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Changelog

Source: NEWS.md

openair (development version)

New Features

  • 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.

  • 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 (https://personal.sron.nl/~pault/), 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.

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

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

  • 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.

Bug fixes

  • 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)))

openair 2.18-2

CRAN release: 2024-03-11

New Features

  • add option to corPlot() to carry through “use” option in cor.

Bug fixes

  • fix date formatting issue in aqStats().
  • fix wrong formula for Euclidian distances in trajCluster() that did not transform coordinates before distance matrix was calculated. Thanks to Dan Jaffe.
  • “15_min” can once again be used as a data_type in the importUKAQ() family.
  • importUKAQ() can now be used to import annual, monthly, and DAQI statistics for multiple combinations of source and year.

openair 2.18-0

CRAN release: 2023-10-09

New Features

  • added a new importUKAQ() function, which supersedes importAURN(), importAQE(), importWAQN(), importSAQN(), importNI() and importLocal(). importUKAQ() brings a lot of new functionality to accessing UK air quality data through openair.

    • importUKAQ() has all of the same arguments as the functions it supersedes, as well as “source” to define the specific network of interest. The “source” argument can either be of length 1 or equal to the length of the “site” argument. This means that importUKAQ() can import statistics from multiple different networks at once.

    • importUKAQ() allows ratified = TRUE and to_narrow = TRUE simultaneously. This will return a tibble with two columns per observation - “value” containing the concentration and “qc” containing TRUE/FALSE which indicates whether the concentration is validated.

    • The AQE, WAQN, SAQN and NI networks now allow for data_type = "daqi". At time of writing, only data from 2022 is present.

    • the site and pollutant arguments of importUKAQ() are respected when data_type is “daqi”, “annual” or “monthly”. The default behaviour to return all available statistics has not changed. (#346)

    • the various arguments which augment import function outputs now behave more consistently with one another. For example, ratified now respects pollutant and only returns the “_qc” columns for the pollutants of interest.

    • importAURN(), importAQE(), importWAQN(), importSAQN(), importNI() and importLocal() are still exported by openair. These are all simply wrappers around importUKAQ() with forced “source” arguments, and remain for back-compatibility and convenience.

    • While importKCL() also imports UK air quality data, it is not currently made available through importUKAQ(). Users should continue to import KCL data via importKCL() for the time being.

  • importMeta() has gained two new “source” options to assist with the new importUKAQ() function:

    • source = "ukaq" will return metadata for all of the “UKAQ” networks.

    • source = "all" will return all available metadata (including KCL and Europe).

  • new function runRegression() for extracting ‘dilution lines’ from air quality and other data. Online manual will be updated with principles and examples.

  • calendarPlot() now automatically creates its own labels if breaks are specified. For example, c(0, 10, 20) will create the labels c("0 - 10", "10 - 20"). labels can still be used to override the default values. (#341)

  • Added the w.abbr.len argument to calendarPlot() which controls the length of the weekday abbreviation. This was requested to help people using written Chinese, but will be more broadly useful (e.g., to use “Mon”, “Tue”, “Wed” in place of “M”, “T”, “W”). (#101)

  • return tibble from timeAverage().

  • add option panel.gap to leave space between panels in timeAverage day-hour plots. Set to 0 for previous behaviour.

  • Move regression formula off main plot for polarPlot() for clarity and label slope as ‘m’.

  • Tweak seasonal trend decomposition using STL to allow the seasonal amplitude to vary more. Affects smoothTrend() and TheilSen().

  • Added colours recommended by the UK Government Analysis Function (https://analysisfunction.civilservice.gov.uk/policy-store/data-visualisation-colours-in-charts/) to openColours().

  • polarCluster now prints the cluster contributions and returns a data frame of them in the output.

Bug Fixes

  • The order of columns in importUKAQ() will remain consistent (metadata, date, pollutants, meteo) regardless of whether hc is TRUE or FALSE.

  • quickText() will now automatically capitalise “no” to “NO”. (#343)

  • The year argument of importMeta() is now respected when source = "kcl" and "europe".

  • Several of the directional analysis plot family (e.g., polarFreq()) have been refactored to use is.null() or is.na() over missing(). While predominantly an internal change, this should be make these functions easier to use inside of other functions (e.g., function(data, breaks = NA) polarFreq(data, breaks = breaks)) will now run successfully).

  • For calendarPlot when annotated with ws or wd arrows, use max ws/wd that corresponds to hour of maximum pollutant concentration and not simple the max ws/wd for a day.

  • summaryPlot() no longer forces time zones to be GMT. (#356)

openair 2.17-0

CRAN release: 2023-05-02

New Features

  • add option meteo to importAURN() family of functions. By default modelled wind speed, direction and ambient temperature are returned if available, but not if meteo = FALSE.

  • added a new column to modStats(), “P”, which represents the P-value of the correlation as reported by cor.test().

  • update processing of ADMS meteorological (.MOP) files to return stability and tidier data.

  • refined the output of pollutionRose() where the ws2 and wd2 options are provided; instead of the misleading N/E/S/W, the markers become 0, +90, +/-180, -90.

  • the timeAverage() progress bar is now powered by cli/purrr and can be silenced using the new progress argument.

  • the polarCluster() progress bar is now also powered by cli/purrr.

  • colours corresponding to the UK daily air quality index (https://uk-air.defra.gov.uk/air-pollution/daqi) have been added as options to openColours().

  • the openair object’s data property returned by the trajLevel() function is now consistently formatted regardless of statistic choice, and contains relevant statistic-specific information (e.g., sigma for "SQTBA").

Bug Fixes

  • fixed issue with modStats() such that “method” can now be changed (e.g., to “spearman”).

  • fixed issue with aqStats() where output wasn’t being properly split by pollutant/type.

  • fixed issue with conditionalQuantile() where the plot would fail to be produced when “type” was not specified.

