Report: Generate a contact tracing `Report`

Description

EpiContatTrace contains report templates to generate pdf- or html reports for the farm specific contacts. These reports can be useful for hands-on disease tracing in the field. The templates are used by Sweave and can be adapted by the end user. However, in the default setting the report has the following layout; first the contacts are visualised graphically in a plot, as to give an immediate signal to the reader of the report of the number of contacts. In the following, the contact data are presented with different levels of detail split by ingoing and outgoing contacts. The first includes collapsed data and the sequential contact structure at group level (i.e. no information on individuals or dates). In this summary, the sequential structure of each part of the chain is included, and a holding that appears in several different parts of the chain can therefore be included more than once in the summary. The reason for this is to facilitate sequential tracing and getting an overview of each part of the chain. After the summary all details of all contacts included in the contact chains is presented, i.e. date of contact and data on individual level when available. To generate pdf files a TeX installation must exist to compile the latex file. The report is saved in the working directory with the name of the root as filename.

Usage

Report(object, format = c("html", "pdf"), dir = ".", template = NULL)
# S4 method for ContactTrace
Report(object, format = c("html", "pdf"), dir = ".", template = NULL)
# S4 method for list
Report(object, format = c("html", "pdf"), dir = ".", template = NULL)

Arguments

object: the object
format: the format to use, can be either 'html' or 'pdf'. The default is 'html'
dir: the generated report is written to the directory folder. The default (".") is the current working directory.
template: the Sweave template file to use. If none is provided, the default is used.

Methods

signature(object = "ContactTrace"): Generate a report for a ContactTrace object.
signature(object = "list"): Generate reports for a list of ContactTrace objects.

References

Dube, C., et al., A review of network analysis terminology and its application to foot-and-mouth disease modelling and policy development. Transbound Emerg Dis 56 (2009) 73-85, doi: 10.1111/j.1865-1682.2008.01064.x
Noremark, M., et al., Network analysis of cattle and pig movements in Sweden: Measures relevant for disease control and riskbased surveillance. Preventive Veterinary Medicine 99 (2011) 78-90, doi: 10.1016/j.prevetmed.2010.12.009
Friedrich Leisch. Sweave: Dynamic generation of statistical reports using literate data analysis. In Wolfgang Hardle and Bernd Ronz, editors, Compstat 2002 - Proceedings in Computational Statistics, pages 575-580. Physica Verlag, Heidelberg, 2002. ISBN 3-7908-1517-9.

Examples

Run this code

## Load data
data(transfers)

## Perform contact tracing
contactTrace <- Trace(movements = transfers,
                      root = 2645,
                      tEnd = "2005-10-31",
                      days = 90)

## Generate an html report showing details of the contact tracing for
## root 2646.
## Creates the file 2645.html in the temporary directory.
Report(contactTrace, dir = tempdir())

## It's possible to generate reports for a list of ContactTrace objects.
## Perform contact tracing for ten of the included herds
root <- sort(unique(c(transfers$source, transfers$destination)))[1:10]

## Perform contact tracing
contactTrace <- Trace(movements = transfers,
                      root = root,
                      tEnd = "2005-10-31",
                      days = 90)

## Generate reports
## Creates the files 1.html, 2.html, ..., 10.html
## in the temporary directory
Report(contactTrace, dir = tempdir())