High-Performance Open-Source Archive
{openair} now suggests {rnaturalearth}
over {rnaturalearthdata}. {rnaturalearthdata}
is still required for a medium map resolution and
{rnaturalearthhires} for a high map resolution, but these
are now managed by {rnaturalearth} directly.strip.position, x.relation, and
y.relation are now no longer function-level arguments and
are handled via ....
The labels argument (as paired with
breaks) is deprecated. If passed through ...
it will be automatically mapped to its new place in the
breakOpts() function.
Refinements to how parameters are passed via ... to
plotting functions:
Graphical parameters are now defined using ggplot2
conventions (e.g., shape over pch).
base/lattice paramters are
automatically remapped to their ggplot2 equivalent with a
warning.
nrow and ncol can now be provided to
control facet layout. As above, layout is automatically
unpacked into ncol and nrow with a
warning.
scales can now be provided to control facet scale
restrictions. As above, x.relation and
y.relation are automatically combined into
scales with a warning.
space, axes, axis.labels,
strip.position and switch are now passed to
ggplot2::facet_wrap() or
ggplot2::facet_grid().
title, subtitle, tag, and
caption can be used throughout openair
(title replacing main and caption
replacing sub). All are passed through
quickText() if auto.text = TRUE.
lineend, linejoin and
linemitre tweak the appearance of line plots; see
ggplot2::geom_line() for more information.
Additional interactions between ... parameters and
various plots:
timePlot() now takes shape to add
markers to the line chart. This can be a vector to vary with
pollutant/group.
timeProp() now takes linewidth and
linetype to control border style.
TheilSen() now takes linewidth,
linetype, shape and
alpha.
smoothTrend() now takes linetype,
linewidth, shape and size. These
can be vectors to vary based on pollutant. The linewidth of the data
will always be half of that of the model.
Refinements to how ref.x and ref.y
behave throughout {openair}:
ref.x and ref.y can now take a vector
rather than a list, which will just use those values as the x/y
intercept with default graphical parameters.
ref.x and ref.y have been added to
timeProp() and TheilSen().
ref.x and ref.y can now take
{ggplot2}-style parameters (intercept,
alpha, colour, linetype,
linewidth). The old parameter names
(h/v, cols, lty and
lwd) are automatically remapped so still work.
The non-intercept arguments passed to ref.x and
ref.y (e.g., alpha) are now automatically
recycled to the length of intercept, similar to how
... parameters are recycled.
Added refOpts() to help construct values for
ref.x and ref.y, similar to
windflowOpts().
Refinements to how breaks are implemented in
functions like trendLevel():
If breaks doesn’t cover the full range of the data
being binned, the maximum and minimum breaks will be
overwritten so that it does.
If breaks is of length 1, the colour
range will be split into breaks categories, defaulting to
using the same logic as running cutData() on a numeric
column.
breaks can now take a named list, defined using the
new breakOpts() function. Most significantly, this allows
for the method of binning to change for single-value breaks
(quantiles, equal range bins, user-defined bin widths, approximate
‘pretty’ breaks and wind direction binning at time of writing).
polarPlot(), polarAnnulus(),
corPlot() and trajLevel() have gained
breaks.
labels is no longer a top-level argument and can be
defined by passing a list to breaks. labels
given to ... will be converted with a warning.
All functions which take breaks also now contain the
trans argument to perform scale transforms on continuous
colour scales. This can take FALSE (no scale transform),
TRUE (an appropriate default transform - usually
"log10"), or a {scales} transform object (or
string shorthand).
Refinements to colours in {openair}:
openColours() gains direction,
alpha, begin, end,
lightness and saturation for better control
over colour palettes.
Added colourOpts(). Any cols argument
in {openair} can now take the colourOpts()
function, which tells each plotting function how to use the new
openColours() arguments.
Added openSchemes() which returns a table of
available colour palettes.
New palettes:
Completed the set of “viridis” palettes with
"rocket" and "mako".