  • fixed issue with cutData() where “season” wouldn’t respect system locale (e.g., would still show “(DJF)” on Italian systems, instead of the correct “(gla)”). Note that the season name itself (e.g., “Winter”) cannot be automatically converted.

  • fixed the theilSen() silent argument. The message “taking bootstrap samples. please wait” is also now sent via message() rather than print() and only appears once per function call.

  • fixed issue where trajCluster() proportions would overlap when clustering forward trajectories. Proportions should now appear at the end of cluster paths, regardless of whether the trajectory is back or forward.

  • fixed issue where not all openair plotting functions would properly return an openair S3 object, and that not all data objects were tibbles.

  • Fixed issue with timeAverage() where date formatting caused problems, possibly due to latest version of R (4.3.0).

openair 2.15

CRAN release: 2023-02-06

  • do not use native pipe yet - does not work with old versions of R

  • fix issue with polarDiff() where the resulting openair object did not contain the plot element.

openair 2.14

CRAN release: 2023-01-25

  • add year as an option to importMeta. This allows the user to select sites that were only open at some point in the chosen year or duration of years.

  • make sure full daily gravimetric data are returned for PM10 and PM2.5 if available when using importAURN family of functions. These data will be returned as gr_pm2.5 and gr_pm10 if data_type = "daily"

  • add alpha argument to all polar directional analysis functions. This is mainly for use in openairmaps but may be of general interest for specific use cases.

  • fix small bug in smoothTrend in returned fit data when data is missing.

openair 2.13

CRAN release: 2023-01-06

  • add importLocal to access locally-managed automatic monitoring data
  • fix bug in pollutionRose when single number of breaks given (was ignored)
  • remove legacy functions import, import.2, importAURNcsv and kernelExceed

openair 2.11

CRAN release: 2022-09-25

  • add sigma to options for SQTBA trajectory analysis for control over plume spread assumptions; set to 1.5 km (in one hour)
  • fix bug introduced in timeAverage for multi-time period averages
  • fix bug in timeProp and simplify code

openair 2.10

  • add Daily Air Quality Index (DAQI) to importAURN as data_type.
  • add rolling 8 and 24 hour statistics to importAURN family as data_type.
  • use https on importing meta data in importMeta
  • fix calendarPlot issue when there are gaps between selected months e.g.month = c(1, 2, 12)
  • fix warning message in calendarPlot
  • don’t pad missing dates in timeAverage if DST
  • deprecate resolution in polarPlot — now uses predictions at a coarser resolution that are interpolated. Will also speed-up plotting
  • add new source method to trajectory analysis (trajlevel), SQTBA — Simplified Quantitative Transport Bias Analysis
  • fix bivariate Gaussian function in polarPlot when two pollutants supplied for different statistics
  • add initial version of ‘York regression’ approach as an option to polarPlot. This regression approach determines a best fit line when there is error in the ‘x’ and the ‘y’. The openair book will be updated to cover this in more detail.

openair 2.9-1

CRAN release: 2022-03-30

  • Do not return hydrocarbon measurements by default for annual and monthly summaries in importAURN.
  • fix issue with class of date-time object for importing some air quality data e.g. importAURN.
  • refine default grid lines in windRose and pollutionRose.

openair 2.9-0

CRAN release: 2022-03-22

  • add option to TaylorDiagram for annotation of observed data.
  • fix issue with timevariation when difference = TRUE
  • fix trajCluster issue to do with dplyr
  • access other time-averaged air quality data using importAURN, importSAQN, importWAQN, importAQE and importNI. New option data_type, which can be “hourly” (default), “annual”, “monthly”, “daily” and “15min” (for SO2). These new data sources should make it much easier to work with long-term time series with many sites. See the openair manual for more details.
  • fix terrible spelling in selectRunning.

openair 2.8-6

CRAN release: 2021-11-22

  • fix annotation bug when comparing two data sets in windRose
  • enhance selectRunning. Now returns full data frame with a new condition column.
  • make sure “hemisphere” argument goes to type “monthyear” and “yearmonth”
  • argument month not passed in calendarPlot

openair 2.8-4

CRAN release: 2021-09-15

  • fix bug in windRose where whole period is calm
  • add optimisation to polarCluster to speed up clustering through option pamonce = 3. This should not appreciably affect results.
  • fix strange bug in aqStats due to lubridate time zone issue.
  • fix bug in TaylorDiagram when group was present.
  • Do not convert times with Daylight Saving Time when checking data — just report presence.
  • add option plot.type to summaryPlot to change line style; most useful for vertical lines in time series with plot.type = "h"

openair 2.8-1

  • Fix bug that crept in for polarCluster

openair 2.8-0

  • New function polarDiff to consider the difference surface between two polar plots.
  • Modify polarCluster to consider clustering of differences in polar plot surfaces.
  • Fix user annotation in windRose and pass on option for number of significant figures used to annotate plots (dig.lab)

openair 2.7-6

  • fix bug with percentileRose when statistic = "cpf" and multiple pollutants
  • fix bug in timeAverage when type = "season" and avg.time = "season"
  • add week to openair default types
  • fix bug in timeVariation when considering difference plots with missing data
  • fix CRAN check when using return

openair 2.7-4

  • add ambient temperature (air_temp) to meteorological variables returned from importAURN, importSAQN and importWAQN (using WRF model).
  • re-format date returned in importAQE due to strange dplyr join issues
  • add statistic = "Spearman" to polarPlot as an option when considering two pollutants.
  • add method option to corPlot to allow different correlation methods (“pearson”, “spearman” or “kendall”)
  • re-factor all UK air quality data import functions i.e. importAURN, importSAQN, importWAQN, importAQE.
  • Add importNI to import data from Northern Ireland.
  • Add option to UK air quality import functions to return information on whether individual pollutants have been quality-assured using option ratified. These functions include importAURN, importSAQN, importWAQN, importAQE and importNI
  • Clean up what is returned from importMeta
  • Return air quality data site name and code as character rather than factor

openair 2.7-2

  • fix tibble recycling issue
  • fix shading issue in lowest percentile range in percentileRose.
  • fix strange bug in importWAQN that would intermittently fail; sometimes crashing R.
  • add option date.format to TheilSen.

