cphsizes_estimate: Estimate CPH sizes
In tpepler/EPIC.SimInf: EPIC Package for Epidemiological Simulation Modelling using SimInf

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

Estimates number of cattle per CPH ("CPH size") from CTS movement data extracted from the EPIC server.

1	cphsizes_estimate(uid = NULL, pwd = NULL, modeldata, outfile = NULL)

`uid`	User ID for the EPIC server. If not specified in the function call, the user will be prompted to supply it.
`pwd`	Password for the EPIC server. If not specified in the function call, the user will be prompted to supply it.
`modeldata`	A list containing the model data. Only the components labelled `model` and `startdate` are used in this function; for more details on how to specify the modeldata object, see the example at the end of this help file.
`outfile`	Name of file on local system where the output should be written to. If none is supplied, a default descriptive file name will be assigned.

For the specified date, the number of cattle per CPH is estimated by counting all animals moved onto a CPH before the date, without any record indicating that they have been moved off of the CPH before the date. Only CTS movement records where is_valid_history = 't' are included in this calculation.

CPH size estimates are returned for all CPHs (in England, Wales and Scotland) for which the estimates are non-zero.

As the data extraction and calculation takes a considerable amount of computational time (~40 minutes), the output can be saved on file for future use.

Returns a data frame with the location IDs (field location_id from the movements table in the CTS database), CPH numbers, and number of cattle at each CPH on the specified date.

The saved output file can be used in the cts_prep function without needing to re-estimate the CPH sizes each time.

Theo Pepler

cts_prep

## -- EXAMPLE NOT RUN --

## Initialise model object
# modeldata1 <- vector('list', 5)
# names(modeldata1) <- c('initdata', 'eventdata', 'model', 'startdate', 'enddate')
# modeldata1$model <- 'SIR'
# modeldata1$startdate <- '2012/01/01'

## Estimate CPH sizes
# cphsizes(modeldata = modeldata1)