Added additional palettes by Paul Tol;
"tol.highcontrast", "tol.vibrant",
"tol.mediumcontrast", "tol.pale" and
"tol.dark".
Added various palettes based on the work of Fabio Crameri - see
openColours() for more details.
Added openColors() and colorOpts()
which are synonymous with their British English equivalents
openColours() and colourOpts().
New Kolmogorov-Zurbenko (KZ) Filter functions
kzFilter() and kzaFilter(). These functions
significantly enhance the capability of {openair} by
allowing different time components to be separated and analysed
separately. The kzFilter() function is considered a good
default for a wide range of problems whereas the
kzaFilter() function is the adaptive version that is
well-suited to capturing abrupt changes, e.g., through an intervention.
The range of uses of the filters will be covered in the
{openair} book.
TheilSen() and smoothTrend() now use a
more straightforward way to input missing data when
deseason = TRUE and missing monthly data are present based
on monthly linear regression by month. The user is alerted to the
imputation and the monthly plot shows the imputed data as a filled grey
circle.
smoothTrend() will now use loess when
it has insufficient data to fit a GAM.
cutData() gains the wd.res argument,
which can take one of 4, 8, or
16, defaulting to 8. 4 cuts the
data into North, East, South and West. 16 cuts the data
into N, NNE, NE, ENE, etc. All plotting function’s type
argument now responds to this, showing only four panels when
wd.res = 4 and a 5x5 grid of sixteen panels when
wd.res = 16.
trajPlot() and trajLevel() regain the
map.res argument. This is passed to
rnaturalearth::ne_countries() so can take three different
resolutions.
polarPlot() will now annotate the identity of the
radial axis as a caption, if annotate = TRUE.
ws and/or wd have been added to
percentileRose(), polarAnnulus(),
polarDiff() and polarFreq() in line with
polarPlot().
angle.scale has been added to
polarFreq() in line with all other polar coordinate
plots.
The default key.position of corPlot()
is now "right".
timePlot() has gained the key.title
argument.
timeAverage() now has a more robust approach to
multi-period averaging time such as “3 day”. Bin boundaries are at fixed
periods of time, which should ensure consistency across data sets that
start at different times. This also means there is less need to use the
argument start.date unless there is a need to extend the
start date of the data for some reason e.g. to the beginning of a year.
THis change may result in slight differences in returned output but
should not affect periods such as “day”, “hour” and “month”.
calendarPlot() will no longer duplicate
windflow arrows when
type != "default".
calendarPlot() now supports
type = "wd".
Fix intercept calculation in TheilSen(). Updated the
intercept formula from median(y) - slope * median(x) to
median(y - slope * x). This resolves a visual bug where
trend lines (especially annual aggregations with negative slopes)
appeared horizontally displaced due to inaccurate intercept estimates on
sparse data. This fix affects the visual display of the trend lines but
not the calculated slopes or uncertainties.
quickText() is once again tolerant of
apostrophes.
windflowOpts() will no longer overwrite the default
range of functions like calendarPlot() and
trendLevel() if range is not supplied by the
user.
polarPlot() will no longer produce a square-shaped
surface when exclude.missing = FALSE.
fontsize is now correctly passed to
scatterPlot(), polarAnnulus(),
variationPlot(), and timePlot().
Strings with line breaks (e.g., the result of
cutData(type="seasonyear"))) will no longer error when used
for facet labels.
name.pol will now correctly map onto the names of
pollutants in timeVariation().
windRose() now respects cols when
ws2 and wd2 are provided.
xlim is now correctly passed to the coordinates of
trajLevel().
openair now depends on R v4.1 and, internally, uses
the base R pipe (|>).
openair now imports ggplot2 and
scales and suggests sf,
geomtextpath, legendry and
rnaturalearthdata.
openair no longer imports lattice,
latticeExtra, hexbin or mapproj
nor suggests mapdata or maps.
