get_time_delay: Get summary statistics of time delay
In timeplyr: Fast Tidy Tools for Date and Date-Time Manipulation

get_time_delay

R Documentation

Get summary statistics of time delay

Description

The output is a list containing summary statistics of time delay between two date/datetime vectors. This can be especially useful in estimating reporting delay for example.

data - A data frame containing the origin, end and calculated time delay.
unit - The chosen time unit.
num - The number of time units.
summary - tibble with summary statistics.
delay - tibble containing the empirical cumulative distribution function values by time delay.
plot - A ggplot of the time delay distribution.

Usage

get_time_delay(
  data,
  origin,
  end,
  timespan = 1L,
  min_delay = -Inf,
  max_delay = Inf,
  probs = c(0.25, 0.5, 0.75, 0.95),
  .by = NULL,
  include_plot = TRUE,
  x_scales = "fixed",
  bw = "sj",
  ...
)

Arguments

`data`	A data frame.
`origin`	Origin date variable.
`end`	End date variable.
`timespan`	timespan.
`min_delay`	The minimum acceptable delay, all delays less than this are removed before calculation. Default is `min_delay = -Inf`.
`max_delay`	The maximum acceptable delay, all delays greater than this are removed before calculation. Default is `max_delay = Inf`.
`probs`	Probabilities used in the quantile summary. Default is `probs = c(0.25, 0.5, 0.75, 0.95)`.
`.by`	(Optional). A selection of columns to group by for this operation. Columns are specified using tidy-select.
`include_plot`	Should a `ggplot` graph of delay distributions be included in the output?
`x_scales`	Option to control how the x-axis is displayed for multiple facets. Choices are "fixed" or "free_x".
`bw`	The smoothing bandwidth selector for the Kernel Density estimator. If numeric, the standard deviation of the smoothing kernel. If character, a rule to choose the bandwidth. See `?stats::bw.nrd` for more details. The default has been set to "SJ" which implements the Sheather & Jones (1991) method, as recommended by the R team `?stats::density`. This differs from the default implemented by `stats::density()` which uses Silverman's rule-of-thumb.
`...`	Further arguments to be passed on to `ggplot2::geom_density()`.

Value

A list containing summary data, summary statistics and an optional ggplot.

Examples

library(timeplyr)
library(outbreaks)
library(dplyr)

ebola_linelist <- ebola_sim_clean$linelist

# Incubation period distribution

# 95% of individuals experienced an incubation period of <= 26 days
inc_distr_days <- ebola_linelist %>%
  get_time_delay(date_of_infection,
                 date_of_onset,
                 time = "days")
head(inc_distr_days$data)
inc_distr_days$unit
inc_distr_days$num
inc_distr_days$summary
head(inc_distr_days$delay) # ECDF and freq by delay
inc_distr_days$plot

# Can change bandwidth selector
inc_distr_days <- ebola_linelist %>%
  get_time_delay(date_of_infection,
                 date_of_onset,
                 time = "day",
                 bw = "nrd")
inc_distr_days$plot

# Can choose any time units
inc_distr_weeks <- ebola_linelist %>%
  get_time_delay(date_of_infection,
                 date_of_onset,
                 time = "weeks",
                 bw = "nrd")
inc_distr_weeks$plot

timeplyr documentation built on April 3, 2025, 6:15 p.m.