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get episode unit tests

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dr. M.S. (Matthijs) Berends 2023-02-24 19:54:56 +01:00
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.8.2.9145
Version: 1.8.2.9146
Date: 2023-02-24
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.2.9145
# AMR 1.8.2.9146
*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*

23
R/get_episode.R
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@ -29,10 +29,10 @@
#' Determine (Clinical or Epidemic) Episodes
#'
#' These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument `episode_days`. This can be used to determine clinical episodes for any epidemiological analysis. The [get_episode()] function returns the index number of the episode per group, while the [is_new_episode()] function returns `TRUE` for every new [get_episode()] index. Both absolute and relative episode determination are supported.
#' These functions determine which items in a vector can be considered (the start of) a new episode. This can be used to determine clinical episodes for any epidemiological analysis. The [get_episode()] function returns the index number of the episode per group, while the [is_new_episode()] function returns `TRUE` for every new [get_episode()] index. Both absolute and relative episode determination are supported.
#' @param x vector of dates (class `Date` or `POSIXt`), will be sorted internally to determine episodes
#' @param episode_days episode length in days, can also be less than a day or `Inf`, see *Details*
#' @param case_free_days length in days after which new episode will start, can also be less than a day or `Inf`, see *Details*
#' @param episode_days episode length in days to specify the time period after which a new episode begins, can also be less than a day or `Inf`, see *Details*
#' @param case_free_days (inter-epidemic) interval length in days after which a new episode will start, can also be less than a day or `Inf`, see *Details*
#' @param ... ignored, only in place to allow future extensions
#' @details Episodes can be determined in two ways: absolute and relative.
#'
@ -44,7 +44,7 @@
#'
#' 2. Relative
#'
#' This method uses `case_free_days` to quantify the duration of (inter-epidemic) intervals, after which a new episode will start. A common use case is infectious disease epidemiology: episodes of norovirus outbreaks in a hospital for example. The case-free period could then be 14 days, so that new norovirus cases after that time will be considered a different (or new) episode.
#' This method uses `case_free_days` to quantify the duration of case-free days (the inter-epidemic interval), after which a new episode will start. A common use case is infectious disease epidemiology: episodes of norovirus outbreaks in a hospital for example. The case-free period could then be 14 days, so that new norovirus cases after that time will be considered a different (or new) episode.
#'
#' Thus, this methods counts **since the last case in the previous episode**.
#'
@ -55,15 +55,17 @@
#' | 2023-01-01 | 1 | 1 |
#' | 2023-01-02 | 1 | 1 |
#' | 2023-01-05 | 1 | 1 |
#' | 2023-01-08 | 2\code{*} | 1 |
#' | 2023-02-21 | 3 | 2\code{**} |
#' | 2023-01-08 | 2** | 1 |
#' | 2023-02-21 | 3 | 2*** |
#' | 2023-02-22 | 3 | 2 |
#' | 2023-02-23 | 3 | 2 |
#' | 2023-02-24 | 3 | 2 |
#' | 2023-03-01 | 4 | 2 |
#'
#' \code{*} This marks the start of a new episode, because 8 January 2023 is more than 7 days since the start of the previous episode (1 January 2023). \cr
#' \code{**} This marks the start of a new episode, because 21 January 2023 is more than 7 days since the last case in the previous episode (8 January 2023).
#' ** This marks the start of a new episode, because 8 January 2023 is more than 7 days since the start of the previous episode (1 January 2023). \cr
#' *** This marks the start of a new episode, because 21 January 2023 is more than 7 days since the last case in the previous episode (8 January 2023).
#'
#' Either `episode_days` or `case_free_days` must be provided in the function.
#'
#' ### Difference between `get_episode()` and `is_new_episode()`
#'
@ -213,8 +215,11 @@ is_new_episode <- function(x, episode_days = NULL, case_free_days = NULL, ...) {
exec_episode <- function(x, episode_days, case_free_days, ...) {
stop_if((is.null(episode_days) && is.null(case_free_days)) || (!is.null(episode_days) && !is.null(case_free_days)),
"either `episode_days` or `case_free_days` must be set.", call = -2)
"either `episode_days` or `case_free_days` must be set.",
call = -2
)
# running as.double() on a POSIXct object will return its number of seconds since 1970-01-01
x <- as.double(as.POSIXct(x)) # as.POSIXct() required for Date classes
# since x is now in seconds, get seconds from episode_days as well