openair 2.7-0

  • fix calendarPlot slowness on MacOS
  • Refine use of Gaussian kernels when two pollutant statistics are considered in polarPlot
  • Add option statistic = "nwr" in polarPlot that implements the Non-parametric Wind Regression based on Henry et al. (2009). The openair implementation is not identical but should yield similar results.
  • NEW importAQE function to import data from Air Quality England sites.
  • NEW importEurope to provide access to some the data from the saqgetr package.

openair 2.6-6

  • fix bug in TheilSen when no missing data and deseason = TRUE
  • fix bug in timeAverage when interval padding dates and date is “Date” class and not “POSIXct”
  • fix example for trajCluster, should be n.cluster not n.clusters
  • fix issue with DST in cutData
  • allow ‘hemisphere’ to be supplied as an argument to timeAverage, used for avg.time = “season”.
  • add option to_narrow to importAURN, importSAQN, importKCL and importWAQN to stack data into a tidy format. The data are now returned as a ‘tibble’
  • Allow meta data to be returned in importSAQN and importWAQN.

openair 2.6-4

  • fix issue with TheilSen when conditioning and < 6 annual measurements
  • remove arrow heads in polarPlot axes.
  • Use a Kalman filter and Kalman smooth to impute missing monthly means when deseason = TRUE in smoothTrend and TheilSen. This replaces simple linear interpolation.
  • fix bug in smoothTrend when ci = FALSE (no smooth was fitted).
  • Add importWAQN to access data from the Welsh air quality network.
  • Add “waqn” as a data source to importMeta.

openair 2.6-1

  • Update handling of meta data in importMeta.

openair 2.6-0

  • In aqStats use default data.thresh = 0 rather than 75% to ensure summaries are calculated
  • Fix confidence intervals in timeVariation when statistic - “median”. Revision will result in narrower range.
  • Change default in corPlot to plot lower and upper triangles; add lower as an option.
  • Update meta data for Scottish Air Quality Network (“saqn”); was badly out of date
  • fix bug in timeAverage when interval more than one time unit e.g. “10 day”

openair 2.5-0

  • add simple versions of viridis colour palettes: “viridis”, “plasma”, “magma”, “inferno” and “cividis” e.g. polarPlot(mydata, cols = "plasma")
  • allow option align to be used in aqStats to determine how rolling means are calculated. Can take the values “centre” (default), “left” and “right”.
  • make sure full year present in importAURN
  • fix issue with multiple pollutants in polarAnnulus
  • fix issues in trajectory functions due to dplyr.

openair 2.4-0

  • use lubridate in timeAverage to improve speed / simplicity
  • make sure all strip colours are white for openair objects
  • fix bug in polarPlot when statistic = "cpf" when using tibbles
  • fix bug in polarCluster with exported data (date was not correctly merged to produce single date column)
  • convert internal mydata to a ‘tibble’ for easier printing.
  • allow npoints = NA in trajPlot to suppress plotting of interval points.
  • fix bias correction bug in windRose when ws/wd have different names
  • fix bug in timeAverage for wind direction (wd) when statistic = "data.cap"
  • New built-in colour palette for the colour blind “cbPalette”. Note maximum number of colours is 8 e.g. windRose(mydata, col = "cbPalette", breaks = 6). Thanks to Jerry Martin.

openair 2.3-0

  • add option plot to TheilSen. FALSE can be useful when analysing data to extract the trend components and plot in other ways and when the TheilSen plot is not required.
  • add option silent to TheilSen to avoid printing updates to trend fitting. By default it is FALSE.
  • fix wrong ordering of names in timeVariation when more than one pollutant
  • fix date parsing issues in selectByDate.
  • fix wrong ordering in timePlot
  • allow calendarPlot to span any time period. The function can now straddle parts of two years or several years.
  • add option col.arrow to calendarPlot to control colour of the wind speed / direction annotation arrows.

openair 2.2-3

CRAN release: 2018-02-26

Main changes

  • refine selectByDate due to changes in lubridate
  • fix issue with importSAQN when no data
  • remove site information from help of importAURN and point users to importMeta
  • fixed bug in scatterPlot when method = "level" due to NSE
  • use tidyr in place of reshape2
  • remove dependency of plyr and reshape2
  • fix bug in percentileRose for method = "cpf" with multiple pollutants

openair 2.1-5

CRAN release: 2017-08-31

Main changes

  • change polarCluster resolution to “normal” rather than “fine” to speed up.
  • fix regression when fitting smooth using trajLevel
  • remove all Airbase functions, will be available via new package that also incorporates newer e-reporting data
  • fix bug in timeAverage when statistic = "sum" and all data in period was missing (would return 0 rather than NA)
  • make sure that same data used in all conditionalEval plots by using data where there are no missing data for all variables used. This is more important of var.obs and var.mod are supplied and hence additional variables are considered relative to only obs and mod.
  • fix date issues in calendarPlot to do with time zones
  • remove missing data when type is a numeric value split up into quantiles
  • fix bug in windRose/pollutionRose when two conditioning variables were given (problem in bias correction)

openair 2.1-0

CRAN release: 2017-04-12

Main changes

  • add angle option to percentileRose to allow wind direction averages for sectors >10 degrees.
  • fix bug in aqStats if only a few lines of data
  • allow statistic to equal “mean”, “median” or “frequency” in scatterPlot, when method = "level"
  • change smoothing in scatterPlot when method = "level" to use tensor interaction to allow for better smoothing when x and y are on different scales.
  • warn when >10% negative data detected in polarPlot and suggest setting force.postive = FALSE
  • make maps Suggests rather than Depends
  • refine check on whether bias correction is needed in windRose
  • still plot data when <6 points in TheilSen and when no trend information is given
  • New function binData to easily summarise mean and 95% confidence intervals for intervals of a variable
  • Export bootMeanDF, used to calculate the bootstrap uncertainty in the mean of a vector.