All plotting functions are now written in ggplot2.
lattice specific options and annotations will no longer
work, but many can now be achieved using ggplot2::theme()
and ggplot2::annotate().
trajPlot(), trajLevel() and
trajCluster() have had their three projection related
arguments removed and replaced with a single crs argument,
which defaults to lat/lng (4326).
As the above three functions no longer call
scatterPlot(), scatterPlot() no longer has the
map argument.
drawOpenKey() has been removed due to being
lattice-specific.
linearRelation() and calcFno2() have
been removed from openair due to using outdated methodology
and assumptions.
summaryPlot() has been removed from
openair. This function was very old and inconsistent with
the rest of openair. It is planned to be replaced in the
future with new summary functions.
key.header and key.footer have been
replaced with a single key.title. This is due to
ggplot2 not supporting a separate “header” and “footer” for
guides.
The key argument has been deprecated, as it now only
exists to overwrite key.position when it is
FALSE. Please use key.position = "none" going
forward.
Argument names have been standardised throughout
openair. For example, instances of col have
been replaced with cols. This may cause some existing code
to break, but will ensure each function behaves more similarly going
into the future.
timeVariation() has been almost completely
rewritten. It is now a thin wrapper around the new
variationPlot(), which can take any arbitrary
x value - passed to cutData() - to use for its
x-axis. Furthermore, it has gained the following changes:
Gained the panels argument. This allows for panels
other than “hour.weekday”, “hour”, “month”, and “weekday” to be
represented in the plot assembly.
When key is FALSE, no key is shown for
any of the four timeVariation() plots. Previously, any
value passed to key would cause all four plots to display a
key.
(!) BREAKING: The order of xlab and
ylim now matches the order of panels.
month.last has also been deprecated; if used and
TRUE, this will override panels with a
warning. The output names output$data will now vary based
on panels, and the type column will be named
{type}_type (e.g., “hour_type”).
(!) BREAKING: The names of the plot and
data objects returned by timeVariation() are
now named after panels and have a more consistent
structure.
timePlot() refinements:
group can now take a character string, passed to
cutData() via timeAverage(). This works
similarly to group in timeVariation() in that
it colours traces within the panel, rather than splitting them into
multiple panels.
Gained the x.relation argument, allowing for
different x ranges on different panels.
smoothTrend() refinements:
Gained the x.relation, date.format, and
key.position arguments, in line with
timePlot().
Gained the progress argument, passed to
timeAverage().
avg.time is also no longer restricted to just three
options (any timeAverage() option is permitted), although
too fine a time resolution may obscure the smooth trend for long running
data.
calendarPlot() refinements:
Gained the type argument. This can take one
type and creates a 2D matrix using month & whatever the
user has selected. type = "year" has special
handling.
Gained the windflow argument, which deprecates
passing "ws" or "wd" to
annotate.
Gained the percentile argument, passed on to
timeAverage().
Gained the show.year argument, defaulting to
TRUE. When FALSE and only one year of data is
given, the strip titles will only read, e.g., “January” instead of
“January-2000”. This can create cleaner plots, as well as being useful
for certain edge cases (e.g., if the calendarPlot is showing day-of-year
averages over multiple years).
When statistic == "min" and
annotation %in% c("ws", "wd"), the ws/wd returned will
correspond to the minimum daily pollutant, rather than the minimum daily
ws/wd.
timeProp() refinements:
proportion is now treated more like
type internally. For a user, this means it can now be
passed "default" to avoid any conditioning and create a
regular period average barchart.
sub can now be defined via ...; set
sub = NA to remove the text annotation which appears by
default at the bottom of a timeProp() plot.
Gained the key argument to remove a legend.
"season" is now a permitted avg.time
option in timeProp(), better aligning it with the options
in timeAverage().
... is now correctly passed to
cutData() when using
type/proportion.
corPlot() refinements:
Added the annotate argument which can change the
correlation annotation to a p-value marker or stars, or remove it
entirely.
Added two new arguments triangle and
diagonal for controlling the plot appearance.
Added arguments key and key.title for
adding and refining a plot legend.
trendLevel() refinements:
(!) BREAKING: type now defaults to
"default", in line with other openair
functions.
