Utility to obtain available fields in a specified table — get_table_field

Note: This will need to be extended when other pathogens are added

Usage

get_table_field_options(
  pathogen,
  table = c("model", "parameter", "outbreak", "article"),
  field = "all"
)

Arguments

pathogen: name of pathogen. Must be one of the priority pathogens You can get a list of the priority pathogens currently included in the package by calling the function priority_pathogens.
table: the table to be loaded. Must be one of "article", "parameter", "outbreak", or "model"
field: can either be "all" to return all fields in the specified table_type, or a specific variable name that the user wants to return

Value

data for specified table_type and field

Examples

get_table_field_options(
                       pathogen = "marburg", "model",
                       field = "all")
#> # A tibble: 11 × 6
#>    `Model type`   Stochastic or determ…¹ `Transmission route` `Compartment type`
#>    <chr>          <chr>                  <chr>                <chr>             
#>  1 "Compartmenta… "Stochastic"           "Airborne or close … "SIS"             
#>  2 "Branching pr… "Deterministic"        "Human to human (di… "SIR"             
#>  3 "Agent / Indi… ""                     "Vector to human"    "SEIR"            
#>  4 "Other"        ""                     "Animal reservoir t… "Other compartmen…
#>  5 "Unspecified"  ""                     "Sexual"             "Not compartmenta…
#>  6 ""             ""                     "Unspecified"        ""                
#>  7 ""             ""                     ""                   ""                
#>  8 ""             ""                     ""                   ""                
#>  9 ""             ""                     ""                   ""                
#> 10 ""             ""                     ""                   ""                
#> 11 ""             ""                     ""                   ""                
#> # ℹ abbreviated name: ¹`Stochastic or deterministic`
#> # ℹ 2 more variables: Assumptions <chr>, Interventions <chr>

get_table_field_options(pathogen = "marburg", "model",
                        field = "Model type")
#> # A tibble: 5 × 1
#>   `Model type`            
#>   <chr>                   
#> 1 Compartmental           
#> 2 Branching process       
#> 3 Agent / Individual based
#> 4 Other                   
#> 5 Unspecified             

get_table_field_options(pathogen = "marburg", "parameter",
                        field = "Reproduction number method")
#> # A tibble: 8 × 1
#>   `Reproduction number method`         
#>   <chr>                                
#> 1 Renewal equations / Branching process
#> 2 Growth rate                          
#> 3 Compartmental model                  
#> 4 Next generation matrix               
#> 5 Empirical (contact tracing)          
#> 6 Genomics                             
#> 7 Other                                
#> 8 Unspecified