openair 2.0-0

CRAN release: 2016-11-23

Main changes

  • silence download progress by default in importAURN
  • update polarPlot to work with pairwise statistics to compare two pollutants. The function can consider Pearson correlation and slopes from ordinary linear regression, robust regression (using MASS function rlm) and quantile regression (requires the quantreg package to be installed). See open access version of the paper.
  • change default polarPlot plot resolution to “fine”.
  • fix windRose problem with some data due to missing data
  • move mapdata package to Suggests
  • add option to return meta data (site type, lat, lon) from importAURN and importKCL.
  • fix statistic = “weighted.mean” issue in polarPlot.
  • make sure y.relation is used when there is no grouping in timePlot. To retain the behaviour of earlier versions use relation = "free"
  • fix issue with type when used with timeProp
  • fix bias correction when not default type in windRose
  • fix pch colour bug in timePlot
  • add option alpha to polarPlot to control transparency of plotted surface. Mostly useful for overlaying polar plots on leaflet maps (see openairmaps package)
  • enhance grid.line option in windRose so that users can control grid spacing, line type and line colour

openair 1.9-9

Main changes

  • correct citation information
  • Now depends on R version of >= 3.2.0 so that download.file can use libcurl for access to https (used in importAURN)
  • add avg.time option to summaryPlot to control the averaging times of the time series lines and print.datacap to control whether the data capture % is shown for each interval.
  • fix bug in selectByDate where a day number would not work
  • remove arrows in windRose, polarPlot to avoid ambiguous interpretation of wind direction
  • add key.position option to timePlot to control the location of the key.
  • fix labels in timeVariation when data for some types is missing.
  • fix trendLevel issue due to dplyr
  • use lubridate package in timeAverage
  • fix bug in summaryPlot related to dplyr use (would not plot missing data correctly)
  • better handling of precision in windRose mean and statistics returned in data (thanks to Dr Ulrich Quass)
  • fix bug in importKCL when incomplete time series (would drop site code and site name)
  • fix bug in pollutionRose due to issue with calms
  • fix bug in smoothTrend where model uncertainties were not returned
  • fix bug in summaryPlot where missing data would not be shown correctly when date was not ordered in sequence
  • fix annotation in windRose when comparing two data sets
  • GoogleMapsPlot is deprecated and will be replaced with a better function.

openair 1.8-6

CRAN release: 2016-06-15

  • Only plot lower triangle for corPlot
  • make sure date class is POSIXct, POSIXt in importAURN
  • fix problem in importMeta for AURN - change in database source format
  • fix pollutionRose plot warning
  • fix NMB in modStats
  • fix bug in timeAverage where estimating the time interval in input data could be unreliable due to low data availability
  • fix time expansion bug in timeAverage
  • add new type “yearseason” (or “seasonyear”). This will split data by every year / season combination, making sure the seasons are contiguous. For example, in winter in the northern hemisphere December 2010 will be considered part of winter 2011, rather than winter 2010. Thanks to Ralf Weisse for the suggestion.
  • fix download issues with importAURN and importMeta when users are within an organisational network. Problems likely due to move from http to https and SSL Certificates.
  • fix TheilSen bug when two types.

openair 1.8-2

CRAN release: 2016-04-25

  • fixes for new version of dplyr
  • adjust legends in conditionalEval to avoid plot error.
  • fix problem on linux and simplify importAURN
  • update importAURN meta data in help function.

openair 1.8-0

CRAN release: 2016-03-24

  • Allow scatterPlot to have control over plot symbol fill and colour (for symbols 21 to 25). Use cols and fill to control.
  • scatterPlot can now fit more than one linear equation when there is a grouping variable
  • give message when using a users’ own type such as month, year etc.
  • fix ordering of bars on timeProp, remove box.width option
  • fix bug introduced in 1.7-4 that affected windRose bias correction (thanks to Eric Christensen)
  • Add option for statistic = "r" in polarPlot for comparing polar plot correlation surfaces between two pollutants using Gaussian kernel weighting.
  • fix bug in type = "daylight" when time zone not UTC.
  • remove cutDaylight as a separate function (cutData works for everything)
  • add w.shift option to calendarPlot to control the first day of the week and subsequent order (thanks to Giovanni Bonafè)

openair 1.7.3

  • Fix regression in timeAverage when expanding time series
  • Remove dplyr warnings in TheilSen
  • Keep season order correct when averaging time is season and type = "season" in TheilSen and smoothTrend
  • add origin marker to trajCluster
  • better date padding when >1 type
  • fix some dplyr bugs where some functions would fail with two types
  • return data frame of cluster information in trajCluster

openair 1.7

CRAN release: 2016-02-22

  • Allow linearRelation to use any arbitrary time averaging period.
  • don’t add line to monthly plot in timeVariation when group = “season”
  • fix NA factors in trajPlot
  • make border black when using maps for improved clarity
  • fix bug in trajPlot that sometimes failed to print map when grouping
  • add percentage total trajectories for trajCluster and option by.type
  • don’t touch existing date-based types in cutData
  • refine date checks
  • speed up timeAverage
  • new dependent package lubridate for easier / faster date-time manipulations
  • fix slow timeProp (lattice panel.barchart is very slow)
  • only remove missing wind speed in windRose (wd can be NA and ws zero i.e. calm)
  • correct order of labels in timeVariation when difference = TRUE for some factor levels (were in alphabetical)

openair 1.6.6

  • Not all labels shown if >25 in trendLevel; make sure strip is white
  • correct bug in timeVariation (vector.ws did not work)
  • fix some cases where background strip was not white

openair 1.6.5

CRAN release: 2015-11-04

  • changes to fix examples not run during the R CMD check
  • make TaylorDiagram more flexible when using two groups and the second is date-based

