mpox incubation period discrepancy

Thanks for reporting.

This has been fixed in PR #346. I believe that only the main text was read when the values were extracted, as a result only the mean and distribution percentiles were included, which were then being used to calculate to the distribution parameters internally, hence the small discrepancy.

In the process of reading the appendix I also noticed that the sample size was incorrectly extracted as 255 (reported as number of PCR confirmed cases), whereas in the appendix table 2 it states "n = 30", so I've corrected the sample size to 30.

As a results the original code snippet above now returns a different Mpox incubation period:

epiparameter::epidist_db(
  disease = "mpox",
  epi_dist = "incubation_period",
  single_epidist = TRUE
)
#> Using Madewell Z, Charniga K, Masters N, Asher J, Fahrenwald L, Still W, Chen
#> J, Kipperman N, Bui D, Shea M, Saathoff-Huber L, Johnson S, Harbi K,
#> Berns A, Perez T, Gateley E, Spicknall I, Nakazawa Y, Gift T, 2022
#> Monkeypox Outbreak Response Team (2022). "Serial interval and
#> incubation period estimates of monkeypox virus infection in 12 U.S.
#> jurisdictions, May – August 2023." _medRxiv_.
#> doi:10.1101/2022.10.26.22281516
#> <https://doi.org/10.1101/2022.10.26.22281516>.. 
#> To retrieve the citation use the 'get_citation' function
#> Disease: Mpox
#> Pathogen: Mpox Virus
#> Epi Distribution: incubation period
#> Study: Madewell Z, Charniga K, Masters N, Asher J, Fahrenwald L, Still W, Chen
#> J, Kipperman N, Bui D, Shea M, Saathoff-Huber L, Johnson S, Harbi K,
#> Berns A, Perez T, Gateley E, Spicknall I, Nakazawa Y, Gift T, 2022
#> Monkeypox Outbreak Response Team (2022). "Serial interval and
#> incubation period estimates of monkeypox virus infection in 12 U.S.
#> jurisdictions, May – August 2023." _medRxiv_.
#> doi:10.1101/2022.10.26.22281516
#> <https://doi.org/10.1101/2022.10.26.22281516>.
#> Distribution: lnorm
#> Parameters:
#>   meanlog: 1.500
#>   sdlog: 0.700

^{Created on 2024-07-02 with reprex v2.1.0}

The Guzzetta et al. parameters can be still be accessed:

epiparameter::epidist_db(
  disease = "mpox", 
  epi_dist = "incubation_period", 
  author = "Guzzetta"
)
#> Returning 1 results that match the criteria (1 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
#> Disease: Mpox
#> Pathogen: Mpox Virus
#> Epi Distribution: incubation period
#> Study: Guzzetta G, Mammone A, Ferraro F, Caraglia A, Rapiti A, Marziano V,
#> Poletti P, Cereda D, Vairo F, Mattei G, Maraglino F, Rezza G, Merler S
#> (2022). "Early Estimates of Monkeypox Incubation Period, Generation
#> Time, and Reproduction Number, Italy, May-June 2022." _Emerging
#> Infectious Diseases_. doi:10.3201/eid2810.221126
#> <https://doi.org/10.3201/eid2810.221126>.
#> Distribution: gamma
#> Parameters:
#>   shape: 2.420
#>   scale: 3.750

^{Created on 2024-07-02 with reprex v2.1.0}

epiverse-trace / epiparameter

mpox incubation period discrepancy #345

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