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actions-user authored and joshwlambert committed Oct 9, 2024
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Expand Up @@ -62,12 +62,12 @@ epiparameters
#> # List of 125 <epiparameter> objects
#> Number of diseases: 23
#> ❯ Adenovirus ❯ Chikungunya ❯ COVID-19 ❯ Dengue ❯ Ebola Virus Disease ❯ Hantavirus Pulmonary Syndrome ❯ Human Coronavirus ❯ Influenza ❯ Japanese Encephalitis ❯ Marburg Virus Disease ❯ Measles ❯ MERS ❯ Mpox ❯ Parainfluenza ❯ Pneumonic Plague ❯ Rhinovirus ❯ Rift Valley Fever ❯ RSV ❯ SARS ❯ Smallpox ❯ West Nile Fever ❯ Yellow Fever ❯ Zika Virus Disease
#> Number of epi distributions: 13
#> 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 Distribution: incubation period
#> 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_.
Expand All @@ -81,7 +81,7 @@ epiparameters
#> [[2]]
#> Disease: Human Coronavirus
#> Pathogen: Human_Cov
#> Epi Distribution: incubation period
#> 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_.
Expand All @@ -95,7 +95,7 @@ epiparameters
#> [[3]]
#> Disease: SARS
#> Pathogen: SARS-Cov-1
#> Epi Distribution: incubation period
#> 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_.
Expand Down Expand Up @@ -124,12 +124,12 @@ The results can be filtered by disease and epidemiological distribution.
Here we set `single_epiparameter = TRUE` as we only want a single
database entry returned, and by default (`single_epiparameter = FALSE`)
it will return all database entries that match the disease (`disease`)
and epidemiological distribution (`epi_dist`).
and epidemiological parameter (`epi_name`).

``` r
influenza_incubation <- epiparameter_db(
disease = "influenza",
epi_dist = "incubation period",
epi_name = "incubation period",
single_epiparameter = TRUE
)
#> Using Virlogeux V, Li M, Tsang T, Feng L, Fang V, Jiang H, Wu P, Zheng J, Lau
Expand All @@ -141,7 +141,7 @@ influenza_incubation <- epiparameter_db(
influenza_incubation
#> Disease: Influenza
#> Pathogen: Influenza-A-H7N9
#> Epi Distribution: incubation period
#> Epi Parameter: incubation period
#> Study: Virlogeux V, Li M, Tsang T, Feng L, Fang V, Jiang H, Wu P, Zheng J, Lau
#> E, Cao Y, Qin Y, Liao Q, Yu H, Cowling B (2015). "Estimating the
#> Distribution of the Incubation Periods of Human Avian Influenza A(H7N9)
Expand All @@ -156,38 +156,38 @@ influenza_incubation
To quickly view the list of epidemiological distributions returned by
`epiparameter_db()` in a table, the `parameter_tbl()` gives a summary of
the data, and offers the ability to subset you data by `disease`,
`pathogen` and epidemiological distribution (`epi_dist`).
`pathogen` and epidemiological parameter (`epi_name`).

``` r
parameter_tbl(epiparameters)
#> # Parameter table:
#> # A data frame: 125 × 7
#> disease pathogen epi_distribution prob_distribution author year sample_size
#> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 Adenovi… Adenovi… incubation peri… lnorm Lessl… 2009 14
#> 2 Human C… Human_C… incubation peri… lnorm Lessl… 2009 13
#> 3 SARS SARS-Co… incubation peri… lnorm Lessl… 2009 157
#> 4 Influen… Influen… incubation peri… lnorm Lessl… 2009 151
#> 5 Influen… Influen… incubation peri… lnorm Lessl… 2009 90
#> 6 Influen… Influen… incubation peri… lnorm Lessl… 2009 78
#> 7 Measles Measles… incubation peri… lnorm Lessl… 2009 55
#> 8 Parainf… Parainf… incubation peri… lnorm Lessl… 2009 11
#> 9 RSV RSV incubation peri… lnorm Lessl… 2009 24
#> 10 Rhinovi… Rhinovi… incubation peri… lnorm Lessl… 2009 28
#> disease pathogen epi_name prob_distribution author year sample_size
#> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 Adenovirus Adenovi… incubat… lnorm Lessl… 2009 14
#> 2 Human Coronavir… Human_C… incubat… lnorm Lessl… 2009 13
#> 3 SARS SARS-Co… incubat… lnorm Lessl… 2009 157
#> 4 Influenza Influen… incubat… lnorm Lessl… 2009 151
#> 5 Influenza Influen… incubat… lnorm Lessl… 2009 90
#> 6 Influenza Influen… incubat… lnorm Lessl… 2009 78
#> 7 Measles Measles… incubat… lnorm Lessl… 2009 55
#> 8 Parainfluenza Parainf… incubat… lnorm Lessl… 2009 11
#> 9 RSV RSV incubat… lnorm Lessl… 2009 24
#> 10 Rhinovirus Rhinovi… incubat… lnorm Lessl… 2009 28
#> # ℹ 115 more rows
parameter_tbl(
epiparameters,
epi_dist = "onset to hospitalisation"
epi_name = "onset to hospitalisation"
)
#> # Parameter table:
#> # A data frame: 5 × 7
#> disease pathogen epi_distribution prob_distribution author year sample_size
#> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 MERS MERS-Cov onset to hospit… <NA> Assir… 2013 23
#> 2 COVID-19 SARS-CoV… onset to hospit… gamma Linto… 2020 155
#> 3 COVID-19 SARS-CoV… onset to hospit… gamma Linto… 2020 34
#> 4 COVID-19 SARS-CoV… onset to hospit… lnorm Linto… 2020 155
#> 5 COVID-19 SARS-CoV… onset to hospit… lnorm Linto… 2020 34
#> disease pathogen epi_name prob_distribution author year sample_size
#> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 MERS MERS-Cov onset to hospi… <NA> Assir… 2013 23
#> 2 COVID-19 SARS-CoV-2 onset to hospi… gamma Linto… 2020 155
#> 3 COVID-19 SARS-CoV-2 onset to hospi… gamma Linto… 2020 34
#> 4 COVID-19 SARS-CoV-2 onset to hospi… lnorm Linto… 2020 155
#> 5 COVID-19 SARS-CoV-2 onset to hospi… lnorm Linto… 2020 34
```

The `<epiparameter>` object can be plotted.
Expand Down

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