cts_prep: Prepare CTS data for modelling with SimInf

In tpepler/EPIC.SimInf: EPIC Package for Epidemiological Simulation Modelling using SimInf

Prepare CTS data for modelling with SimInf

Description

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

Usage

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

Arguments

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.

Details

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.

Value

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.

Note

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

Author(s)

Theo Pepler

See Also

cphsizes_estimate, cts_events_extract

Examples

## -- 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 Sept. 19, 2024, 5:09 a.m.