openair 1.6.4

CRAN release: 2015-10-23

  • fix bug in GoogleMapsPlot when pollutant not given
  • don’t clutter up working directory with GoogleMapsPlot; write to temporary file instead
  • fix bug when trying to access multiple sites with no data in
  • fix problem with multiple sites in aqStats
  • TheilSen should always give trend in units/year (would use xlab if supplied)
  • fix cutData bug where quantile cuts are made
  • don’t remove missing data in scatterPlot so that factors with no data still shown
  • TheilSen should always give trend in units/year (would use xlab if supplied)
  • New option slope.text in TheilSen to allow users to add their own text i.e. not the default “units/year”
  • refine check on DST
  • Always report data capture % in aqStats

openair 1.6

CRAN release: 2015-07-23

  • Don’t force integer results for importAURN
  • fix bug with period = "months" in summaryPlot
  • allow linear fit with method = "hexbin" in scatterPlot
  • allow users to define own map limits in trajectory functions and better scaled map grids
  • fix renaming bug in airbaseStats
  • bug in windRose when all calm
  • date bug fixes in scatterPlot
  • add option windflow to scatterPlot and timePlot to allow wind flow plots
  • suppress harmless warnings in smoothTrend
  • fix bug in some functions when type more than one
  • add support in pollutionRose for option normalise to show probability by wind sector (0 to 1).
  • timeAverage now has an option type similar to other functions. A common use would be to apply timeAverage to a data frame with multiple sites where there is a column representing site name e.g. type = "site".
  • Add receptor location for trajectory plots trajLevel and trajPlot.
  • Add an option trend to TheilSen to control how the trend lines are drawn.
  • fix bug in calendarPlot when partial month available
  • fix bug in calendarPlot, don’t need to cut data first
  • add npoints option to trajPlot to control time spacing of dots shown on back trajectories
  • don’t include missing data when statistic = "frequency in timeAverage
  • fix bug in timeProp due to point above
  • fix bug in timeVariation with type = "season" when space in pollutant name

openair 1.5

CRAN release: 2015-04-14

  • Add ‘days’ as a time unit to summaryPlot - useful for shorter time series
  • Initial changes to use dplyr to speed up some of the code e.g. timeAverage
  • Automate x.inc and y.inc if not supplied by user in scatterPlot
  • Fix regression in trajLevel frequency calculation
  • Fix a few problems with trajectory plotting - some methods would fail given recent updates
  • Make trajectory gridded analysis faster
  • Fix bug in importMeta introduced since using dplyr
  • Add angle.scale to windRose to control placement of radial scale (helps to avoid clash with wind rose paddles)
  • Fix bug in timePlot when avg.time given (regression)
  • Allow TaylorDiagram to have group of length two. This will show all group combinations but will only differentiate them by colour/symbol according to the first grouping variable.
  • timeVariation can now take a ylim list to control the y-limits on each individual plot
  • For trajectory plotting allow map.res to be “state” to show the US States.
  • Fix bug in importKCL when date was not at beginning of the year

in openair 1.1-2

  • Fix regression for openair methods e.g. affected plot method for timeVariation subsets
  • Check data are numeric before applying running mean (would crash R if not)
  • Begin transition to Github, more details to follow
  • Add option dist to scatterPlot for surface modelling
  • Sort out package dependencies etc. to make maps easier to load
  • Add fontsize option to all openair plot functions
  • Change contact details, fix citation problem
  • Make sure importKCL is file of full year
  • Fix warning messages in aqStats when multiple pollutants selected

openair 1.1

  • Add ref.y option to timeVariation for y references line(s)
  • Fix type = “wd” labelling to corPlot
  • Refine airbaseStats to include site type and city by default
  • Make trendLevel colour scaling consistent with other functions and allow missing data to be shown in different colour
  • Allow categorical scales in trendLevel
  • Fix type = ‘season’ in trajLevel (winter period not properly calculated)
  • Allow multiple reference lines to be added to timePlot, scatterPlot, timeVariation and add to smoothTrend together with full control of their properties. Note - ref.x and ref.y must now be lists; see help file for details.
  • Don’t open graphics window in aqStats
  • Add more flexibility to timeAverage for irregular time intervals
  • Add 12-hour interval points on back trajectory lines
  • Fix bug in percentileRose with stat = “cpf” and non-default type (now uses single percentile based on all data, not each panel)
  • Check if date is in POSIXt format and throw error if TRUE
  • Improve date checks in selectByDate
  • Add dendrogram option to corPlot (thanks to James Durant for the suggestion)
  • Remove strip in corPlot when type = “default”
  • Remove statistic description in pollutionRose when annotate = FALSE.
  • Fix colour scaling bug in scatterPlot/trajPlot when user limits supplied
  • Check period = “years” or “months” in summaryPlot; some users supplied “year” resulting in incorrect statistics
  • Give mean and percent calm in pollutionRose when statistic = “prop.mean” (was erroneously percentage)
  • getMet function for downloading Hysplit met files in manual did not download as binary files; now corrected
  • Add name.pol argument to smoothTrend for more control over names used for plotting
  • Show first few dates when import fails to apply correct date format (helps to provide a clue as to actual date format)
  • Updates to trajectory plots to allow for different map projections using the mapproj package (new dependency)
  • Fix trajectory frequency calculation - underestimated frequencies.

