annulusMap: Polar annulus plots on dynamic and static maps

In davidcarslaw/openairmaps: Create Maps of Air Pollution Data

Polar annulus plots on dynamic and static maps

Description

The annulusMap() function creates a map using polar annulus plots as markers. Any number of pollutants can be specified using the pollutant argument, and multiple layers of markers can be created using type. By default, these maps are dynamic and can be panned, zoomed, and otherwise interacted with. Using the static argument allows for static images to be produced instead.

Usage

annulusMap(
  data,
  pollutant = NULL,
  period = "hour",
  limits = "free",
  latitude = NULL,
  longitude = NULL,
  crs = 4326,
  type = NULL,
  popup = NULL,
  label = NULL,
  provider = "OpenStreetMap",
  cols = "turbo",
  alpha = 1,
  key = FALSE,
  legend = TRUE,
  legend.position = NULL,
  legend.title = NULL,
  legend.title.autotext = TRUE,
  control.collapsed = FALSE,
  control.position = "topright",
  control.autotext = TRUE,
  d.icon = 200,
  d.fig = 3.5,
  static = FALSE,
  static.nrow = NULL,
  ...
)

Arguments

data	Input data table with pollutant, wind, and geo-spatial information. required | scope: dynamic & static A data frame. The data frame must contain the data to plot the directional analysis marker, which includes wind speed (ws), wind direction (wd), and the column representing the concentration of a pollutant. In addition, data must include a decimal latitude and longitude (or X/Y coordinate used in conjunction with crs).
pollutant	Pollutant name(s). required | scope: dynamic & static The column name(s) of the pollutant(s) to plot. If multiple pollutants are specified the type argument will no longer be able to be used, and: Dynamic: The pollutants can be toggled between using a "layer control" menu. Static:: The pollutants will each appear in a different panel. Multiple pollutants prohibit the use of the type argument.
period	Temporal period for radial axis. default: "hour" | scope: dynamic & static Options are "hour" (the default, to plot diurnal variations), "season" to plot variation throughout the year, "weekday" to plot day of the week variation and "trend" to plot the trend by wind direction.
limits	Specifier for the plot colour scale bounds. default: "free" | scope: dynamic & static One of: "fixed" which ensures all of the markers use the same colour scale. "free" (the default) which allows all of the markers to use different colour scales. 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.
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.
type	A method to condition the data for separate plotting. default: NULL | scope: dynamic & static Used for splitting the input data into different groups, passed to the type argument of openair::cutData(). When type is specified: Dynamic: The different data splits can be toggled between using a "layer control" menu. Static:: The data splits will each appear in a different panel. type cannot be used if multiple pollutant columns have been provided.
popup	Content for marker popups on dynamic maps. default: NULL | scope: dynamic Columns to be used as the HTML content for marker popups on dynamic maps. Popups may be useful to show information about the individual sites (e.g., site names, codes, types, etc.). If a vector of column names are provided they are passed to buildPopup() using its default values.
label	Content for marker hover-over on dynamic maps. default: NULL | scope: dynamic Column to be used as the HTML content for hover-over labels. Labels are useful for the same reasons as popups, though are typically shorter.
provider	The basemap(s) to be used. default: "OpenStreetMap" | scope: dynamic & static The base map(s) to be used beneath the polar markers. 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. Read more about this palette at https://research.google/blog/turbo-an-improved-rainbow-colormap-for-visualization/.
alpha	Transparency value for polar markers. default: 1 | scope: dynamic & static A value between 0 (fully transparent) and 1 (fully opaque).
key	Transparency value for polar markers. default: FALSE | scope: dynamic & static Draw a key for each individual marker? Potentially useful when limits = "free", but of limited use otherwise.
legend	Draw a shared legend? default: TRUE | scope: dynamic & static When all markers share the same colour scale (e.g., when limits != "free" in polarMap()), should a shared legend be created at the side of the map?
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).
control.collapsed	Show the layer control as a collapsed? default: FALSE | scope: dynamic For dynamic maps, should the "layer control" interface be collapsed? If TRUE, users will have to hover over an icon to view the options.
control.position	Position of the layer control menu default: "topright" | scope: dynamic When type != NULL, or multiple pollutants are specified, where should the "layer control" interface be placed? One of "topleft", "topright", "bottomleft" or "bottomright". Passed to the position argument of leaflet::addLayersControl().
control.autotext	Automatically format the content of the layer control menu? default: TRUE | scope: dynamic When control.autotext = TRUE, the content of the "layer control" interface will be first run through quickTextHTML().
d.icon	The diameter of the plot on the map in pixels. default: 200 | scope: dynamic & static This will affect the size of the individual polar markers. Alternatively, a vector in the form c(width, height) can be provided if a non-circular marker is desired.
d.fig	The diameter of the plots to be produced using {openair} in inches. default: 3.5 | scope: dynamic & static This will affect the resolution of the markers on the map. Alternatively, a vector in the form c(width, height) can be provided if a non-circular marker is desired.
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).
static.nrow	Number of rows in a static map. default: NULL | scope: static Controls the number of rows of panels on a static map when multiple pollutants or type are specified; passed to the nrow argument of ggplot2::facet_wrap(). The default, NULL, results in a roughly square grid of panels.
...	Arguments passed on to openair::polarAnnulus resolution Two plot resolutions can be set: “normal” and “fine” (the default). local.tz Should the results be calculated in local time that includes a treatment of daylight savings time (DST)? The default is not to consider DST issues, provided the data were imported without a DST offset. Emissions activity tends to occur at local time e.g. rush hour is at 8 am every day. When the clocks go forward in spring, the emissions are effectively released into the atmosphere typically 1 hour earlier during the summertime i.e. when DST applies. When plotting diurnal profiles, this has the effect of “smearing-out” the concentrations. Sometimes, a useful approach is to express time as local time. This correction tends to produce better-defined diurnal profiles of concentration (or other variables) and allows a better comparison to be made with emissions/activity data. If set to FALSE then GMT is used. Examples of usage include local.tz = "Europe/London", local.tz = "America/New_York". See cutData and import for more details. statistic The statistic that should be applied to each wind speed/direction bin. Can be “mean” (default), “median”, “max” (maximum), “frequency”. “stdev” (standard deviation), “weighted.mean” or “cpf” (Conditional Probability Function). Because of the smoothing involved, the colour scale for some of these statistics is only to provide an indication of overall pattern and should not be interpreted in concentration units e.g. for statistic = "weighted.mean" where the bin mean is multiplied by the bin frequency and divided by the total frequency. In many cases using polarFreq will be better. Setting statistic = "weighted.mean" can be useful because it provides an indication of the concentration * frequency of occurrence and will highlight the wind speed/direction conditions that dominate the overall mean. percentile If statistic = "percentile" or statistic = "cpf" then percentile is used, expressed from 0 to 100. Note that the percentile value is calculated in the wind speed, wind direction ‘bins’. For this reason it can also be useful to set min.bin to ensure there are a sufficient number of points available to estimate a percentile. See quantile for more details of how percentiles are calculated. width The width of the annulus; can be “normal” (the default), “thin” or “fat”. min.bin The minimum number of points allowed in a wind speed/wind direction bin. The default is 1. A value of two requires at least 2 valid records in each bin an so on; bins with less than 2 valid records are set to NA. Care should be taken when using a value > 1 because of the risk of removing real data points. It is recommended to consider your data with care. Also, the polarFreq function can be of use in such circumstances. exclude.missing Setting this option to TRUE (the default) removes points from the plot that are too far from the original data. The smoothing routines will produce predictions at points where no data exist i.e. they predict. By removing the points too far from the original data produces a plot where it is clear where the original data lie. If set to FALSE missing data will be interpolated. date.pad For type = "trend" (default), date.pad = TRUE will pad-out missing data to the beginning of the first year and the end of the last year. The purpose is to ensure that the trend plot begins and ends at the beginning or end of year. force.positive The default is TRUE. Sometimes if smoothing data with steep gradients it is possible for predicted values to be negative. force.positive = TRUE ensures that predictions remain positive. This is useful for several reasons. First, with lots of missing data more interpolation is needed and this can result in artefacts because the predictions are too far from the original data. Second, if it is known beforehand that the data are all positive, then this option carries that assumption through to the prediction. The only likely time where setting force.positive = FALSE would be if background concentrations were first subtracted resulting in data that is legitimately negative. For the vast majority of situations it is expected that the user will not need to alter the default option. k The smoothing value supplied to gam for the temporal and wind direction components, respectively. In some cases e.g. a trend plot with less than 1-year of data the smoothing with the default values may become too noisy and affected more by outliers. Choosing a lower value of k (say 10) may help produce a better plot. normalise If TRUE concentrations are normalised by dividing by their mean value. This is done after fitting the smooth surface. This option is particularly useful if one is interested in the patterns of concentrations for several pollutants on different scales e.g. NOx and CO. Often useful if more than one pollutant is chosen. key.header Adds additional text/labels to the scale key. For example, passing the options key.header = "header", key.footer = "footer1" adds addition text above and below the scale key. These arguments are passed to drawOpenKey via quickText, applying the auto.text argument, to handle formatting. key.footer see key.footer. key.position Location where the scale key is to plotted. Allowed arguments currently include "top", "right", "bottom" and "left". auto.text Either TRUE (default) or FALSE. If TRUE titles and axis labels will automatically try and format pollutant names and units properly e.g. by subscripting the ‘2’ in NO2.

