A helper function when creating an <epiparameter> object to
create a metadata list with sensible defaults, type checking and arguments
to help remember metadata list structure (element names).
Usage
create_metadata(
sample_size = NA_integer_,
region = NA_character_,
transmission_mode = NA_character_,
vector = NA_character_,
extrinsic = FALSE,
inference_method = NA_character_
)Arguments
- sample_size
The sample of the data used to fit the delay distribution. This is usually the number of people with data on a primary and possibly secondary event of interest. In cases where the sample size is not stated NA can be used.
- region
The geographical location the data was collected. This can either be given at sub-national, national, continental. Multiple nested regions can be given and are comma separated. When the region is not specified NA can be given.
- transmission_mode
A character string specifying how the pathogen is transmitted. This information is used to determine whether the epidemiological parameters are from a vector-borne disease (i.e. is transmitted between humans through an intermediate vector), this is specified by
transmission_mode = "vector_borne".- vector
The name of the vector transmitting the vector-borne disease. This can be a common name, or a latin binomial name of a specific vector species. Both the common name and taxonomic name can be given with one given in parentheses. When a disease is not vector-borne NA should be given.
- extrinsic
A boolean value defining whether the data entry is an extrinsic delay distribution, such as the extrinsic incubation period. This field is required because intrinsic and extrinsic delay distributions are stored as separate entries in the database and can be linked. When the disease is not vector-borne FALSE should be given. See Details for explanation of extrinsic distribution.
- inference_method
The type of inference used to fit the delay distribution to the data. Abbreviations of model fitting techniques can be specified as long as they are non-ambiguous. This field is only used to determine whether the uncertainty intervals possibly specified in the other fields are: confidence intervals (in the case of maximum likelihood), or credible intervals (in the case of bayesian inference). Uncertainty bounds for another types of inference methods, or if the inference method is unstated are assumed to be confidence intervals. When the inference method is unknown or a disease does not have a probability distribution NA can be given.
Value
A named list containing information on the sample size of the study, geography, whether the disease is vector-borne and if so whether it is the intrinsic or extrinsic distribution as well as method of distribution parameter estimation.
Details
In vector-borne diseases the transmissibility of a disease is dependent on both the time taken for a host (i.e. human) to become infectious, but also on the time it takes the vector to become infectious. Therefore, the extrinsic delay, in which the vector has been infected by is not yet infectious can have a role in the spread of a disease.
Examples
# it will automatically populate the fields with defaults if left empty
create_metadata()
#> $sample_size
#> [1] NA
#>
#> $region
#> [1] NA
#>
#> $transmission_mode
#> [1] NA
#>
#> $vector
#> [1] NA
#>
#> $extrinsic
#> [1] FALSE
#>
#> $inference_method
#> [1] NA
#>
# supplying each field
create_metadata(
sample_size = 10,
region = "UK",
transmission_mode = "vector_borne",
vector = "mosquito",
extrinsic = FALSE,
inference_method = "MLE"
)
#> $sample_size
#> [1] 10
#>
#> $region
#> [1] "UK"
#>
#> $transmission_mode
#> [1] "vector_borne"
#>
#> $vector
#> [1] "mosquito"
#>
#> $extrinsic
#> [1] FALSE
#>
#> $inference_method
#> [1] "MLE"
#>