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Recent Releases of openair

openair - openair 2.19.0

Deprecations

importEurope() relies on the same back-end database as the saqgetr package (https://github.com/skgrange/saqgetr), which was retired in February 2024. importEurope() will now warn users of this, and outright error if year >= 2025. Users are instead encouraged to use the EEA Air Quality Download Service https://eeadmz1-downloads-webapp.azurewebsites.net to obtain European data for the time being. An R package, https://github.com/openair-project/euroaq, has been developed to facilitate its use.

New Features

Data Access

  • The source argument of importUKAQ() now defaults to NULL. This option allows the function to assign the source of each site itself, with some caveats:

    • Ambiguous codes (e.g., "AD1", which corresponds to a SAQN and locally managed site) will preferentially import from the national networks (AURN, then AQE/SAQN/WAQN/NIAQN) over locally-managed networks. To override this users should manually define source.

    • Incorrect codes not found in importMeta() will error if importUKAQ() is left to assign the source.

    • When data_type is one of the aggregate types (e.g., "annual") and a site isn't defined, a source must be provided.

    • It is likely slightly slower for the function to assign source itself than for users to specify it themselves.

  • The specific metadata columns appended when importUKAQ(meta = TRUE) can now be controlled using the meta_columns argument. For example, setting meta_columns to c("zone", "agglomeration") will append the zone/agglomeration information instead of the default site type/latitude/longitude.

  • DAQI information imported using importUKAQ(data_type = "daqi") will be returned with the relevant DAQI band appended as an additional factor column; either "Low" (1-3), "Moderate" (4-6), "High" (7-9), or "Very High" (10). See https://uk-air.defra.gov.uk/air-pollution/daqi for more information.

  • importImperial() has been added, superseding importKCL(). They are functionally identical, but reflect that londonair is now managed by Imperial College London. Function arguments have been renamed in importImperial() to better match importUKAQ().

Utility Functions

  • cutData() gained numerous new features:

    • Added the names argument to specify the name of the appended columns. For example, cutData(mydata, "wd", names = c("windDir")) will append a column named "windDir".

    • Added the suffix argument as an alternative to names. If a new column would otherwise overwrite an existing column, suffix will be appended. For example, cutData(mydata, c("nox", "o3"), suffix = "_cuts") would append nox_cuts and o3_cuts columns.

    • cutData() is now less destructive and better cleans up after itself. For example, when type = "yearseason", it will no longer leave 'year' and 'season' columns behind, or overwrite existing 'year' and 'season' columns.

    • cutData() will now give an informative error message if the user provides a type which is in neither an in-built option nor a column in their dataframe.

  • calcPercentile() gained the following arguments:

    • Added the type argument, in line with timeAverage().

    • Added the prefix argument to control the naming of the returned columns.

  • binData() gained the following arguments:

    • Added the type argument, passed to cutData().

    • Added the B and conf.int arguments, passed to bootMeanDF().

  • selectRunning() gained the following arguments:

    • Added the type argument, passed to cutData().

    • Added the name argument, which changes the name of the new column appended by the function.

    • Added the mode argument, which allows selectRunning() to filter the dataset rather than append a column.

  • rollingMean() has gained the type argument. This will likely be of most use for distinguishing between - and calculating separate statistics for - different monitoring stations within the same data frame.

  • splitByDate() can now more consistently take Date / POSIXct inputs as well as characters, and provides more flexibility over inputs with a new format argument.

  • aqStats() gained the progress argument, in line with timeAverage().

  • Many 'data utility' functions will now either warn or error if duplicate dates are detected, which is suggestive of a mix of either sites or averaging times within the same dataframe. The following functions have new behaviour:

    • selectRunning() and rollingMean() will error (duplicate dates break the logic of 'rolling window' functions).

    • aqStats() will also error, as it relies on rollingMean().

    • timeAverage() will warn the user but proceed with calculations, as averaging across different sites may be a legitimate action.

    • Functions which rely on timeAverage() will also warn but not error (notably calcPercentile() but also many plotting functions with avg.time arguments).

Plotting Functions

  • Added new features for openColours():

    • Added new qualitative colour palettes: the "tol" family are colour-blind friendly palettes based on the work of Paul Tol, and "tableau" and "observable" provide access to the "Tableau10" and "Observable10" palettes to aid in consistency with plots made in those platforms.

    • When n isn't defined for a qualitative palette (e.g., "Dark2"), the full qualitative palette will be returned. Previously this errored with the default of 100.

    • openColours() will now check whether the provided scheme is either a known scheme name or a vector of valid R colours, and provide an informative error if this is not the case.

  • polarDiff() has gained the type argument, and correctly responds to main, key.footer and key.header via the ... options.

  • trendLevel() has gained new statistic types to match timeAverage(), including "mean", "median", "min", "max", "sd", "sum", "frequency" and "percentile".

  • trendLevel() will now automatically generate appropriate labels if breaks are provided. The labels argument can still be used to provide custom labels per break.

  • The formula.label argument of polarPlot() will now control whether concentration information is printed when statistic = "cpf".

  • Added calm.thresh as an option to windRose(). This change allows users to set a non-zero wind speed threshold that is considered as calm.

  • Added the map.lwd, map.lty and map.border arguments to trajPlot(), trajLevel() and trajCluster() for greater control over the 'basemap' of each plot.

Bug fixes

  • Fixed repeated day number in calendarPlot() when statistic = max.

  • Fixed annotate = FALSE in windRose() where axes and labels were not shown

  • Fixed an issue wherein importUKAQ() would drop sites if importing from local sites and another network.

  • polarCluster() will no longer error with multiple pollutants and a single n.clusters.

  • importUKAQ() will correctly append site meta data when meta = TRUE, source is a length greater than 1, and a single site is repeated in more than one source (e.g., importUKAQ(source = c("waqn", "aurn"), data_type = "daqi", year = 2024L)))

  • calcPercentile() will now correctly pass its arguments (e.g., date.start) to timeAverage().

  • timeAverage() will now more consistently return NA values rather than NaN or Inf when all values are NA. This specifically affects the "mean" and "min" statistics.

  • importUKAQ() will now correctly label a measurement as ratified when it is on the day of ratified_to. i.e., if a site is ratified to 2020/01/01, the measurement at 2020/01/01 23:00 will now be labelled as ratified.

  • Fixed importImperial() URLs.

Natural Resources - Air Quality - R
Published by jack-davison 6 months ago