From c316732b7e052502c4e512c7f0fa2cae9f5b46d6 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Tue, 8 Oct 2024 12:46:05 +0100 Subject: [PATCH] clarify PERG work in data_from_epireview vignette --- vignettes/articles/data_from_epireview.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vignettes/articles/data_from_epireview.Rmd b/vignettes/articles/data_from_epireview.Rmd index c15a8cc18..97b5e6479 100644 --- a/vignettes/articles/data_from_epireview.Rmd +++ b/vignettes/articles/data_from_epireview.Rmd @@ -125,7 +125,7 @@ The `as_epiparameter()` function is an S3 generic. If you are not familiar with ## Multi-row {epireview} entries -In general, all required values for a parameter are represented as a _single_ entry in epireview. In some of cases, e.g. for Marburg Virus Disease and Ebola Virus Disease (as the first pathogens we extracted), values captured for a parameter are on multiple rows. We are trying to avoid this as _linking_ these entries is very challenging, but there are still some cases in which there are linked parameters on different rows. We provide further information in the limitations section below. +In general, all required values for a parameter are represented as a _single_ entry in epireview. In some of cases, e.g. for Marburg Virus Disease and Ebola Virus Disease (as the first pathogens the PERG team extracted), values captured for a parameter are on multiple rows. We are trying to avoid this as _linking_ these entries is very challenging, but there are still some cases in which there are linked parameters on different rows. We provide further information in the limitations section below. The way the {epireview} data is stored means that some epidemiological parameter entries require multiple rows. This can be, for example, because they contain two summary statistics (e.g. mean and standard deviation) that are kept on separate rows. In order to create `` objects that contains the full information for each entry multiple rows of the epidemiological parameters table from {epireview} can be given to `as_epiparameter()` to create a single `` object. @@ -282,7 +282,7 @@ generate(ebola_si_epiparameter, times = 10) * The _database schema_ of {epireview} has evolved over time as the Imperial PERG team has extracted more pathogens. * A list of [parameter types](https://mrc-ide.github.io/epireview/articles/pathogen_database_field_options.html) is available in the {epireview} package -* It is important to differentiate between variability of the sample (e.g. sample standard deviation) and uncertainty of the estimate (e.g. 95% confidence interval or credible interval). From the database version of {epireview} of Zika, we will explicitly expose this to remove any ambiguity of the extracted data. Please note that in the Marburg, Lassa, and Ebola datasets, there may be some ambiguity between variability and uncertainty. +* It is important to differentiate between variability of the sample (e.g. sample standard deviation) and uncertainty of the estimate (e.g. 95% confidence interval or credible interval). From the database version of {epireview} of Zika, the PERG team will explicitly expose this to remove any ambiguity of the extracted data. Please note that in the Marburg, Lassa, and Ebola datasets, there may be some ambiguity between variability and uncertainty. * This is functionality in {epiparameter} and {epireview} which will be developed and improved over the coming months. ## References