8
inst/tinytest/test-episode.R → inst/tinytest/test-get_episode.R
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@ -27,6 +27,14 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
x <- data.frame(dates = as.Date(c("2021-01-01", "2021-01-02", "2021-01-05", "2021-01-08", "2021-02-21", "2021-02-22", "2021-02-23", "2021-02-24", "2021-03-01", "2021-03-01")))
x$absolute <- get_episode(x$dates, episode_days = 7)
x$relative <- get_episode(x$dates, case_free_days = 7)
expect_equal(x$absolute, c(1, 1, 1, 2, 3, 3, 3, 3, 4, 4))
expect_equal(x$relative, c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2))
expect_equal(get_episode(as.Date(c("2022-01-01", "2020-01-01")), 365), c(2, 1))
expect_equal(get_episode(as.Date(c("2020-01-01", "2022-01-01")), 365), c(1, 2))
test_df <- rbind(
data.frame(
date = as.Date(c("2015-01-01", "2015-10-01", "2016-02-04", "2016-12-31", "2017-01-01", "2017-02-01", "2017-02-05", "2020-01-01")),

18
man/get_episode.Rd
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@ -12,9 +12,9 @@ is_new_episode(x, episode_days = NULL, case_free_days = NULL, ...)
\arguments{
\item{x}{vector of dates (class \code{Date} or \code{POSIXt}), will be sorted internally to determine episodes}
\item{episode_days}{episode length in days, can also be less than a day or \code{Inf}, see \emph{Details}}
\item{episode_days}{episode length in days to specify the time period after which a new episode begins, can also be less than a day or \code{Inf}, see \emph{Details}}
\item{case_free_days}{length in days after which new episode will start, can also be less than a day or \code{Inf}, see \emph{Details}}
\item{case_free_days}{(inter-epidemic) interval length in days after which a new episode will start, can also be less than a day or \code{Inf}, see \emph{Details}}
\item{...}{ignored, only in place to allow future extensions}
}
@ -25,7 +25,7 @@ is_new_episode(x, episode_days = NULL, case_free_days = NULL, ...)
}
}
\description{
These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument \code{episode_days}. This can be used to determine clinical episodes for any epidemiological analysis. The \code{\link[=get_episode]{get_episode()}} function returns the index number of the episode per group, while the \code{\link[=is_new_episode]{is_new_episode()}} function returns \code{TRUE} for every new \code{\link[=get_episode]{get_episode()}} index. Both absolute and relative episode determination are supported.
These functions determine which items in a vector can be considered (the start of) a new episode. This can be used to determine clinical episodes for any epidemiological analysis. The \code{\link[=get_episode]{get_episode()}} function returns the index number of the episode per group, while the \code{\link[=is_new_episode]{is_new_episode()}} function returns \code{TRUE} for every new \code{\link[=get_episode]{get_episode()}} index. Both absolute and relative episode determination are supported.
}
\details{
Episodes can be determined in two ways: absolute and relative.
@ -37,7 +37,7 @@ This method uses \code{episode_days} to define an episode length in days, after
Thus, this method counts \strong{since the start of the previous episode}.
\item Relative
This method uses \code{case_free_days} to quantify the duration of (inter-epidemic) intervals, after which a new episode will start. A common use case is infectious disease epidemiology: episodes of norovirus outbreaks in a hospital for example. The case-free period could then be 14 days, so that new norovirus cases after that time will be considered a different (or new) episode.
This method uses \code{case_free_days} to quantify the duration of case-free days (the inter-epidemic interval), after which a new episode will start. A common use case is infectious disease epidemiology: episodes of norovirus outbreaks in a hospital for example. The case-free period could then be 14 days, so that new norovirus cases after that time will be considered a different (or new) episode.
Thus, this methods counts \strong{since the last case in the previous episode}.
}
@ -47,8 +47,8 @@ In a table:\tabular{ccc}{
2023-01-01 \tab 1 \tab 1 \cr
2023-01-02 \tab 1 \tab 1 \cr
2023-01-05 \tab 1 \tab 1 \cr
2023-01-08 \tab 2\code{*} \tab 1 \cr
2023-02-21 \tab 3 \tab 2\code{**} \cr
2023-01-08 \tab 2** \tab 1 \cr
2023-02-21 \tab 3 \tab 2*** \cr
2023-02-22 \tab 3 \tab 2 \cr
2023-02-23 \tab 3 \tab 2 \cr
2023-02-24 \tab 3 \tab 2 \cr
@ -56,8 +56,10 @@ In a table:\tabular{ccc}{
}
\code{*} This marks the start of a new episode, because 8 January 2023 is more than 7 days since the start of the previous episode (1 January 2023). \cr
\code{**} This marks the start of a new episode, because 21 January 2023 is more than 7 days since the last case in the previous episode (8 January 2023).
** This marks the start of a new episode, because 8 January 2023 is more than 7 days since the start of the previous episode (1 January 2023). \cr
*** This marks the start of a new episode, because 21 January 2023 is more than 7 days since the last case in the previous episode (8 January 2023).
Either \code{episode_days} or \code{case_free_days} must be provided in the function.
\subsection{Difference between \code{get_episode()} and \code{is_new_episode()}}{
The \code{\link[=get_episode]{get_episode()}} function returns the index number of the episode, so all cases/patients/isolates in the first episode will have the number 1, all cases/patients/isolates in the second episode will have the number 2, etc.