epiparameter_db {epiparameter} | R Documentation |
Create <epiparameter>
object(s) directly from the epiparameter library
(database)
Description
Extract <epiparameter>
object(s) directly from
the library of epidemiological parameters. The epiparameter
library of epidemiological parameters is compiled from primary literature
sources. The list output from epiparameter_db()
can be subset by the data
it contains, for example by: disease, pathogen, epidemiological distribution,
sample size, region, etc.
If a distribution from a specific study is required, the author
argument
can be specified.
Multiple entries (<epiparameter>
objects) can be returned, use the
arguments to subset entries and use single_epiparameter = TRUE
to force a
single <epiparameter>
to be returned.
Usage
epiparameter_db(
disease = "all",
pathogen = "all",
epi_name = "all",
author = NULL,
subset = NULL,
single_epiparameter = FALSE
)
Arguments
disease |
A |
pathogen |
A |
epi_name |
A |
author |
A |
subset |
Either Subsetting (using The The expression should be specified without using the data object name
(e.g. |
single_epiparameter |
A boolean Note: If multiple entries match the arguments supplied and
|
Details
disease
, epi_name
and author
are given as individual arguments
as these are the most common variables to subset the parameter library by.
The subset
argument facilitates all other subsetting of rows to select the
<epiparameter>
object(s) desired. To subset based on multiple variables
separate each expression with &
.
List of epidemiological parameters:
"all" (default, returns all entries in library)
"incubation period"
"onset to hospitalisation"
"onset to death"
"serial interval"
"generation time"
"offspring distribution"
"hospitalisation to death"
"hospitalisation to discharge"
"notification to death"
"notification to discharge"
"onset to discharge"
"onset to ventilation"
Value
An <epiparameter>
object or list of <epiparameter>
objects.
Examples
epiparameter_db(disease = "influenza", epi_name = "serial_interval")
# example using custom subsetting
eparam <- epiparameter_db(
disease = "SARS",
epi_name = "offspring_distribution",
subset = sample_size > 40
)
# example using functional subsetting
eparam <- epiparameter_db(
disease = "COVID-19",
epi_name = "incubation_period",
subset = is_parameterised
)
# example forcing a single <epiparameter> to be returned
eparam <- epiparameter_db(
disease = "SARS",
epi_name = "offspring_distribution",
single_epiparameter = TRUE
)