cts_prep: Prepare CTS data for modelling with SimInf
In tpepler/EPIC.SimInf: EPIC Package for Epidemiological Simulation Modelling using SimInf

Description Usage Arguments Details Value Note Author(s) See Also Examples

View source: R/cts_prep.R

Reads in and prepares CTS data for modelling with the SimInf simulation framework.

1	cts_prep(uid = NULL, pwd = NULL, startdate, enddate, model = c("SIR"), cphsizes_file = NULL, initdata_file = NULL, events_file = NULL)

`uid`	User ID for the EPIC server. If not specified in the function call, the user may be prompted to supply it if required.
`pwd`	Password for the EPIC server. If not specified in the function call, the user may be prompted to supply it if required.
`startdate`	Date for the start of the simulation model; specify in the format `'YYYY/MM/DD'`.
`enddate`	Date for the end of the simulation model; specify in the format `'YYYY/MM/DD'`.
`model`	Compartmental model type; currently only `'SIR'` is implemented.
`cphsizes_file`	Name of file containing CPH size data (i.e. numbers of animals per CPH on the start date of the simulation model) on the local file system, if available. Ignored if `inidata_file` is given. If both `cphsizes_file` and `initdata_file` are `NULL`, the required data will be extracted from the `cts201404` databased on the EPIC server.
`initdata_file`	Name of the file on the local file system containing the formatted initialisation data. If `NULL`, the `cphsizes_file` (if available) will be used to construct the initialisation data set.
`events_file`	Name of the file on the local file system containing the formatted events data. If `NULL`, the required data will be extracted from the EPIC server.

Initialisation and events data can be imported from files on the local file system, or extracted directly from the EPIC server. However, data extraction from the EPIC server takes considerably longer.

If data extraction from the EPIC server is necessary (in the case where either initdata_file and/or events_file are NULL), the user will be prompted to supply their user ID and password to access the EPIC server.

Returns a model data object (list) containing the following components:

`initdata`	Initialisation data (number of animals at each location at the start of the simulation).
`eventdata`	Observed event data to be used in the simulation model.
`model`	Compartment model type.
`startdate`	Start date for the simulation model.
`enddate`	End date for the simulation model.

Currently data preparation procedures are implemented for only the SIR model.

Theo Pepler

cphsizes_estimate, cts_events_extract

## -- EXAMPLE NOT RUN --

## Extract and prepare CTS data from the EPIC server
# cts_prep(startdate = '2012/01/01', enddate = '2012/03/31', model = 'SIR')

tpepler/EPIC.SimInf documentation built on July 29, 2021, 4:11 p.m.