openair 1.0-0

  • Pass all arguments in corPlot
  • Enhance timeVariation to consider median + quantiles through option ‘statistic’
  • Do not remove NA results from modStats
  • Better scaling in polarCluster; consistent with polarPlot
  • Fix importKCL where dates were filled if two non contiguous years were chosen
  • Refine scaling of ws in polarPlot when upper is set
  • Fix bug when type = “weekday” but not all days of the week are present
  • Add annotate option to TaylorDiagram
  • Allow modStat statistics to be chosen by user and add Index of Agreement
  • Needs to be >24 months to deseason in smoothTrend/TheilSen (was >=)
  • Refine names returned by importADMS when used with .pst file
  • Fix trajectory code in appendix D in the manual (some function arguments were not passed)
  • Better user defined limits scaling in polarPlot, scatterPlot, polarAnnulus when limits within data range
  • Clarify time zone for importing data to openair and checking (see manual for details)
  • Initial versions of functions to import EEA airbase data - see newsletter/manual for details
  • Better treatment of daylight saving time in cutData, timeVariation and polarAnnulus (allow any local time zone to be used; was just GMT/BST before)
  • Remove existing date-based columns in cutData to ensure date is used instead
  • Allow users to shade/not shade alternate years in smoothTrend and TheilSen
  • Do not smooth percentileRose by wind direction by default.
  • Add option ‘wd’ to percentileRose
  • Fix trajPlot bug when trajectory data was not at 3-hour intervals
  • Return data and smooth fit information in smoothTrend

openair 0.9-0

CRAN release: 2013-11-12

  • Fix bug introduced in 0.8-0 for scatterPlot surfaces
  • Add statistic and percentile option to polarAnnulus; allow Conditional Probability Functions
  • Allow percentile intervals to be considered in polarPlot when statistic = “cpf”
  • Correct calculation of AOT40 in aqStats to take account of daylight hours and growing season (Apr. to Sep.). Can use latitude/longitude, if supplied
  • Fix bug in aqStats when non predefined pollutant used
  • Allow log10 factor of 2 lines in scatterPlot when x and/or y are on a log scale
  • Allow users to supply own transform/inverse functions to hexbin
  • Don’t try and pad-out missing data in rollingMean when returning results
  • Make latticeExtra a ‘depends’
  • Don’t copy-down data by default in timeAverage when requested averaging time is < original. Better handling when ‘site’ is present
  • Update AURN help file site information; add site type
  • Show where data removed when min.bin > 1 for polarPlot
  • Add ‘trim’ value to percentiles in polarPlot to extract more source information.
  • Add ‘weights’ argument to polarPlot to down-weight bins with few data points - alternative to min.bin
  • Use more wd sectors for surface modelling when wd is not already rounded to 10 degree intervals in polarPlot
  • Fix bug in timePlot when pch supplied and group = TRUE.
  • Add Air Quality Standard for O3 in aqStats (days >120 ug/m3) not to be exceeded more than 10 days a year.
  • Add max.freq option to windRose/pollutionRose to control extent of radial limits
  • Add map.res option to trajPlot and trajLevel and make default lower resolution. Make default pollutant ‘height’ (always present)
  • Add Oslo and Rotterdam to trajectory database for 2010-2012
  • Better limits control on calendarPlot, use first year if not supplied, add option month to allow only selected month(s)
  • Fix bug when type = “wd” and some are missing (remove them)
  • Don’t open up graphic window in timeAverage
  • Fix indexing problem in polarCluster which sometimes caused the function to trip up
  • Only plot full length trajectories in trajPlot
  • Allow smoothing parameter k to be used when smooth = TRUE for more control in scatterPlot
  • Add a bias correction to windRose (thanks to Philippe Barneoud from Environment Canada for pointing out the need and solution)
  • Better treatment of pollutionRose when comparing two met datasets when ws bias is zero
  • Fix conditionalEval to use COE, not IOA and other minor changes
  • Allow method = “density” in trajLevel

openair 0.8-0

CRAN release: 2013-02-13

  • make sure missing dates are plotted properly in scatterPlot
  • fix regression in corPlot - main did not work
  • remove time zone options in import - users must supply data in GMT (UTC). Too many problems introduced due to daylight saving time
  • Use Legates and McCabe Coefficient of Efficiency in modStats in place of the Index of Agreement - easier to interpret.
  • Allow type = “month” etc to be used in timeVariation (was variable clash). Allow more flexibility when group and type are used
  • Better handling of user-defined limits in polarPlot and scatterPlot (method = “level”)
  • Add optional mean line option to percentileRose.
  • Correct pollutionRose documentation about comparing 2 data sets (first subtracted from second)
  • Fix bug in timeVariation that showed extra NA level for certain groups/types
  • Fix scaling bug in polarCluster when there is negative data e.g. x = “temp”
  • Allow statistic = “median” in trajLevel
  • NEW FUNCTION timeProp to plot time series by category as a bar chart
  • Fix windRose bug when wind direction name was not wd
  • Fix bug in importAURN when pollutant = “all” was specified
  • Allow minimum value of breaks in ws to be above minimum ws value, but warn.
  • Allow day to be numeric in selectByDate to select days of the month
  • Better base maps with trajectory plotting (filled and alpha transparency)
  • Fix windRose bug where all data are missing
  • Use higher resolution mapdata not maps package for trajectory plots
  • Allow method = “hexbin” in trajLevel for hexagonal binning of trajectory frequencies
  • Refine rollingMean to allow moving window to be aligned centre/center, left or right + better treatment of ends when data capture threshold used. Use option ‘width’ rather than ‘hours’ because non-hourly data can be considered.
  • Fix pollutionRose scaling issue, which sometimes missed the lower interval
  • Fix timeAverage data capture issue - was not always setting data to NA
  • Output clusters as C1, C2 etc. not 1, 2.
  • Use same labelling in calendarPlot as other functions (wrong month order in non-English locales)
  • Export dendogram in corPlot - see example in help file
  • Fix scaling bug in polarPlot when radial variable was negative and small
  • Update ‘mydata’ to set negative data to NA
  • Add method = CPF to percentile rose and polarPlot
  • Update trajectory analysis to allow Potential Source Contribution Function (PSCF) and Concentration Weighted Trajectory (CWT) to be considered

