From a78971142d5b8cff56a528d48d7bf32c9371e742 Mon Sep 17 00:00:00 2001 From: athowes Date: Thu, 21 Nov 2024 11:30:41 +0000 Subject: [PATCH] Edits to Ebola vignette --- vignettes/ebola.Rmd | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/vignettes/ebola.Rmd b/vignettes/ebola.Rmd index 536ebd4f5..0e3592597 100644 --- a/vignettes/ebola.Rmd +++ b/vignettes/ebola.Rmd @@ -163,7 +163,7 @@ That is, $\mu$ and $\sigma$ such that when $x \sim \mathcal{N}(\mu, \sigma)$ the ## Data preparation -To prepare the data, we begin by filtering for the relevant columns and converting the date columns to `Date` objects: +To prepare the data, we begin by converting the date columns to `Date` objects and selecting the relevant columns: ```{r} obs_cens <- sierra_leone_ebola_data |> @@ -193,7 +193,7 @@ subsample <- 0.2 ``` Additionally, to speed up computation, we take a random `r 100 * subsample`% subsample of the complete data. -(In a real analysis, we'd recommend using all the available data). +(In a real analysis, we'd recommend using all the available data.) ```{r} obs_cens <- obs_cens |> @@ -210,7 +210,9 @@ linelist_data <- obs_cens |> ) ``` -Note that this has made some assumptions about the data in that it has assumed that as we did not supply upper bounds for the primary and secondary events, that the upper bounds are one day after the lower bounds. It has also assumed that the observation time is the maximum of the secondary event upper bound as we also did not supply an observation time column. +In this call to [as_epidist_linelist_data()] it has made some assumptions about the data. +First, because we did not supply upper bounds for the primary and secondary events (`pdate_upr` and `sdate_upr`), it has assumed that the upper bounds are one day after the lower bounds. +Second, because we also did not supply an observation time column (`obs_date`), it has assumed that the observation time is the maximum of the secondary event upper bounds. ## Model fitting