Retrieve all incubation period parameters for a given pathogen

Retrieve all serial interval estimates for a given pathogen

Retrieve all generation time estimates for a given pathogen

Retrieve all delay parameters for a given pathogen

Retrieve all CFR parameters for a given pathogen

Retrieve all risk factor parameters for a given pathogen

Retrieve all genomic parameters for a given pathogen

Retrieve all reproduction number parameters for a given pathogen

Retrieve all seroprevalence parameters for a given pathogen

Retrieve all doubling time parameters for a given pathogen

Retrieve all attack rate parameters for a given pathogen

Retrieve all growth rate parameters for a given pathogen

Retrieve all overdispersion parameters for a given pathogen

Usage

get_incubation_period(data, all_columns)

get_serial_interval(data, all_columns)

get_generation_time(data, all_columns)

get_delays(data, all_columns)

get_cfr(data, all_columns)

get_risk_factors(data, all_columns)

get_genomic(data, all_columns)

get_reproduction_number(data, all_columns)

get_seroprevalence(data, all_columns)

get_doubling_time(data, all_columns)

get_attack_rate(data, all_columns)

get_growth_rate(data, all_columns)

get_overdispersion(data, all_columns)

get_relative_contribution(data, all_columns)

Arguments

data: parameter dataframe output from load_epidata
all_columns: The default is FALSE meaning that only the key columns specified for the specific parameter will be retrieved. If TRUE, then all columns in the data.frame will be retrieved.

Value

dataframe with all parameter estimates of this type and key columns (see get_key_columns)

Examples

df <- load_epidata(pathogen = "lassa")
#> 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 lassa
get_incubation_period(data = df$params, all_columns = FALSE)
#> # A tibble: 5 × 15
#>   article_label  article_info          population_country population_sample_size
#>   <chr>          <chr>                 <chr>                               <int>
#> 1 John D. 1970   John D. 1970 (Americ… Nigeria                                 3
#> 2 N.A. 2013      10.1016/j.ijid.2013.… Nigeria                                20
#> 3 Andrei R. 2019 10.1098/rstb.2018.02… Nigeria                                NA
#> 4 A 2019         A 2019 (Annals Of Me… Nigeria                                62
#> 5 P. E. 1973     10.4269/ajtmh.1973.2… Liberia                                11
#> # ℹ 11 more variables: population_sample_type <chr>, population_group <chr>,
#> #   method_disaggregated <lgl>, parameter_type <chr>, parameter_value <dbl>,
#> #   parameter_unit <chr>, distribution_type <chr>,
#> #   distribution_par1_value <dbl>, distribution_par2_value <dbl>,
#> #   other_delay_start <chr>, other_delay_end <chr>