Package 'sugrrants'

sugrrants: supporting graphs for analysing time series

Description

Provides 'ggplot2' graphics for analysing time series data. It aims to fit into the 'tidyverse' and grammar of graphics framework for handling temporal data.

Author(s)

Maintainer: Earo Wang [email protected] (ORCID)

Authors:

• Di Cook (ORCID) [thesis advisor]

• Rob Hyndman (ORCID) [thesis advisor]

See Also

Useful links:

• https://pkg.earo.me/sugrrants/

• Report bugs at https://github.com/earowang/sugrrants/issues

---

Lay out panels in a calendar format

Description

Lay out panels in a calendar format

Usage

facet_calendar(
  date,
  format = "%b %d",
  week_start = getOption("lubridate.week.start", 1),
  nrow = NULL,
  ncol = NULL,
  scales = "fixed",
  shrink = TRUE,
  dir = "h",
  labeller = "label_value",
  strip.position = "top"
)

Arguments

date	A variable that contains dates or an expression that generates dates will be mapped in the calendar.
format	A character string, such as ⁠%Y-%b-%d⁠ and ⁠%a (%d)⁠, formatting the display of facet strips. See ?strptime for details.
week_start	Day on which week starts following ISO conventions - 1 means Monday (default), 7 means Sunday. You can set lubridate.week.start option to control this parameter globally.
nrow, ncol	Number of rows and columns defined for "monthly" calendar layout. If NULL, it computes a sensible layout.
scales	Should scales be fixed ("fixed", the default), free ("free"), or free in one dimension ("free_x", "free_y")?
shrink	If TRUE, will shrink scales to fit output of statistics, not raw data. If FALSE, will be range of raw data before statistical summary.
dir	Direction of calendar: "h" for horizontal (the default) or "v" for vertical.
labeller	A function that takes one data frame of labels and returns a list or data frame of character vectors. Each input column corresponds to one factor. Thus there will be more than one with vars(cyl, am). Each output column gets displayed as one separate line in the strip label. This function should inherit from the "labeller" S3 class for compatibility with labeller(). You can use different labeling functions for different kind of labels, for example use label_parsed() for formatting facet labels. label_value() is used by default, check it for more details and pointers to other options.
strip.position	By default, the labels are displayed on the top of the plot. Using strip.position it is possible to place the labels on either of the four sides by setting strip.position = c("top", "bottom", "left", "right")

Details

A monthly calendar is set up as a 5 by 7 layout matrix. Each month could extend over six weeks but in these months is to wrap the last few days up to the top row of the block.

See Also

frame_calendar for a compact calendar display, by quickly transforming the data.

Examples

fs <- hourly_peds %>%
  dplyr::filter(Date < as.Date("2016-05-01"))

fs %>%
  ggplot(aes(x = Time, y = Hourly_Counts)) +
  geom_line(aes(colour = Sensor_Name)) +
  facet_calendar(~ Date, nrow = 2) + # or ~ as.Date(Date_Time)
  theme(legend.position = "bottom")

---

Rearrange a temporal data frame to a calendar-based data format using linear algebra

Description

Temporal data of daily intervals or higher frequency levels can be organised into a calendar-based format, which is useful for visually presenting calendar-related activities or multiple seasonality (such as time of day, day of week, day of month). The function only returns a rearranged data frame, and ggplot2 takes care of the plotting afterwards. It allows more flexibility for users to visualise the data in various ways.

Usage

frame_calendar(
  data,
  x,
  y,
  date,
  calendar = "monthly",
  dir = "h",
  week_start = getOption("lubridate.week.start", 1),
  nrow = NULL,
  ncol = NULL,
  polar = FALSE,
  scale = "fixed",
  width = 0.95,
  height = 0.95,
  margin = NULL,
  ...
)

prettify(plot, label = c("label", "text"), locale, abbr = TRUE, ...)

