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")
#> ✔ 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 Frame 1970        Frame 1970 (Ameri… Nigeria                                 3
#> 2 Ajayi 2013        10.1016/j.ijid.20… Nigeria                                20
#> 3 Akhmetzhanov 2019 10.1098/rstb.2018… Nigeria                                NA
#> 4 Joseph 2019       Joseph 2019 (Anna… Nigeria                                62
#> 5 Mertens 1973      10.4269/ajtmh.197… 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>