tests/testthat/_snaps/print.md

In epiparameter: Classes and Helper Functions for Working with Epidemiological Parameters

epiparameter_db print method works as expected for > 5

Code
  epiparameter_db()
Message
  Returning 125 results that match the criteria (100 are parameterised). 
  Use subset to filter by entry variables or single_epiparameter to return a single entry. 
  To retrieve the citation for each use the 'get_citation' function
Output
  # List of 125 <epiparameter> objects
  Number of diseases: 23
  > Adenovirus > COVID-19 > Chikungunya > Dengue > Ebola Virus Disease > Hantavirus Pulmonary Syndrome > Human Coronavirus > Influenza > Japanese Encephalitis > MERS > Marburg Virus Disease > Measles > Mpox > Parainfluenza > Pneumonic Plague > RSV > Rhinovirus > Rift Valley Fever > SARS > Smallpox > West Nile Fever > Yellow Fever > Zika Virus Disease
  Number of epi parameters: 13
  > case fatality risk > generation time > hospitalisation to death > hospitalisation to discharge > incubation period > notification to death > notification to discharge > offspring distribution > onset to death > onset to discharge > onset to hospitalisation > onset to ventilation > serial interval
  [[1]]
  Disease: Adenovirus
  Pathogen: Adenovirus
  Epi Parameter: incubation period
  Study: Lessler J, Reich N, Brookmeyer R, Perl T, Nelson K, Cummings D (2009).
  "Incubation periods of acute respiratory viral infections: a systematic
  review." _The Lancet Infectious Diseases_.
  doi:10.1016/S1473-3099(09)70069-6
  <https://doi.org/10.1016/S1473-3099%2809%2970069-6>.
  Distribution: lnorm (days)
  Parameters:
    meanlog: 1.723
    sdlog: 0.231

  [[2]]
  Disease: Human Coronavirus
  Pathogen: Human_Cov
  Epi Parameter: incubation period
  Study: Lessler J, Reich N, Brookmeyer R, Perl T, Nelson K, Cummings D (2009).
  "Incubation periods of acute respiratory viral infections: a systematic
  review." _The Lancet Infectious Diseases_.
  doi:10.1016/S1473-3099(09)70069-7
  <https://doi.org/10.1016/S1473-3099%2809%2970069-7>.
  Distribution: lnorm (days)
  Parameters:
    meanlog: 1.163
    sdlog: 0.140

  [[3]]
  Disease: SARS
  Pathogen: SARS-Cov-1
  Epi Parameter: incubation period
  Study: Lessler J, Reich N, Brookmeyer R, Perl T, Nelson K, Cummings D (2009).
  "Incubation periods of acute respiratory viral infections: a systematic
  review." _The Lancet Infectious Diseases_.
  doi:10.1016/S1473-3099(09)70069-8
  <https://doi.org/10.1016/S1473-3099%2809%2970069-8>.
  Distribution: lnorm (days)
  Parameters:
    meanlog: 1.386
    sdlog: 0.593

  # i 122 more elements
  # i Use `print(n = ...)` to see more elements.
  # i Use `parameter_tbl()` to see a summary table of the parameters.
  # i Explore database online at: https://epiverse-trace.github.io/epiparameter/articles/database.html

epiparameter_db print method works as expected for <= 5

Code
  epiparameter_db(disease = "SARS", epi_name = "offspring distribution")
Message
  Returning 2 results that match the criteria (2 are parameterised). 
  Use subset to filter by entry variables or single_epiparameter to return a single entry. 
  To retrieve the citation for each use the 'get_citation' function
Output
  # List of 2 <epiparameter> objects
  Number of diseases: 1
  > SARS
  Number of epi parameters: 1
  > offspring distribution
  [[1]]
  Disease: SARS
  Pathogen: SARS-Cov-1
  Epi Parameter: offspring distribution
  Study: Lloyd-Smith J, Schreiber S, Kopp P, Getz W (2005). "Superspreading and
  the effect of individual variation on disease emergence." _Nature_.
  doi:10.1038/nature04153 <https://doi.org/10.1038/nature04153>.
  Distribution: nbinom (No units)
  Parameters:
    mean: 1.630
    dispersion: 0.160

  [[2]]
  Disease: SARS
  Pathogen: SARS-Cov-1
  Epi Parameter: offspring distribution
  Study: Lloyd-Smith J, Schreiber S, Kopp P, Getz W (2005). "Superspreading and
  the effect of individual variation on disease emergence." _Nature_.
  doi:10.1038/nature04153 <https://doi.org/10.1038/nature04153>.
  Distribution: nbinom (No units)
  Parameters:
    mean: 0.940
    dispersion: 0.170

  # i Use `parameter_tbl()` to see a summary table of the parameters.
  # i Explore database online at: https://epiverse-trace.github.io/epiparameter/articles/database.html

epiparameter.print works as expected

Code
  epiparameter(disease = "ebola", epi_name = "incubation", prob_distribution = create_prob_distribution(
    prob_distribution = "gamma", prob_distribution_params = c(shape = 1, scale = 1)))
Message
  Citation cannot be created as author, year, journal or title is missing
Output
  Disease: ebola
  Pathogen: NA
  Epi Parameter: incubation
  Study: (????). "No citation."
  Distribution: gamma (NA)
  Parameters:
    shape: 1.000
    scale: 1.000

Code
  epiparameter(disease = "ebola", epi_name = "incubation", prob_distribution = create_prob_distribution(
    prob_distribution = "gamma", prob_distribution_params = c(shape = 1, scale = 1),
    discretise = TRUE))
Message
  Citation cannot be created as author, year, journal or title is missing
Output
  Disease: ebola
  Pathogen: NA
  Epi Parameter: incubation
  Study: (????). "No citation."
  Distribution: discrete gamma (NA)
  Parameters:
    shape: 1.000
    scale: 1.000

epiparameter documentation built on April 3, 2025, 5:50 p.m.