From 91286578306f249a66ce386bdc50d7ac1e71f280 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Fri, 5 Jan 2024 14:08:38 +0000 Subject: [PATCH] update get started vignette Co-authored-by: Adam Kucharski --- vignettes/simulist.Rmd | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/vignettes/simulist.Rmd b/vignettes/simulist.Rmd index bca5e675..a9d6d876 100644 --- a/vignettes/simulist.Rmd +++ b/vignettes/simulist.Rmd @@ -18,18 +18,18 @@ knitr::opts_chunk$set( ) ``` -This is an introductory vignette to the {simulist} R package. {simulist} simulates epidemiological data, either a line list, to provide a row-by-row account of cases in an infectious disease outbreak, or a contacts table, to provide a history of which individuals were in contact with which others. +This is an introductory vignette to the {simulist} R package. {simulist} simulates two types of common epidemiological data collected during infectious disease outbreaks: 1) a line list, which provides individual-level descriptions of cases in an outbreak; 2) a contact dataset, which provides details of which others individuals were in contact with each of the cases. The main function in the {simulist} package is `sim_linelist()`. This functions takes in arguments that control the dynamics of the outbreak, such as the serial interval, and outputs a line list table (``) with case information for each infected individual. -For this introduction we will simulate a line list for a COVID-19 (SARS-CoV-2) outbreak. This will require two R packages: {simulist}, to produce the line list, and {epiparameter} to provide epidemiological parameters, such as onset-to-death delays. +For this introduction we will simulate a line list for the early stages of a COVID-19 (SARS-CoV-2) outbreak. This will require two R packages: {simulist}, to produce the line list, and {epiparameter} to provide epidemiological parameters, such as onset-to-death delays. ```{r setup} library(simulist) library(epiparameter) ``` -First we load in some data that is required for the line list simulation. Data on epidemiological parameters and distributions is read from the {epiparameter} R package. +First we load in some data that is required for the line list simulation. Data on epidemiological parameters and distributions are read from the {epiparameter} R package. ```{r read-epidist} # get serial interval from {epiparameter} database @@ -70,7 +70,7 @@ head(linelist) ## Case type -In the midst of an infectious disease outbreak it may not be possible to confirm every case. A confirmed case is usually done via a diagnostic test which may or may not need to be carried out in the laboratory. There are several reasons why a case may not be confirmed, one example is limited testing capacity, especially in fast growing epidemics. The other categories for cases are: probable and suspected. Probable cases are those that show clinical evidence for the disease but have not, or cannot, be confirmed by a diagnostic test. Suspected cases are those that are possibly infected but do not show clear clinical or epidemiological evidence, nor has a diagnostic test been performed. +During an infectious disease outbreak it may not be possible to confirm every infection as a case. A confirmed case is typically defined via a diagnostic test. There are several reasons why a case may not be confirmed, including limited testing capacity and mild or non-specific early symptoms, especially in fast growing epidemics. We therefore include two other categories for cases: probable and suspected. For example, probable cases may those that show clinical evidence for the disease but have not, or cannot, be confirmed by a diagnostic test. Suspected cases are those that are possibly infected but do not show clear clinical or epidemiological evidence, nor has a diagnostic test been performed. Hence the distribution of suspected/probable/confirmed will depend on the pathogen characteristics, outbreak-specific definitions, and resources available. The line list output from the {simulist} simulation contains a column (`case_type`) with the type of case.