openair 0.7-0

CRAN release: 2012-09-19

  • Allow more flexible layout when two or more pollutants are used with polarPlot and type is default
  • Fix colour scale problem for windRose when interval does not exist
  • Added ‘nativeRaster’ class handler for GoogleMapsPlots
  • (test) Fix for GoogleMapsPlot xlim, ylim
  • Do not remove missing data from timeVariation
  • Fix bug in FAC2 in modStats when observations = 0 (exclude from calculation because indeterminate)
  • Fix bug in windRose for empty panels and panel labelling when data missing
  • New option start.day in cutData that affects most plots; allows users to set start day when type = “weekday”
  • Allow categorical scales in calendarPlot
  • Allow two met data sets to be compared in pollutionRose
  • Allow statistic = “percentile” to be used with polarPlot
  • Allow ‘method’ to be passed to cor in corPlot
  • Added more back trajectory locations.
  • Try harder to plot polarPlots when there is insufficient data to calculate a smooth surface.
  • Rename some variables in timeAverage to avoid variable clash.
  • Add gridded frequency capability to trajLevel
  • Fix bug in colour scaling in polarFreq when statistic = “stdev” (0 would not be plotted)
  • Fix bug in summaryPlot: type = “density” broken in recent versions

openair 0.6-0

CRAN release: 2012-05-11

  • Add y.relation option to timePlot
  • Fix interpolation bug in calcFno2 and names in documentation.
  • Refine conditionalQuantile scales
  • Provide volatile and non-volatile components for FDMS PM10 and PM2.5 in importKCL - now consistent with importAURN
  • NEW FUNCTION conditionalEval for model evaluation - allows other variable performance to be assessed.
  • Make lattice strips white by default for cleaner look on complicated plots
  • Complete re-write of import to simplify - changes are NOT backward compatible but will allow more developments
  • Allow line breaks in titles using to work with quickText
    • thanks to Karl
  • Allow better annotation of calendarPlot - highlight values above/below a certain threshold.

openair 0.5-25

CRAN release: 2012-03-19

  • Fix bug when type = “wd” - would add missing data to north sector
  • Add observed histogram to conditionalQuantile
  • Fix bug in timeAverage when ws was not available but wd was
  • Temporary fix to GoogleMapsPlot documentation due to new package version

openair 0.5-23

CRAN release: 2012-03-05

  • Fix bug in windRose when paddle = FALSE

openair 0.5-22

  • Fix scaling bug that could sometime affect polarPlot grid lines
  • Fix regression in importKCL that was introduced in 0.5-21
  • Make sure wd data are rounded to 10 degrees in polarFreq
  • Fix date padding issue in smoothTrend when type = “site”
  • windRose now gives mean ws in each panel rather than count
  • add option date.format to timePlot for more control over date format on axis

openair 0.5-21

CRAN release: 2012-02-22

  • Use C++ code for rolling mean calcs. Much faster, more to follow
  • NEW function trajCluster to carry out cluster analysis on back trajectories
  • Simple model ranking available in modStats # Changes in openair 0.5-18 [2012-01-16]
  • Update trajectory files to 2011 and add Berlin, Paris
  • Add option seg to pollutionRose to control the width of the segments
  • Add option start.day to timeVariation to control the order of weekdays.
  • Fixed bug in polarAnnulus where 360 degree winds were absent.
  • Remove dependency on zoo and proto.
  • Allow importAURN to import new ws/wd from pre-calculated WRF data at AURN sites

openair 0.5-17

  • Update to [IN DEVELOPMENT] GoogleMapsPlot. (1 lat,lon default handling)

openair 0.5-15

  • Update imports etc.

openair 0.5-15

  • Update to [IN DEVELOPMENT] GoogleMapsPlot.
  • Tidy up calcFno2 plotting.
  • Improve speed of timeAverage by removing date.pad.
  • Add vector averaging option to timeAverage for wind speed.

openair 0.5-14

  • NEW FUNCTION polarCluster for undertaking k-means clustering of bivariate polar plots

  • Remove any considerations of time zones in selectByDate. If start and end are supplied, whole days based on Date format are used to select. Now accepts start/end in the form “YYYY-mm-dd” as well as UK format e.g. dd/mm/YYYY.

openair 0.5-13

  • Major update to polarPlot allowing variables other than “ws” to be plotted with wind direction.
  • Improve documentation for polarPlot/TaylorDiagram
  • Update openair citation information to Journal article

openair 0.5-12

  • do not clip polarPlot concentrations unless upper is supplied
  • new option ‘intervals’ for percentileRose
  • add min.bin option to polarAnnulus
  • add Index of Agreement to modStats
  • new averaging time “season” for timeAverage
  • better treatment of avg.time = “season” and type = “season” in TheilSen and smoothTrend
  • use bootstrap methods to calculate 95% confidence intervals in the mean for timeVariation
  • New option ‘difference’ in timeVariation to show difference between two variables with bootstrap 95% CI in the mean
  • Byte-compile package
  • Place key on right be default in scatterPlot to avoid clash with x or y axis labels.
  • Include all colour schemes defined in the RColorBrewer package

openair 0.5-11

CRAN release: 2011-10-05

  • update to corPlot, scatterPlot, smoothTrend, linearRelation, percentileRose, trajPlot, trajLevel, timeVariation, TaylorDiagram, timePlot, summaryPlot improved … handling
  • remove warnings when importing air pollution data
  • additional update to corPlot added pollutant option, and openair class output
  • tweak scaling on percentileRose deal with negative data
  • change MannKendall to use TheilSen for all estimates for consistency. May slightly affect some p estimates.