Added windflow and min.bin arguments,
in line with similar functions.
Two type values are now supported.
TaylorDiagram() refinements:
pos.cor argument which controls whether the
negative correlation quadrant is shown.New function WhittakerSmooth() to do
Whittaker-Eilers Smoothing. This is a fast and general smoothing
technique, well-suited to a wide range of problems. The function can be
used to flexibly smooth and interpolate missing data. Additionally, the
function can flexibly define a baseline (and hence increment) for a time
series.
New function windflowOpts() which can be passed to
the windflow argument of various openair
functions to thoroughly customise the “windflow” arrows.
All openair plotting functions have gained
strip.position to control the placement of the facet
strip.
trajPlot() and trajLevel() have gained
the grid.nx and grid.ny arguments which can be
used to control the number of ticks on the coordinate grid, or remove it
altogether.
cutData() now contains the drop
argument. This allows for greater control over factor levels for
appended columns. For example, consider a situation in which
data only contains dates in March and May and
type = "month" is used:
drop = "empty" will ensure the resulting vector only
has factor levels "March" and "May".
drop = "none" will ensure the vector has all twelve
months (January, February, March, etc.).
drop = "outside" will retain ‘inclusive’ factor
levels within the range of the data - in this case "March",
"April", and "May".
drop = "default" is the existing
cutData() behaviour - in the case of
type = "month", it is equivalent to
drop = "empty".
cutData() also gains the "quarter" and
"quarteryear"/"yearquarter" type
options. These split a year cleanly into quarters, as an alternative to
"season" and
"seasonyear"/"yearseason". While seasons
better align with meteorology, quarters more cleanly fit into a single
calendar year and may better align with other relevant periods (e.g.,
reporting schedules, ratification calendars, economic activity,
etc.).
is.axis now has an effect on weekday,
season, seasonyear and
monthyear.
quickText() now converts air_temp (a
common worldmet variable) into
"temperature".
timeAverage() is much faster with the bulk of the
calculations made using C++.
runRegression() is now much faster with a new
algorithm.
timePlot() now allows duplicate dates when
time.avg is used. The user will still receive a warning
from timeAverage(), which is used internally, but the plot
will still be created.
The windflow argument of timePlot() now
works when "ws" and/or "wd" are in
pollutant.
importUKAQ() now closes its url()
connections and generally fails more gracefully when
data_type %in% c("annual", "monthly", "daqi"). This was
already the case for other data types.
timeAverage() will no longer leave Uu
and Vv columns behind when
statistic = "data.cap".
timeAverage() now correctly passes ...
to cutData().
timeAverage() now properly calculates wind speed and
direction when vector.ws = TRUE.
selectByDate() now correctly handles the
end date if supplied when in a date format (i.e.,
dd/mm/yyyy) and selects all hours in that day if present.
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.
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().
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).
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 and
key.title 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.
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.
corPlot() to carry through “use” option
in cor.aqStats().trajCluster() that did not transform coordinates before
distance matrix was calculated. Thanks to Dan Jaffe.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.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.
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)
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").
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).
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.
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.