Arguments

data	A data frame or a grouped data frame including a Date variable.
x	A bare (or unquoted) variable mapping to x axis, for example time of day. If integer 1 is specified, it simply returns calendar grids on x without transformation.
y	A bare (or unquoted) variable or more mapping to y axis. More than one variable need putting to vars(). If integer 1 is specified, it returns calendar grids on y without transformation.
date	A Date variable mapping to dates in the calendar.
calendar	Type of calendar. (1) "monthly" calendar (the default) organises the data to a common format comprised of day of week in the column and week of month in the row. A monthly calendar is set up as a 5 by 7 layout matrix. Each month could extend over six weeks but in these months is to wrap the last few days up to the top row of the block. (2) "weekly" calendar consists of day of week and week of year. (3) "daily" calendar refers to day of month and month of year.
dir	Direction of calendar: "h" for horizontal (the default) or "v" for vertical.
week_start	Day on which week starts following ISO conventions - 1 means Monday (default), 7 means Sunday. You can set lubridate.week.start option to control this parameter globally.
nrow, ncol	Number of rows and columns defined for "monthly" calendar layout. If NULL, it computes a sensible layout.
polar	FALSE (the default) for Cartesian or TRUE for polar coordinates.
scale	"fixed" (the default) for fixed scale. "free" for scaling conditional on each daily cell, "free_wday" for scaling on weekdays, "free_mday" for scaling on day of month.
width, height	Numerics between 0 and 1 to specify the width/height for each glyph.
margin	Numerics of length two between 0 and 1 to specify the horizontal and vertical margins between month panels.
...	Extra arguments passed to geom_label() and geom_text()
plot	A "ggplot" object or "plotly".
label	If "label" is specified, it will add month/week text on the ggplot object, which is actually passed to geom_label(). If "text" is specified, it will add weekday/day of month text on the ggplot object, which is actually passed to geom_text(). By default, both "label" and "text" are used. If "text2" is specified for the "monthly" calendar only, it will add day of month to the ggplot object.
locale	ISO 639 language code. The default is "en" (i.e. US English). For other languages support, package readr needs to be installed. See readr::locale for more details.
abbr	Logical to specify if the abbreviated version of label should be used.

Details

The calendar-based graphic can be considered as small multiples of sub-series arranged into many daily cells. For every multiple (or facet), it requires the x variable mapped to be time of day and y to value. New x and y are computed and named with a . prefixed to variable according to x and y respectively, and get ready for ggplot2 aesthetic mappings. In conjunction with group_by(), it allows the grouped variable to have their individual scales. For more details, see vignette("frame-calendar", package = "sugrrants")

Value

A data frame or a dplyr::tibble with newly added columns of .x, .y. .x and .y together give new coordinates computed for different types of calendars. date groups the same dates in a chronological order, which is useful for geom_line or geom_path. The basic use is ⁠ggplot(aes(x = .x, y = .y, group = date)) + geom_*⁠. The variable names .x and .y reflect the actual x and y with a prefix ..

See Also

facet_calendar for a fully-fledged faceting calendar with formal labels and axes.

Examples

library(dplyr, warn.conflicts = FALSE)
# compute the calendar layout for the data frame
calendar_df <- hourly_peds %>%
  filter(Sensor_ID == 13, Year == 2016) %>%
  frame_calendar(x = Time, y = Hourly_Counts, date = Date, nrow = 4)

# ggplot
p1 <- calendar_df %>%
  ggplot(aes(x = .Time, y = .Hourly_Counts, group = Date)) +
  geom_line()
prettify(p1, size = 3, label.padding = unit(0.15, "lines"))

# use in conjunction with group_by()
grped_calendar <- hourly_peds %>%
  filter(Year == "2017", Month == "March") %>%
  group_by(Sensor_Name) %>%
  frame_calendar(x = Time, y = Hourly_Counts, date = Date, week_start = 7)

p2 <- grped_calendar %>%
  ggplot(aes(x = .Time, y = .Hourly_Counts, group = Date)) +
  geom_line() +
  facet_wrap(~ Sensor_Name, nrow = 2)
prettify(p2)
## Not run: 
# allow for different languages
# below gives simplied Chinese labels with STKaiti font family,
# assuming this font installed in user's local system
prettify(p2, locale = "zh", family = "STKaiti")

