Package 'gghourglass'

Annotate a period in an hourglass plot

Description

Adds rectangles to a geom_hourglass() plot layer. It can be used to mark specific periods. The example shows how this annotation can be used to mark the periods when detector (used for the observations) was active. Note that this may not work correctly when displaying data that uses datetime objects with daylight saving time. In those cases you could split the periods into parts with and without daylight saving. Or convert your data to a timezone without daylight saving time (e.g. UTC).

Usage

annotate_periodstates(mapping, data, hour_center = 0, ...)

Arguments

mapping	A ggplot2::aes() object that maps the periods. It needs x, y, xend and yend, which mark the conrners of the rectangles (i.e. periods)
data	A data.frame containing information about the periods.
hour_center	The hour at which the time of day is centred. Default is 0, meaning midnight. -12 centres around noon of the preceding day, +12 centres around noon of the next day.
...	Passed to layer parameters.

Author(s)

Pepijn de Vries

Examples

library(ggplot2)
library(dplyr)
library(lubridate)

## Extract monitoring periods from 'bats' data
monitoring_periods <-
  attr(bats, "monitoring") |>
  mutate(time_on  = as_datetime(time_on),
         time_off = as_datetime(time_off))

ggplot(bats, aes(x = RECDATETIME, col = SPECDESCSCI)) +

  ## Set background to transparent red to contrast with
  ## monitoring periods
  theme(panel.background = element_rect(fill = "#FF000044")) +
  
  ## Annotate periods in which the detector was active with
  ## white rectangles
  annotate_periodstates(
    aes(x    = start,   xend = end,
        y    = time_on, yend = time_off),
    monitoring_periods,
    fill = "white") +
    
 ## plot observations
  geom_hourglass(hour_center = -6)

---

Annotate ggplot with a band indicating solar events

Description

Annotate a ggplot (currently only plots using coord_hourglass() is supported) with a coloured band indicating solar events, such as sunset and sunrise.

Usage

AnnotateDaylight

annotate_daylight(
  longitude = 0,
  latitude = 60,
  sun_prop = c("sunrise", "sunset"),
  ...
)

Arguments

longitude, latitude	Geographical location that will be used to calculate sunlight times.
sun_prop	A vector of two solar events that should be captured by the annotation. It will be shown as a coloured band between these two events. Default is c("sunrise", "sunset"), but could also be c("dusk", "dawn"). See suncalc::getSunlightTimes() for all allowed solar events.
...	Passed to the list of layer parameters.

Format

An object of class AnnotateDaylight (inherits from GeomPolygon, Geom, ggproto, gg) of length 6.

Value

Returns a ggplot2::layer() which can be added to a ggplot2::ggplot()

Author(s)

Pepijn de Vries

Examples

library(ggplot2)
data(bats)

monitoring <- attr(bats, "monitoring")

ggplot(subset(bats, format(RECDATETIME, "%Y") == "2018"),
       aes(x = RECDATETIME, col = SPECDESCSCI)) +
  annotate_daylight(monitoring$longitude[1], monitoring$latitude[1]) +
  annotate_daylight(monitoring$longitude[1], monitoring$latitude[1], c("dusk", "dawn")) +
  geom_hourglass()

---

Observations from a bat detector

Description

A dataset containing detections of audio call sequences from bats. It is a small subset of the data published by Lagerveld et al. (2023)

Format

A data.frame with 1,037 rows and 2 columns:

• RECDATETIME: datetime of the recorded bat call sequence

• SPECDESCSCI: scientific species name

It also contains an attribute named monitoring which is a data.frame containing monitoring periods at which the bat detector was active. Each row is a monitoring period, and it holds the following columns:

• start: start datetime of the monitoring period

• end: end datetime of the monitoring period

• time_on: time of day at which the detector is activated during the monitoring period

• time_off: time of day at which the detector is deactivated during the monitoring period

• longitude and latitude: coordinates of the detector's location

• altitude: altitude in meters above sea level of the detector.