importLocal to access locally-managed automatic
monitoring datapollutionRose when single number of breaks
given (was ignored)import, import.2,
importAURNcsv and kernelExceedsigma to options for SQTBA trajectory analysis for
control over plume spread assumptions; set to 1.5 km (in one hour)timeAverage for multi-time period
averagestimeProp and simplify codeimportAURN as
data_type.importAURN
family as data_type.importMetacalendarPlot issue when there are gaps between
selected months e.g.month = c(1, 2, 12)calendarPlottimeAverage if DSTresolution in polarPlot — now
uses predictions at a coarser resolution that are interpolated. Will
also speed-up plottingtrajlevel), SQTBA — Simplified Quantitative Transport Bias
AnalysispolarPlot when two
pollutants supplied for different statisticspolarPlot. 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.importAURN.importAURN.windRose and
pollutionRose.TaylorDiagram for annotation of observed
data.timevariation when
difference = TRUEtrajCluster issue to do with
dplyrimportAURN, 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.selectRunning.windRoseselectRunning. Now returns full data frame with
a new condition column.month not passed in
calendarPlotwindRose where whole period is calmpolarCluster to speed up clustering
through option pamonce = 3. This should not appreciably
affect results.aqStats due to
lubridate time zone issue.TaylorDiagram when group was present.plot.type to summaryPlot to
change line style; most useful for vertical lines in time series with
plot.type = "h"polarClusterpolarDiff to consider the difference
surface between two polar plots.polarCluster to consider clustering of
differences in polar plot surfaces.windRose and pass on option for
number of significant figures used to annotate plots
(dig.lab)percentileRose when
statistic = "cpf" and multiple pollutantstimeAverage when
type = "season" and avg.time = "season"week to openair default typestimeVariation when considering difference
plots with missing datareturnair_temp) to meteorological
variables returned from importAURN, importSAQN
and importWAQN (using WRF model).importAQE due to strange
dplyr join issuesstatistic = "Spearman" to polarPlot as
an option when considering two pollutants.method option to corPlot to allow
different correlation methods (“pearson”, “spearman” or “kendall”)importAURN, importSAQN,
importWAQN, importAQE.importNI to import data from Northern Ireland.ratified. These functions include importAURN,
importSAQN, importWAQN, importAQE
and importNIimportMetapercentileRose.importWAQN that would intermittently
fail; sometimes crashing R.date.format to TheilSen.calendarPlot slowness on MacOSpolarPlotstatistic = "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.importAQE function to import data from Air Quality England
sites.importEurope to provide access to some the data
from the saqgetr package.TheilSen when no missing data and
deseason = TRUEtimeAverage when interval padding dates and
date is “Date” class and not “POSIXct”trajCluster, should be
n.cluster not n.clusterscutDatatimeAverage, used for avg.time = “season”.to_narrow to importAURN,
importSAQN, importKCL and
importWAQN to stack data into a tidy format. The data are
now returned as a ‘tibble’importSAQN and
importWAQN.TheilSen when conditioning and < 6
annual measurementspolarPlot axes.deseason = TRUE in smoothTrend and
TheilSen. This replaces simple linear interpolation.smoothTrend when ci = FALSE (no
smooth was fitted).importWAQN to access data from the Welsh air quality network.importMeta.importMeta.aqStats use default data.thresh = 0
rather than 75% to ensure summaries are calculatedtimeVariation when
statistic - “median”. Revision will result in narrower range.corPlot to plot lower and upper
triangles; add lower as an option.timeAverage when interval more than one time
unit e.g. “10 day”polarPlot(mydata, cols = "plasma")align to be used in aqStats
to determine how rolling means are calculated. Can take the values
“centre” (default), “left” and “right”.importAURNpolarAnnulusdplyr.lubridate in timeAverage to improve
speed / simplicityopenair
objectspolarPlot when
statistic = "cpf" when using tibblespolarCluster with exported data (date was
not correctly merged to produce single date column)mydata to a ‘tibble’ for easier
printing.npoints = NA in trajPlot to suppress
plotting of interval points.windRose when ws/wd have
different namestimeAverage for wind direction
(wd) when statistic = "data.cap"windRose(mydata, col = "cbPalette", breaks = 6).
