "osm" to specify "OpenStreetMap". When static providers are provided to dynamic maps or vice versa, {openairmaps} will attempt to substitute the correct provider string.

cols

Colours to use for plotting.

default: "turbo" | scope: dynamic & static

The colours used for plotting, passed to openair::openColours(). The default, "turbo", is a rainbow palette with relatively perceptually uniform colours.

alpha

Transparency value for interpolated surface.

default: 1 | scope: dynamic & static

A value between 0 (fully transparent) and 1 (fully opaque).

show.markers

Show original monitoring site markers?

default: TRUE | scope: dynamic & static

When TRUE, the coordinates in the input data will be shown as coloured markers.

marker.border, voronoi.border

Border colour to use for markers and voronoi tiles.

default: "white" | scope: dynamic & static

Any valid HTML colour (e.g., a hex code). Use NA for no border.

legend

Draw a legend?

default: TRUE | scope: dynamic & static

When TRUE, a legend will appear on the map identifying the colour scale.

legend.position

Position of the shared legend.

default: NULL | scope: dynamic & static

When legend = TRUE, where should the legend be placed?

  • Dynamic: One of "topright", "topright", "bottomleft" or "bottomright". Passed to the position argument of leaflet::addLegend().

  • Static:: One of "top", "right", "bottom" or "left". Passed to the legend.position argument of ggplot2::theme().

legend.title

Title of the legend.

default: NULL | scope: dynamic & static

By default, when legend.title = NULL, the function will attempt to provide a sensible legend title. legend.title allows users to overwrite this - for example, to include units or other contextual information. For dynamic maps, users may wish to use HTML tags to format the title.

legend.title.autotext

Automatically format the title of the legend?

default: TRUE | scope: dynamic & static

When legend.title.autotext = TRUE, legend.title will be first run through quickTextHTML() (dynamic) or openair::quickText() (static).

static

Produce a static map?

default: FALSE

This controls whether a dynamic or static map is produced. The former is the default and is broadly more useful, but the latter may be preferable for DOCX or PDF outputs (e.g., academic papers).

vgm

A variogram model

default: gstat::vgm(psill = 1, model = "Exp", range = 50000, nugget = 1) | scope: dynamic & static

The variogram model to use when method = "kriging". Must be the output of gstat::vgm().

args.idw, args.variogram, args.fit.variogram, args.krige

Extra arguments to pass to spatial interpolation functions for krigingMap().

scope: dynamic & static

Extra arguments passed to gstat::idw(), gstat::vgm(), gstat::fit.variogram(), and gstat::krige().

args.voronoi

Extra arguments to pass to spatial interpolation functions for voronoiMap().

scope: dynamic & static

Extra arguments passed to terra::voronoi(), with the exception of x which is dealt with by voronoiMap().

Value

Either:

  • Dynamic: A leaflet object

  • Static: A ggplot2 object using ggplot2::coord_sf() coordinates with a ggspatial basemap

Examples

if (FALSE) { # \dontrun{
# import ozone DAQI
daqi <-
  openair::importUKAQ(
    pollutant = "o3",
    year = 2020,
    source = "aurn",
    data_type = "daqi",
    meta = TRUE
  )

# get a UK shapefile
uk <- rnaturalearth::ne_countries(scale = 10, country = "united kingdom")

# create spatially interpolated map
voronoiMap(
  daqi,
  pollutant = "poll_index",
  newdata = uk,
  statistic = "max",
  breaks = seq(0.5, 10.5, 1),
  labels = as.character(1:10),
  legend.title = "Max O3 DAQI",
  cols = "daqi"
)

krigingMap(
  daqi,
  pollutant = "poll_index",
  newdata = uk,
  statistic = "max",
  legend.title = "Max O3 DAQI",
  cols = openair::openColours("daqi", n = 10),
  limits = c(1, 10)
)
} # }