how to subset multi_epidist object from epidist_db() by the prob_distribution?

[avallecam]

I want to extract the distribution for COVID-19 serial interval from Nishiura. If I use the single_epidist = T I get the lnorm. If I want the weibull, how can I do it? or is there a reason to prefer one over the other? or, how should I write the subset?

library(epiparameter)
library(tidyverse)

# from code below, I identify that prob_distribution column can be used to subset

epiparameter::epidist_db(
  disease = "covid",
  epi_dist = "serial",
  author = "Nishiura") %>%
  epiparameter::list_distributions()
#> Returning 2 results that match the criteria (2 are parameterised). 
#> Use subset to filter by entry variables or single_epidist to return a single entry. 
#> To retrieve the short citation for each use the 'get_citation' function
#>    disease epi_distribution prob_distribution       author year
#> 1 COVID-19  serial interval             lnorm Hiroshi .... 2020
#> 2 COVID-19  serial interval           weibull Hiroshi .... 2020

# I use subset, but this notation does not work

epiparameter::epidist_db(
  disease = "covid",
  epi_dist = "serial",
  author = "Nishiura",
  subset = prob_distribution == "lnorm")
#> Error in epiparameter::epidist_db(disease = "covid", epi_dist = "serial", : object 'prob_distribution' not found

# I get lnorm with single_epidist = T
# if interested in weibull, how to do it?

epiparameter::epidist_db(disease = "covid",
                         epi_dist = "serial",
                         author = "Nishiura",
                         single_epidist = T)
#> 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
#> Disease: COVID-19
#> Pathogen: SARS-CoV-2
#> Epi Distribution: serial interval
#> Study: 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>.
#> Distribution: lnorm
#> Parameters:
#>   meanlog: 1.386
#>   sdlog: 0.568

^{Created on 2023-11-30 with reprex v2.0.2}

[joshwlambert]

The feature you are after does not currently exist in {epiparameter}, I will convert this to an issue and make the required changes in order to subset by distribution type using non-standard evaluation.

[avallecam]

tagging #225 here for tracking this. I just found out that issues are not automatically cited in discussions