Thanks to Jerry Martin.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.silent to TheilSen to avoid
printing updates to trend fitting. By default it is
FALSE.timeVariation when more
than one pollutantselectByDate.timePlotcalendarPlot to span any time period. The
function can now straddle parts of two years or several years.col.arrow to calendarPlot to
control colour of the wind speed / direction annotation arrows.selectByDate due to changes in
lubridateimportSAQN when no dataimportAURN and
point users to importMetascatterPlot when
method = "level" due to NSEtidyr in place of reshape2plyr and
reshape2percentileRose for
method = "cpf" with multiple pollutantspolarCluster resolution to “normal” rather than
“fine” to speed up.trajLeveltimeAverage when
statistic = "sum" and all data in period was missing (would
return 0 rather than NA)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.calendarPlot to do with time
zoneswindRose/pollutionRose when two
conditioning variables were given (problem in bias correction)angle option to percentileRose to
allow wind direction averages for sectors >10 degrees.aqStats if only a few lines of datastatistic to equal “mean”, “median” or
“frequency” in scatterPlot, when
method = "level"scatterPlot when
method = "level" to use tensor interaction to allow for
better smoothing when x and y are on different scales.polarPlot
and suggest setting force.postive = FALSEmaps Suggests rather than DependswindRoseTheilSen and when
no trend information is givenbinData to easily summarise mean and 95%
confidence intervals for intervals of a variablebootMeanDF, used to calculate the bootstrap
uncertainty in the mean of a vector.importAURNpolarPlot 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).polarPlot plot resolution to
“fine”.windRose problem with some data due to missing
datamapdata package to SuggestsimportAURN and importKCL.polarPlot.y.relation is used when there is no grouping
in timePlot. To retain the behaviour of earlier versions
use relation = "free"type when used with
timePropwindRosetimePlotalpha to polarPlot to control
transparency of plotted surface. Mostly useful for overlaying polar
plots on leaflet maps (see openairmaps
package)grid.line option in windRose so
that users can control grid spacing, line type and line colourdownload.file can use libcurl for access to
https (used in importAURN)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.selectByDate where a day number would not
workwindRose, polarPlot to
avoid ambiguous interpretation of wind directionkey.position option to timePlot to
control the location of the key.timeVariation when data for some types is
missing.trendLevel issue due to dplyrlubridate package in timeAveragesummaryPlot related to dplyr
use (would not plot missing data correctly)windRose mean and
statistics returned in data (thanks to Dr Ulrich Quass)importKCL when incomplete time series (would
drop site code and site name)pollutionRose due to issue with calmssmoothTrend where model uncertainties were
not returnedsummaryPlot where missing data would not be
shown correctly when date was not ordered in sequencewindRose when comparing two data
setsGoogleMapsPlot is deprecated and will be replaced with
a better function.corPlotimportAURNimportMeta for AURN - change in database
source formatpollutionRose plot warningmodStatstimeAverage where estimating the time
interval in input data could be unreliable due to low data
availabilitytimeAveragetype “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.importAURN and
importMeta when users are within an organisational network.
Problems likely due to move from http to https and SSL
Certificates.TheilSen bug when two types.dplyrconditionalEval to avoid plot
error.importAURNimportAURN meta data in help function.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 variabletype such as
month, year etc.timeProp, remove
box.width optionwindRose bias
correction (thanks to Eric Christensen)statistic = "r" in
polarPlot for comparing polar plot correlation surfaces
between two pollutants using Gaussian kernel weighting.type = "daylight" when time zone not
UTC.cutDaylight as a separate function
(cutData works for everything)w.shift option to calendarPlot to
control the first day of the week and subsequent order (thanks to
Giovanni Bonafè)timeAverage when expanding time
seriesdplyr warnings in TheilSentype = "season" in TheilSen and
smoothTrendtrajClusterdplyr bugs where some functions would fail
with two typestrajClusterlinearRelation to use any arbitrary time
averaging period.timeVariation when
group = “season”NA factors in trajPlottrajPlot that sometimes failed to print map
when groupingtrajCluster and
option by.typecutDatatimeAveragelubridate for easier / faster
date-time manipulationstimeProp (lattice panel.barchart
is very slow)windRose (wd can be
NA and ws zero i.e. calm)timeVariation when
difference = TRUE for some factor levels (were in
alphabetical)trendLevel; make sure
strip is whitetimeVariation (vector.ws
did not work)TaylorDiagram more flexible when using two groups
and the second is date-basedGoogleMapsPlot when pollutant not givenGoogleMapsPlot;
write to temporary file insteadaqStatsTheilSen should always give trend in units/year (would
use xlab if supplied)cutData bug where quantile cuts are madescatterPlot so that
