epiparameter
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show if epiparameter is `extrinsic` TRUE or FALSE
Is your feature request related to a problem? Please describe.
The extrinsic incubation periods are only two, but the current interface does not show the variable "extrinsic" yet
library(epiparameter)
library(tidyverse)
epidist_db(subset = extrinsic == TRUE)
#> 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 citation for each use the 'get_citation' function
#> # List of 2 <epidist> objects
#> Number of diseases: 1
#> ❯ Dengue
#> Number of epi distributions: 1
#> ❯ incubation period
#> [[1]]
#> Disease: Dengue
#> Pathogen: Dengue Virus
#> Epi Distribution: incubation period
#> Study: Chan M, Johansson M (2012). "The Incubation Periods of Dengue Viruses."
#> _PLoS One_. doi:10.1371/journal.pone.0050972
#> <https://doi.org/10.1371/journal.pone.0050972>.
#> Distribution: lnorm
#> Parameters:
#> meanlog: 2.553
#> sdlog: 0.481
#>
#> [[2]]
#> Disease: Dengue
#> Pathogen: Dengue Virus
#> Epi Distribution: incubation period
#> Study: Chan M, Johansson M (2012). "The Incubation Periods of Dengue Viruses."
#> _PLoS One_. doi:10.1371/journal.pone.0050972
#> <https://doi.org/10.1371/journal.pone.0050972>.
#> Distribution: lnorm
#> Parameters:
#> meanlog: 1.792
#> sdlog: 0.468
#>
#> # ℹ Use `parameter_tbl()` to see a summary table of the parameters.
#> # ℹ Explore database online at: https://epiverse-trace.github.io/epiparameter/dev/articles/database.html
epidist_db(subset = extrinsic == TRUE) %>%
parameter_tbl()
#> 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 citation for each use the 'get_citation' function
#> # Parameter table:
#> # A data frame: 2 × 7
#> disease pathogen epi_distribution prob_distribution author year sample_size
#> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 Dengue Dengue Vi… incubation peri… lnorm Chan … 2012 146
#> 2 Dengue Dengue Vi… incubation peri… lnorm Chan … 2012 146
Created on 2024-08-02 with reprex v2.1.0
Describe the solution you'd like
Possibly related with #50, the solution could include a line in the epidist/epiparameter class object print saying extrinsic: FALSE
or extrinsic: TRUE
. Also a column in the parameter_tbl()
output
Additional context It's not urgent, but it's for your consideration. Although {epiparameter} currently only has Denge extrinsic incubation period, when Zika values be added we can showcase them in how-to guides about the usage of {epiparameter} to access inputs to a Zika model build with {deSolve} as a next step for learners after reading the "building a simple mathematical model for Zika" (Spanish, English)