References

Lagerveld, S., Wilkes, T., van Puijenbroek, M.E.B., Noort, B.C.A., Geelhoed, S.C.V. Acoustic monitoring reveals spatiotemporal occurrence of Nathusius’ pipistrelle at the southern North Sea during autumn migration. Environ Monit Assess 195, 1016 (2023) doi:10.1007/s10661-023-11590-2

Examples

data("bats")

---

Hourglass coordinates for a ggplot

Description

A Cartesian coordinate system that adds sensible guides to axes in a geom_hourglass() layer. It is added automatically to geom_hourglass(). There is no need to explicitly add it to a ggplot, unless you wish to tweak the coordinate system.

Usage

CoordHourglass

coord_hourglass(
  xlim = NULL,
  ylim = NULL,
  expand = TRUE,
  default = FALSE,
  clip = "on",
  date_labels = "%H:%M",
  layer = NULL,
  ...
)

Arguments

xlim, ylim	Limits for the x and y axes.
expand	If TRUE, the default, adds a small expansion factor to the limits to ensure that data and axes don't overlap. If FALSE, limits are taken exactly from the data or xlim/ylim.
default	Is this the default coordinate system? If FALSE (the default), then replacing this coordinate system with another one creates a message alerting the user that the coordinate system is being replaced. If TRUE, that warning is suppressed.
clip	Should drawing be clipped to the extent of the plot panel? A setting of "on" (the default) means yes, and a setting of "off" means no. In most cases, the default of "on" should not be changed, as setting clip = "off" can cause unexpected results. It allows drawing of data points anywhere on the plot, including in the plot margins. If limits are set via xlim and ylim and some data points fall outside those limits, then those data points may show up in places such as the axes, the legend, the plot title, or the plot margins.
date_labels	Formating string for formatting the time labels on the axis. By default it is "%H:%M".
layer	This argument allows you to pass the hourglass layer to which the coordinate system should be applied. It is used to derive the orientation of the plot. By default it is NULL and an attempt is made to derive the orientation of the plot from its axes scales.
...	Arguments passed as extra params to ggplot2::layer()

Format

An object of class CoordHourglass (inherits from CoordCartesian, Coord, ggproto, gg) of length 3.

Value

Returns a ggproto object inheriting from coord_cartesian().

Author(s)

Pepijn de Vries

Examples

coord_hourglass()

---

Add an 'hourglass' layer to a ggplot

Description

geom_hourglass() takes a continuous datetime object, splits in in discrete dates and time of day with stat_hourglass(). This geometry is a wrapper to add it as a layer to a ggplot. GeomHourglass is a ggproto object inheriting from ?ggplot2::GeomPoint. It should not be used directly. Instead call geom_hourglass().

Usage

GeomHourglass

geom_hourglass(
  mapping = NULL,
  data = NULL,
  stat = "hourglass",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  hour_center = 0,
  inherit.aes = TRUE,
  ...
)

Arguments

mapping	Set of aesthetic mappings created by ggplot2::aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping. The hourglass stat and geom requires either the x axis or the y axis to be mapped. The mapped aesthetic will show the date of the variable, whereas the opposite axis will show the time of day.
data	The data to be displayed in this layer. If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot2::ggplot(). Otherwise, a data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See ggplot2::fortify() for which variables will be created. The data should contain a column with datetime values (e.g., ?POSIXct)
stat	Can be used to overwrite the default connection between geom_hourglass and stat_hourglass().
position	A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following: The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position. A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter". For more information and other ways to specify the position, see the layer position documentation.
na.rm	If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.
show.legend	logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.
hour_center	The hour at which the time of day is centred. Default is 0, meaning midnight. -12 centres around noon of the preceding day, +12 centres around noon of the next day.
inherit.aes	If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().
...	Arguments passed to geometry.

Format

An object of class GeomHourglass (inherits from GeomPoint, Geom, ggproto, gg) of length 3.