factors with no data still shownTheilSen should always give trend in units/year (would
use xlab if supplied)slope.text in TheilSen to allow
users to add their own text i.e. not the default “units/year”aqStatsimportAURNperiod = "months" in
summaryPlotmethod = "hexbin" in
scatterPlotairbaseStatswindRose when all calmscatterPlotwindflow to scatterPlot and
timePlot to allow wind flow plotssmoothTrendpollutionRose 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".trajLevel
and trajPlot.trend to TheilSen to control
how the trend lines are drawn.calendarPlot when partial month
availablecalendarPlot, don’t need to cut data
firstnpoints option to trajPlot to control
time spacing of dots shown on back trajectoriesstatistic = "frequency
in timeAveragetimeProp due to point abovetimeVariation with
type = "season" when space in pollutant namesummaryPlot - useful for
shorter time seriesdplyr to speed up some of the
code e.g. timeAveragex.inc and y.inc if not supplied
by user in scatterPlottrajLevel frequency calculationimportMeta introduced since using
dplyrangle.scale to windRose to control
placement of radial scale (helps to avoid clash with wind rose
paddles)timePlot when avg.time given
(regression)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 plotmap.res to be “state” to
show the US States.importKCL when date was not at beginning of
the yeartimeVariation subsetsscatterPlot for surface
modellingimportKCL is file of full yearaqStats when multiple
pollutants selectedtimeVariation for y references
line(s)corPlottrajLevel (winter period not
properly calculated)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.timeAverage for irregular time
intervalspercentileRose with stat = “cpf” and
non-default type (now uses single percentile based on all data, not each
panel)corPlot (thanks to James
Durant for the suggestion)corPlot when type = “default”pollutionRose when
annotate = FALSE.scatterPlot/trajPlot when user limits
suppliedsummaryPlot; some
users supplied “year” resulting in incorrect statisticspollutionRose when
statistic = “prop.mean” (was erroneously percentage)smoothTrend for more control
over names used for plottingcorPlottimeVariation to consider median + quantiles
through option ‘statistic’polarPlotimportKCL where dates were filled if two non
contiguous years were chosenpolarPlot when upper is
setsmoothTrend/TheilSen (was >=)polarPlot,
scatterPlot, polarAnnulus when limits within data
rangetimeVariation and polarAnnulus (allow any local time zone
to be used; was just GMT/BST before)smoothTrend and TheilSenpercentileRose by wind direction by
default.percentileRosetrajPlot bug when trajectory data was not at 3-hour
intervalssmoothTrendscatterPlot
surfacespolarPlot when statistic = “cpf”scatterPlot when x
and/or y are on a log scaletimeAverage when
requested averaging time is < original. Better handling when ‘site’
is presentpolarPlotpolarPlot to extract
more source information.polarPlot to down-weight bins
with few data points - alternative to min.binpolarPlottimePlot when pch supplied and group =
TRUE.windRose/pollutionRose to control extent of
radial limitstrajPlot and
trajLevel and make default lower resolution. Make default
pollutant ‘height’ (always present)calendarPlot, use first year
if not supplied, add option month to allow only selected month(s)timeAveragetrajPlotscatterPlotwindRose (thanks to Philippe
Barneoud from Environment Canada for pointing out the need and
solution)pollutionRose when comparing two
met datasets when ws bias is zerotrajLevelscatterPlotcorPlot - main did not worktimeVariation
(was variable clash). Allow more flexibility when group and type are
usedpolarPlot and
scatterPlot (method = “level”)percentileRose.pollutionRose documentation about comparing 2
data sets (first subtracted from second)timeVariation that showed extra NA level for
certain groups/typestrajLevelwindRose bug when wind direction name was not
wdimportAURN when pollutant = “all” was
specifiedwindRose bug where all data are missingtrajLevel for hexagonal
binning of trajectory frequenciespollutionRose scaling issue, which sometimes missed
the lower intervaltimeAverage data capture issue - was not always
setting data to NAcalendarPlot as other functions
(wrong month order in non-English locales)corPlot - see example in help
filepolarPlot when radial variable was
negative and smallpolarPlotpolarPlot and type is defaultwindRose when interval
does not existtimeVariationwindRose for empty panels and panel
labelling when data missingcalendarPlotpollutionRosepolarPlotcorPlotpolarPlots when there is
insufficient data to calculate a smooth surface.timeAverage to avoid variable
clash.trajLevelsummaryPlot: type = “density” broken in
recent versionstimePlotimportKCL - now consistent with
importAURNcalendarPlot - highlight
values above/below a certain threshold.timeAverage when ws was not available but wd
waswindRose when paddle = FALSEpolarPlot
grid linesimportKCL that was introduced in
0.5-21smoothTrend when type =
“site”windRose now gives mean ws in each panel rather than
counttimePlot for more control
over date format on axispollutionRose to control the width of
the segmentstimeVariation to control the
order of weekdays.importAURN to import new ws/wd from
pre-calculated WRF data at AURN sitestimeAverage by removing date.pad.timeAverage for wind
speed.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.