# plotly example
if (!requireNamespace("plotly", quietly = TRUE)) {
  stop("Please install the 'plotly' package to run these following examples.")
}
library(plotly)
pp <- calendar_df %>%
  group_by(Date) %>%
  plot_ly(x = ~ .Time, y = ~ .Hourly_Counts) %>%
  add_lines(text = ~ paste("Count: ", Hourly_Counts, "<br> Time: ", Time))
prettify(pp)

## End(Not run)

---

Autocorrelation for temporal data

Description

Since the data input is data.frame, it's better to sort the date-times from early to recent and make implicit missing values explicit before using geom_acf.

Usage

geom_acf(
  mapping = NULL,
  data = NULL,
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  lag.max = NULL,
  type = "correlation",
  level = 0.95,
  ...
)

Arguments

mapping	Set of aesthetic mappings created by 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.
data	The data to be displayed in this layer. There are three options: If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot(). A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created. A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).
position	Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.
na.rm	Logical. If TRUE, missing values are removed. default is the "correlation" and other options are "covariance" and "partial".
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().
lag.max	An integer indicating the maximum lag at which to calculate the acf.
type	A character string giving the type of the acf to be computed. The
level	A numeric defining the confidence level. If NULL, no significant line to be drawn.
...	Other arguments passed on to layer(). These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "red" or size = 3. They may also be parameters to the paired geom/stat.

Examples

library(dplyr)
fstaff <- hourly_peds %>%
  filter(Sensor_ID == 13)

# use ggplot2 
fstaff %>%
  ggplot(aes(x = ..lag.., y = Hourly_Counts)) +
  geom_acf()

---

Pedestrian counts in Melbourne city

Description

A dataset containing the pedestrian counts at hourly intervals from 2016-01-01 to 2017-04-20 at 7 sensors in the city of Melbourne. The variables are as follows:

Usage

hourly_peds

Format

A tibble with 78755 rows and 9 variables:

Date_Time

Date time when the pedestrian counts are recorded

Year

Year associated with Date_Time

Month

Month associated with Date_Time

Mdate

Day of month associated with Date_Time

Day

Weekday associated with Date_Time

Time

Hour associated with Date_Time

Sensor_ID

Sensor identifiers

Sensor_Name

Sensor names

Hourly_Counts

Hourly pedestrian counts

Examples

hourly_peds

---

Autocorrelation for temporal data

Description

Since the data input is data.frame, it's better to sort the date-times from early to recent and make implicit missing values explicit before using stat_acf.

Usage

stat_acf(
  mapping = NULL,
  data = NULL,
  geom = "bar",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  lag.max = NULL,
  type = "correlation",
  level = 0.95,
  ...
)

Arguments

mapping	Set of aesthetic mappings created by 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.
data	The data to be displayed in this layer. There are three options: If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot(). A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created. A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).
geom	The geometric object to use to display the data, either as a ggproto Geom subclass or as a string naming the geom stripped of the geom_ prefix (e.g. "point" rather than "geom_point")
position	Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.
na.rm	Logical. If TRUE, missing values are 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.
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().
lag.max	An integer indicating the maximum lag at which to calculate the acf.
type	A character string giving the type of the acf to be computed. The default is the "correlation" and other options are "covariance" and "partial".
level	A numeric defining the confidence level. If NULL, no significant line to be drawn.
...	Other arguments passed on to layer(). These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "red" or size = 3. They may also be parameters to the paired geom/stat.

Examples

library(dplyr)
fstaff <- hourly_peds %>%
  filter(Sensor_ID == 13)

# use ggplot2 
fstaff %>%
  ggplot(aes(x = ..lag.., y = Hourly_Counts)) +
  stat_acf(geom = "bar")

---