knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.width=7, fig.height=5 )
This vignette details the structure of incidence objects, as produced by the
We generate a toy dataset of dates to examine the content of incidence objects.
library(incidence) set.seed(1) dat <- sample(1:50, 200, replace = TRUE, prob = 1 + exp(1:50 * 0.1)) sex <- sample(c("female", "male"), 200, replace = TRUE)
The incidence by 48h period is computed as:
i <- incidence(dat, interval = 2) i plot(i)
We also compute incidence by gender:
i.sex <- incidence(dat, interval = 2, group = sex) i.sex plot(i.sex)
i is a
list with the class incidence:
class(i) is.list(i) names(i)
i can be accessed using the same indexing as any lists, but it's
safer to use the accessors for each item:
## use name head(i$dates) head(get_dates(i))
In the following sections, we examine each of the components of the object.
$dates component contains a vector for all the dates for which incidence
have been computed, in the format of the input dataset (e.g.
date_bins <- get_dates(i) class(date_bins) class(dat) date_bins
The dates correspond to the lower bounds of the time intervals used as bins for the incidence. Bins always include the lower bound and exclude the upper bound. In the example provided above, this means that the first bin counts events that happened at day 5-6, the second bin counts events from 7-8, etc.
Note that if we had actual
Date-class dates, they would be returned as dates
dat_Date <- as.Date("2018-10-31") + dat head(dat_Date) i.date <- incidence(dat_Date, interval = 2, group = sex) i.date get_dates(i.date) class(get_dates(i.date))
These can be converted to integers, counting the number of days from the first date.
get_dates(i.date, count_days = TRUE) get_dates(i, count_days = TRUE)
To facilitate modelling, it's also possible to get the center of the interval by
position = "center" argument:
get_dates(i.date, position = "center") get_dates(i.date, position = "center", count_days = TRUE)
$counts component contains the actual incidence, i.e. counts of events
for the defined bins. It is a
integers where rows correspond to
time intervals, with one column for each group for which incidence is computed
(a single, unnamed column if no groups were provided). If groups were provided,
columns are named after the groups. We illustrate the difference comparing the
counts <- get_counts(i) class(counts) storage.mode(counts) counts get_counts(i.sex)
You can see the dimensions of the incidence object by using
nrow(), which returns the dimensions of the counts matrix:
dim(get_counts(i.sex)) dim(i.sex) nrow(i.sex) # number of date bins ncol(i.sex) # number of groups
There are also accessors for handling groups:
# Number of groups ncol(i.sex) ncol(i) # Names of groups group_names(i.sex) group_names(i) # You can also rename the groups group_names(i.sex) <- c("F", "M") group_names(i.sex)
Note that a
data.frame containing dates and counts can be obtained using
## basic conversion as.data.frame(i) as.data.frame(i.sex) ## long format for ggplot2 as.data.frame(i.sex, long = TRUE)
incidence has an argument called
na_as_group which is
default, which will pool all missing groups into a separate group, in which
case it will be a separate column in
$timespan component stores the length of the time period covered by the
get_timespan(i) print(date_range <- range(get_dates(i))) diff(date_range) + 1
$interval component contains the length of the time interval for the bins:
$n component stores the total number of events in the data:
Note that to obtain the number of cases by groups, one can use:
$weeks component is optional, and used to store
aweek objects whenever they have
been used. Weeks are used by default when weekly incidence is computed from
dates (see argument
library(outbreaks) dat <- ebola_sim$linelist$date_of_onset i.7 <- incidence(dat, "1 epiweek", standard = TRUE) i.7 i.7$weeks
$weeks is an optional element, it does not have a dedicated
accessor. If the element is not present, attempting to access it will result in
Both dates and weeks are returned when converting an
incidence object to
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