openair 0.5-10

  • update to calendarPlot, kernelExceed, MannKendall and conditionalQuantile improved … handling
  •   minor update to GoogleMapsPlot

openair 0.5-9

  • allow model performance change to be considered in TaylorDiagram
  • update to windRose and pollutionRose stat related annotation
  • update to polarPlot, ploarFreq and polarAnnulus improved … handling

openair 0.5-8

  • NEW FUNCTION importMeta to import site meta data from air pollution networks

openair 0.5-7

  • update to trendLevel: improved … handling
  • update to windRose/pollutionRose: added statistic option “abs.count”; improved scaling of segment widths; improved … handling

openair 0.5-6

  • NEW FUNCTIONS importTraj, trajPlot, trajLevel for importing and plotting pre-defined HYSPLIT back trajectories. These functions are under active development and are for testing purposes only!
  • Fix error in % upper/lower uncertainty intervals for MannKendall
  • More control over trend information placement for MannKendall
    • arguments text.col, lab.frac (for vertical position) and lab.cex (for font size)

openair 0.5-4

  • Use roxygen2 for package documentation and future maintainability
  • Allow splitByDate to handle multiple sites and output a new column controlled by argument ‘name’
  • More options for MannKendall: control of colour and variable x-axis scales

openair 0.5-0

  • NEW FUNCTION corPlot for correlation matrices
  • add sep argument to import

openair 0.4-23

CRAN release: 2011-07-26

  • enhance ‘normalise’ option in timePlot
  • add annotate option to windRose/pollutionRose
  • NEW FUNCTION TaylorDiagram for model evaluation.

openair 0.4-22

  • NOTE - use reshape2 in place of reshape for speed and reliability
  • allow more than one pollutant with percentileRose
  • fixed title bug with scatterPlot - not shown for some methods
  • modified key handling on plots using drawOpenKey, so key = NULL or FALSE now removes colour key.
  • added method = “level” to scatterPlot for binning data with optional smoothing, plus other code clean-ups
  • fix bug in conditionalQuantile that labelled plots wrongly when site(s) has missing data
  • added ref.x and ref.y to timePlot to allow reference lines to be added
  • do not remove calm wind speed conditions in any functions where this is not necessary

openair 0.4-21

  • fixed bug in polarAnnulus that resulted in a failure to annotate the plot properly with period = “trend” and less than 1 year of data; improved smoothing default options used
  • new ‘statistic’ option to pollutionRose to show contribution to counts and contribution to the mean. The latter is useful for displaying those wind directions that make most contribution to the overall mean. Panel mean is also now shown.
  • small change to final example of re-shaping data in importKCL
  • timeAverage can now expand data to shorter time periods e.g. hourly to 15-minute. This makes it more flexible to combine data sets with differing averaging times. For example, daily mean particle data can be expanded to 1-hour means and combined with an hourly meteorological data set.
  • Fix treatment of calms in checkPrep, which affected cases with zero wind speeds in timeAverage
  • Fix to vector averaging in timeAverage (did not include wind speed in calculations). For most data this will make very little difference, but will be more important for low wind speeds and/or variable wind directions.
  • allow type = ‘variable’ in smoothTrend
  • Add avg.time to smoothTrend for “month” or “year” averages

openair 0.4-20

  • Do not remove calms in timeAverage
  • NEW FUNCTION importSAQN to import data from the Scottish Air Quality Network

openair 0.4-19

  • improved import date.name/time.name handling of spaces
  • Improved scaling for polarFreq
  • scatterPlot type = “wd” labels aligned
  • Added option “statistic” to polarPlot, which can now consider “mean”, “median”, “max” (maximum), “frequency”. “stdev” (standard deviation) or “weighted.mean” in a similar way to polarFreq
  • Fixed bad.24 and international tz bugs in import
  • updated import/import.2

openair 0.4-18

  • Better handling of missing data in smoothTrend/MannKendall; particularly when there are multiple sites
  • Do not run checkPrep on selectByDate because it removes calms
  • Fixed scaling bug in polarFreq when ws.int != 1
  • use avg.time in calcPercentile instead of ‘period’ to ensure consistency with other functions (timePlot would fail with percentiles)
  • return NA in aqStats when no data present; previously it tried to calculate quantities, returning -Inf etc

openair 0.4-17

CRAN release: 2011-04-24

  • use readRDS and not .readRDS (caused failure on R Dev)
  • openair now depends on >=R2.13.0
  • NEW FUNCTION sqStats to calculate common and pollutant-specific air quality statistics by year and site.
  • Changed option data.capture in rollingMean to data.thresh to be consistent with other functions.

openair 0.4-16

  • Fixed bugs in cutData when a partial year was used with type = “month”. Also affected type = “season” and “weekday”. The plots were labelled in the wrong order.
  • Ensure that missing wind sectors are skipped in type = “wd” for smoothTrend, MannKendall, timePlot and scatterPlot

openair 0.4-15

CRAN release: 2011-04-12

  • Preparation for CRAN release
  • removed some restrictions on type/period combinations in polarAnnulus

openair 0.4-14

  • Added preliminary greyscale method to openColours and linked in strip background and other text and line colour control for standard openair plots.

openair 0.4-13

  • Removed ad-hoc sites from importKCL, added site classification to the help file and ensured GMT is exported.

openair 0.4-12

  • Added y.relation option to smoothTrend and MannKendall to allow flexible y-scales.
  • NEW FUNCTION ‘percentileRose’ for flexible plotting of percentiles by wind direction
  • NEW FUNCTION selectRunning for selecting run lengths of a numeric variable above a certain threshold.
  • Modified plot layout in polarPlot to maximise plotting area
  • Initial fixes to functions affected by time zone settings
  • polarFreq now has consistent annotation cf. windRose and percentileRose; new option grid.line to control radial axes.
  • Fixed couple of minor auto.text bugs in summaryPlot and timePlot
  • Removed dependency of date for polar functions where time-based types are not required.

openair 0.4-11

  • More consistent use of strips in default plot (remove them)
  • Add percentage units to windRose and pollutionRose on radial scale

openair 0.4-10

CRAN release: 2011-03-08

  • Fixed calendarPlot main/quickText handling.
  • Fixed calendarPlot first day of month error.
  • Fixed summaryPlot site ordering when more than one site.

openair 0.4-9

  • Added new options to scatterPlot (plot.type, lwd, and lty) making it possible to add points and/or lines

openair 0.4-8

  • Added new cutData type option ‘daylight’, enabled using new function cutDaylight.

openair 0.4-7

CRAN release: 2011-02-17

  • Added new function conditionalQuantile for model
evaluation purposes.
  • Fixed `importAURN` to account for a change in web domain
address at AEA.