retrieve all parameters of specified type or class
Arguments
- data
parameter dataframe output from
load_epidata- parameter_name
name of the parameter type or parameter class to retrieve, ensuring the name matches that in data
Examples
df <- load_epidata(pathogen = "ebola")
#> ℹ ebola does not have any extracted outbreaks
#> information. Outbreaks will be set to NULL.
#> Rows: 107 Columns: 2
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ";"
#> chr (2): parameter_type_short, parameter_type_full
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> ✔ Data loaded for ebola
get_parameter(data = df$params, parameter_name = "Human delay - serial interval")
#> # A tibble: 19 × 78
#> id parameter_data_id covidence_id pathogen parameter_type parameter_value
#> <chr> <chr> <int> <chr> <chr> <dbl>
#> 1 f49a9… 466f684ff8286fbd… 506 Ebola v… Human delay -… 12
#> 2 c1e68… cb37cc4599953d47… 1471 Ebola v… Human delay -… 19.4
#> 3 08e06… 20eb9e7d7714183c… 1876 Ebola v… Human delay -… 11
#> 4 5a250… 115c169147af31f7… 1891 Ebola v… Human delay -… 11.1
#> 5 54159… 6fca288e3bca7dc0… 3138 Ebola v… Human delay -… 16.1
#> 6 f044b… 89e334ec3622ed27… 3776 Ebola v… Human delay -… 14
#> 7 df908… e62da97ac8648211… 4966 Ebola v… Human delay -… 14.2
#> 8 df908… d46ff8b0c2ff67b7… 4966 Ebola v… Human delay -… 7.1
#> 9 1b9d9… abb8b6aabf43ac86… 5924 Ebola v… Human delay -… 13.7
#> 10 39354… 2b270d400af4fcce… 5939 Ebola v… Human delay -… NA
#> 11 39354… 8a18cde4823cf9f7… 5939 Ebola v… Human delay -… NA
#> 12 39354… 10f3384f1550a778… 5939 Ebola v… Human delay -… NA
#> 13 50dea… 631ec65830a82fbe… 6346 Ebola v… Human delay -… 15.3
#> 14 86e39… 5c8d68c39d1c3b98… 15896 Ebola v… Human delay -… 15.3
#> 15 40a29… 7f4ab651c48511df… 17077 Ebola v… Human delay -… 15.3
#> 16 b76dc… 0c3e02f80addfccc… 17730 Ebola v… Human delay -… 12
#> 17 b76dc… c2e0739d6bc652e9… 17730 Ebola v… Human delay -… 11.7
#> 18 74b62… e2a59f5aa40ddbdf… 18536 Ebola v… Human delay -… 12.3
#> 19 66e1b… 4da557e3c2c22a10… 19083 Ebola v… Human delay -… NA
#> # ℹ 72 more variables: exponent <dbl>, parameter_unit <chr>,
#> # parameter_lower_bound <dbl>, parameter_upper_bound <dbl>,
#> # parameter_value_type <chr>, parameter_uncertainty_single_value <dbl>,
#> # parameter_uncertainty_singe_type <chr>,
#> # parameter_uncertainty_lower_value <dbl>,
#> # parameter_uncertainty_upper_value <dbl>, parameter_uncertainty_type <chr>,
#> # cfr_ifr_numerator <int>, cfr_ifr_denominator <int>, …
df <- load_epidata(pathogen = "marburg")
#> Warning: There is 1 article with missing first author surname.
#> Warning: There is 1 article with missing first author surname and first author first
#> name.
#> Warning: There is 1 article with missing year of publication.
#> Rows: 107 Columns: 2
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ";"
#> chr (2): parameter_type_short, parameter_type_full
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Warning: Unknown or uninitialised column: `other_delay_start`.
#> Warning: Unknown or uninitialised column: `other_delay_end`.
#> Note: the params dataframe does not have a covidence_id column
#> Note: the models dataframe does not have a covidence_id column
#> Note: the outbreaks dataframe does not have a covidence_id column
#> ✔ Data loaded for marburg
get_parameter(data = df$params, parameter_name = "Attack rate")
#> # A tibble: 1 × 61
#> parameter_data_id article_id parameter_type parameter_value parameter_unit
#> <chr> <int> <chr> <dbl> <chr>
#> 1 aaee8bee0e1498de490f… 21 Attack rate 21 Percentage (%)
#> # ℹ 56 more variables: parameter_lower_bound <dbl>,
#> # parameter_upper_bound <dbl>, parameter_value_type <chr>,
#> # parameter_uncertainty_single_value <dbl>,
#> # parameter_uncertainty_singe_type <chr>,
#> # parameter_uncertainty_lower_value <dbl>,
#> # parameter_uncertainty_upper_value <dbl>, parameter_uncertainty_type <chr>,
#> # cfr_ifr_numerator <int>, cfr_ifr_denominator <int>, …