diff --git a/README.md b/README.md index 72a62c3..0da4d6c 100644 --- a/README.md +++ b/README.md @@ -86,8 +86,8 @@ head(linelist) ``` However, to simulate a more realistic line list using epidemiological -parameters estimated for a infectious disease we can use previously -estimated epidemiological parameters. These can be from the +parameters estimated for an infectious disease outbreak we can use +previously estimated epidemiological parameters. These can be from the `{epiparameter}` R package if available, or if these are not in the `{epiparameter}` database yet (such as the contact distribution for COVID-19) we can define them ourselves. Here we define a contact @@ -107,9 +107,6 @@ contact_distribution <- epiparameter::epidist( prob_distribution_params = c(mean = 2) ) #> Citation cannot be created as author, year, journal or title is missing -``` - -``` r # create COVID-19 infectious period infectious_period <- epiparameter::epidist( @@ -119,9 +116,6 @@ infectious_period <- epiparameter::epidist( prob_distribution_params = c(shape = 1, scale = 1) ) #> Citation cannot be created as author, year, journal or title is missing -``` - -``` r # get onset to hospital admission from {epiparameter} database onset_to_hosp <- epiparameter::epidist_db( @@ -136,9 +130,6 @@ onset_to_hosp <- epiparameter::epidist_db( #> Case Data." _Journal of Clinical Medicine_. doi:10.3390/jcm9020538 #> .. #> To retrieve the citation use the 'get_citation' function -``` - -``` r # get onset to death from {epiparameter} database onset_to_death <- epiparameter::epidist_db( @@ -290,9 +281,6 @@ head(outbreak$linelist) #> 4 2023-01-21 2023-01-07 2023-01-08 23.9 #> 5 2023-01-01 2023-01-01 23.9 #> 6 2023-01-02 2023-01-05 NA -``` - -``` r head(outbreak$contacts) #> from to age sex date_first_contact #> 1 Okatomi Reish Jesse Lynn 44 f 2023-01-04