Value

Either:

• Dynamic: A leaflet object

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

Customisation of static maps using ggplot2

As the outputs of the static directional analysis functions are ggplot2 figures, further customisation is possible using functions such as ggplot2::theme(), ggplot2::guides() and ggplot2::labs().

If multiple pollutants are specified, subscripting (e.g., the "x" in "NOx") is achieved using the ggtext package. Therefore if you choose to override the plot theme, it is recommended to use ⁠[ggplot2::theme()]⁠ and ⁠[ggtext::element_markdown()]⁠ to define the strip.text parameter.

When arguments like limits, percentile or breaks are defined, a legend is automatically added to the figure. Legends can be removed using ggplot2::theme(legend.position = "none"), or further customised using ggplot2::guides() and either color = ggplot2::guide_colourbar() for continuous legends or fill = ggplot2::guide_legend() for discrete legends.

See Also

openair::polarAnnulus()

Other directional analysis maps: diffMap(), freqMap(), percentileMap(), polarMap(), pollroseMap(), windroseMap()

Examples

## Not run: 
annulusMap(polar_data,
  pollutant = "nox",
  period = "hour",
  provider = "CartoDB.Voyager"
)

## End(Not run)

davidcarslaw/openairmaps documentation built on April 28, 2024, 3 p.m.