Value

Returns a ggplot2::layer() which can be added to a ggplot2::ggplot()

Author(s)

Pepijn de Vries

Examples

library(ggplot2)
data(bats)

monitoring <- attr(bats, "monitoring")

ggplot(subset(bats, format(RECDATETIME, "%Y") == "2019"),
       aes(x = RECDATETIME, col = SPECDESCSCI)) +
  geom_hourglass()

ggplot(dplyr::mutate(bats, YEAR = format(RECDATETIME, "%Y")),
       aes(x = RECDATETIME, col = SPECDESCSCI)) +
  geom_hourglass() +
  facet_wrap(~YEAR, scales = "free_x")

---

Functions to split datetime into date and time of day

Description

Split a datetime object in a date component (get_date()) and time of day (get_hour()) component, centred around a specific hour of the day. They are used by stat_hourglass().

Usage

get_hour(x, hour_center = 0, ...)

get_date(x, hour_center = 0, ...)

Arguments

x	A datetime object (e.g., as.POSIXct()) to extract day of time from
hour_center	The hour at which the time of day is centred. Default is 0, meaning midnight. -12 centres around noon of the preceding day, +12 centres around noon of the next day.
...	Ignored

Value

Returns a period (lubridate::as.period()) in case of get_hour(). Returns a datetime object in case of get_date()

Author(s)

Pepijn de Vries

Examples

my_datetime <- as.POSIXct("2020-02-02 02:20:02 UTC", tz = "UTC")
get_hour(my_datetime)
get_hour(my_datetime, -12)

get_date(my_datetime)
get_date(my_datetime, -12)

## This will return the original `my_date`
get_date(my_datetime) + get_hour(my_datetime)

## This will too
get_date(my_datetime, -12) + get_hour(my_datetime, -12)

---

A ggplot2 stat function to wrangle data for geom_hourglass.

Description

Splits mapped x or y aesthetic from a continuous datetime into discrete date values on the mapped axis. The hour of day is mapped to the opposite axis.

Usage

StatHourglass

stat_hourglass(
  mapping = NULL,
  data = NULL,
  geom = "hourglass",
  position = "identity",
  show.legend = NA,
  inherit.aes = TRUE,
  hour_center = 0,
  na.rm = FALSE,
  ...
)

Arguments

mapping	Set of aesthetic mappings created by ggplot2::aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping. The hourglass stat and geom requires either the x axis or the y axis to be mapped. The mapped aesthetic will show the date of the variable, whereas the opposite axis will show the time of day.
data	The data to be displayed in this layer. If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot2::ggplot(). Otherwise, a data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See ggplot2::fortify() for which variables will be created. The data should contain a column with datetime values (e.g., ?POSIXct)
geom	Can be used to overwrite the default connection between stat_hourglass and ⁠[geom_hourglass]⁠.
position	A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following: The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position. A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter". For more information and other ways to specify the position, see the layer position documentation.
show.legend	logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.
inherit.aes	If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().
hour_center	The hour at which the time of day is centred. Default is 0, meaning midnight. -12 centres around noon of the preceding day, +12 centres around noon of the next day.
na.rm	If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.
...	Arguments passed as extra params to ggplot2::layer()

Format

An object of class StatHourglass (inherits from Stat, ggproto, gg) of length 7.

Value

Returns a ggplot2::layer() which can be added to a ggplot2::ggplot()

Author(s)

Pepijn de Vries

Examples

stat_hourglass()

---

Test if datetime object potentially uses daylight saving time

Description

Function to check if a datetime object potentially uses daylight saving time. It is not the same as lubridate::dst(), which will determine if daylight saving time is set for the requested date.

Usage

uses_dst(x)

Arguments

x	A datetime object.

Value

Returns a logical value indicating of the time zone used by the datetime object potentially uses daylight saving time.

Author(s)

Pepijn de Vries

Examples

uses_dst(as.POSIXct("2020-03-29 02:00:00 CET", tz = "CET"))
uses_dst(as.POSIXct("2020-03-29 02:00:00 UTC", tz = "UTC"))

---