library(epiparameter)
covid_serialint <-
epiparameter::epidist_db(
disease = "covid",
epi_dist = "serial",
author = "Nishiura",
single_epidist = TRUE
)
#> Using Nishiura H, Linton N, Akhmetzhanov A (2020). "Serial interval of novel
#> coronavirus (COVID-19) infections." _International Journal of
#> Infectious Diseases_. doi:10.1016/j.ijid.2020.02.060
#> <https://doi.org/10.1016/j.ijid.2020.02.060>..
#> To retrieve the short citation use the 'get_citation' function
covid_serialint_discrete <-
epiparameter::discretise(covid_serialint)
# get quantiles
# for discrete distribution
# from discretised distribution object
covid_serialint_discrete$prob_dist$q(0.6)
#> [1] 4
# get quantiles
# for continuous distribution
# (but)
# from the discretise distribution object
covid_serialint_discrete$prob_dist$qf(0.6)
#> [1] 4.618906
# as in
quantile(covid_serialint,0.6)
#> [1] 4.618906
When we use
si$prob_dist$qf()
from a discretised function we are using the output from the continuous function. I reported this in https://github.com/epiverse-trace/epiparameter/issues/233. I copied here the reprex:Line in {episoap} of issue: https://github.com/epiverse-trace/episoap/blob/fe73f6bd4395c2b349034568881f53f08edc60b5/inst/rmarkdown/templates/transmissibility/skeleton/skeleton.Rmd#L408-L409
Reprex from {epiparameter}:
Created on 2024-02-01 with reprex v2.0.2
Tagging @joshwlambert @Degoot-AM @adamkucharski @jamesmbaazam as interest group from devday and as devs of this @Bisaloo @CarmenTamayo