Polar annulus plots on dynamic and static maps

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,
  progress = TRUE,
  ...,
  control = 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 and a non-pairwise statistic is supplied, 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 for non-pairwise statistics.

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 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 polar markers.

default: 1 | scope: dynamic & static

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

key

Draw individual marker legends?

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.

progress

Show a progress bar?

default: TRUE | scope: dynamic & static

By default, a progress bar is shown to visualise the function's progress creating individual polar markers. This option allows this to be turned off, if desired.

...

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.

control

Deprecated. Please use type.

Value

Either:

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

Parallel processing with mirai

Creating a directional analysis map can take a lot of time; each polar marker needs to be plot individually, and many of these require some expensive computations. openairmaps supports parallel processing with {mirai} to speed these computations up. Users may create workers by running mirai::daemons() in their R session.

mirai::daemons(4)
polarMap(polar_data, "no2")

Typically, spawning one fewer daemons than your number of available cores is a useful rule of thumb. Parallel processing will be most useful for the most computationally intensive plotting functions - i.e., polarMap() and annulusMap().

Customisation of static maps using ggplot2

As all static plots functions are ggplot2 figures, further customisation is possible using functions such as ggplot2::theme(), ggplot2::guides() and ggplot2::labs().

Subscripting pollutants (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.

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 color = ggplot2::guide_legend() for discrete legends.

The extent of a map can be adjusted using the xlim and ylim arguments of ggplot2::coord_sf().

polarMap(polar_data, "no2", static = TRUE) +
    ggplot2::coord_sf(
        xlim = c(-0.3, 0.2),
        ylim = c(51.2, 51.8)
    )

Examples

if (FALSE) { # \dontrun{
annulusMap(polar_data,
  pollutant = "nox",
  period = "hour",
  provider = "CartoDB.Voyager"
)
} # }

Polar annulus plots on dynamic and static maps

Usage

Arguments

Value

Parallel processing with mirai

Customisation of static maps using ggplot2

See also

Examples