polarPlot allowing variables other than
“ws” to be plotted with wind direction.polarPlot/TaylorDiagrampolarPlot concentrations unless upper is
suppliedpercentileRosetimeAverageTheilSen and smoothTrendtimeVariationtimeVariation to show
difference between two variables with bootstrap 95% CI in the meanscatterPlot to avoid
clash with x or y axis labels.corPlot, scatterPlot,
smoothTrend, linearRelation, percentileRose,
trajPlot, trajLevel,
timeVariation, TaylorDiagram, timePlot,
summaryPlot improved … handlingcorPlot added pollutant option,
and openair class outputpercentileRose deal with negative
dataTheilSen for all estimates
for consistency. May slightly affect some p estimates.calendarPlot, kernelExceed, MannKendall and
conditionalQuantile improved … handling minor update to GoogleMapsPlotwindRose and pollutionRose stat
related annotationpolarPlot, ploarFreq and polarAnnulus
improved … handlingimportMeta to import site meta data from
air pollution networkswindRose/pollutionRose: added
statistic option “abs.count”; improved scaling of segment widths;
improved … handlingtrajPlot,
trajLevel for importing and plotting pre-defined HYSPLIT
back trajectories. These functions are under active development and are
for testing purposes only!corPlot for correlation matricestimePlotwindRose/pollutionRosepercentileRosescatterPlot - not shown for some
methodsscatterPlot for binning data
with optional smoothing, plus other code clean-upstimePlot to allow reference
lines to be addedpollutionRose 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.importKCLtimeAverage 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.timeAveragetimeAverage (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.smoothTrendsmoothTrend for “month” or “year”
averagestimeAveragescatterPlot type = “wd” labels alignedpolarPlot, which can now
consider “mean”, “median”, “max” (maximum), “frequency”. “stdev”
(standard deviation) or “weighted.mean” in a similar way to
polarFreqsmoothTrend/MannKendall; particularly when there are
multiple sitestimePlot would fail with
percentiles)smoothTrend, MannKendall, timePlot and
scatterPlotimportKCL, added site
classification to the help file and ensured GMT is exported.smoothTrend and MannKendall
to allow flexible y-scales.percentileRose’ for flexible plotting of
percentiles by wind directionselectRunning for selecting run lengths of
a numeric variable above a certain threshold.polarPlot to maximise plotting
areawindRose
and percentileRose; new option grid.line to control radial
axes.summaryPlot and
timePlotwindRose and
pollutionRose on radial scalecalendarPlot main/quickText handling.calendarPlot first day of month error.summaryPlot site ordering when more than one
site.scatterPlot (plot.type, lwd, and
lty) making it possible to add points and/or linesAdded new function conditionalQuantile for model
evaluation purposes.Fixed `importAURN` to account for a change in web domain
address at AEA.
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