epidist_db: Create `<epiparameter>` object(s) directly from the epiparameter library (database)

Description

epidist_db() has been renamed epiparameter_db(). Please use epiparameter_db() instead as the epidist_db() alias will be removed from the package in the future.

Usage

epidist_db(
  disease = "all",
  pathogen = "all",
  epi_name = "all",
  author = NULL,
  subset = NULL,
  single_epiparameter = FALSE
)

Value

An <epiparameter> object or list of <epiparameter> objects.

Arguments

disease

A character string specifying the disease.

pathogen

A character string specifying the pathogen.

epi_name

A character string specifying the epidemiological parameter. See details for full list of epidemiological distributions.

author

A character string specifying the author of the study reporting the distribution. Only the first author will be matched. It is recommended to use the family name as first names may or may not be initialised.

subset

Either NULL or a valid R expressions that evaluates to logicals to subset the list of <epiparameter>, or a function that can be applied over a list of <epiparameter> objects.

Subsetting (using subset) can be combined with the subsetting done with the disease and epi_name arguments (and author if specified). If left as NULL (default) no subsetting is carried out.

The subset argument is similar to subsetting a <data.frame>, but the difference is that fixed comparisons and not vectorised comparisons are needed. For example sample_size > 10 is a valid subset expression, but sample_size == max(sample_size), which would be a valid subset expression for a <data.frame> does not work. The vectorised expression will often not error, but will likely return unexpected results. For the sample_size == max(sample_size) example it will always return TRUE (except for NAs) as it is a single numeric so will be equal to it's max value.

The expression should be specified without using the data object name (e.g. df$var) and instead just var should be supplied. In other words, this argument uses non-standard evaluation, just as the subset argument in subset(), and is similar to <data-masking> used by the dplyr package.

single_epiparameter

A boolean logical determining whether a single <epiparameter> or multiple entries from the library can be returned if matched by the other arguments (disease, epi_name, author). This argument is used to prevent multiple sets of parameters being returned when only one is wanted.

Note: If multiple entries match the arguments supplied and single_epiparameter = TRUE then the <epiparameter> that is parameterised (and accounts for truncation if available) and has the largest sample size will be returned (see is_parameterised()). If multiple entries are equal after this sorting the first entry will be returned.