runEpiSDReport {EpiSignalDetection}

Run the EpiSignalDetection report (HTML markdown)

Description

Function to render the markdown report of alarms in HTML format for ECDC Signal Detection Report

Usage

runEpiSDReport(input, stratified, outputfile, run_pandoc = TRUE)

Arguments

input

list of parameters as defined in the Signal Detection Application (see runEpiSDApp)

(i.e. list(disease, country, indicator, stratification, unit, daterange, algo, testingperiod))

(see also default parameters in system.file("SignalDetectionReport_HTML", "SignalDetectionReport.Rmd", package = "EpiSignalDetection"))

stratified

a logical value indicating whether the report should be stratified by Population variable or not (default FALSE)

outputfile

output file name (e.g. 'C:/R/report.html')

(default value is a temporary folder - file.path(tempdir(), "SignalDectectionReport.html"))

run_pandoc

An option for whether to run pandoc to convert Markdown output.

Details

Datasets to use in the report:

• Default dataset included in the package (Salmonellosis 2007-2016 or Measles 1999-2018 data) (i.e. input$file = NULL);

• External dataset:

  • –> An export (csv format) from the ECDC Surveillance Atlas of Infectious Diseases: http://atlas.ecdc.europa.eu/public/index.aspx.

    On the ECDC "Surveillance Atlas of Infectious Diseases" web site:

    • 1- Choose the disease/health topic to analyse

    • 2- Export the data (csv) using the default settings

    • 3- Specify the location of this external dataset in the input argument of the runEpiSDReport() function (e.g. input <- list(file = list(datapath = "C:/Users/Downloads/ECDC_surveillance_data_Pertussis.csv"), disease = "Pertussis", country = "Greece", indicator = "Reported cases", stratification = "All cases", unit = "Month", daterange = c("2011-12-01", "2016-12-01"), algo = "FarringtonFlexible", testingperiod = 3))

    • 4- You can now render the re markdown report... (e.g. runEpiSDReport(input = input))

  • –> Any dataset specified as described in the package vignette.

Value

An HTML report. When run_pandoc = TRUE, the compiled document is written into the output file, and the path of the output file is returned. When run_pandoc = FALSE, the path of the Markdown output file, with attributes knit_meta (the knitr meta data collected from code chunks) and intermediates (the intermediate files/directories generated by render())

See Also

Default dataset used in the report SignalData

Signal Detection Application runEpiSDApp

Examples

## Not run: 
#-- Running the report as a standalone function
runEpiSDReport()    #Definition of each input parameter
                     #is done one by one through the R console

#---> OR

#-- First setting the parameters to run the report for
input <- list(
disease = "Salmonellosis",
country = "Portugal",
indicator = "Reported cases",
stratification = "Confirmed cases",
unit = "Month",
daterange = c("2011-01-01", "2016-12-31"),
algo = "FarringtonFlexible",
testingperiod = 6
)

#-- Second running the report based on the EpiSignalDetection::SignalData dataset
#-- and store it in a temporary folder
runEpiSDReport(input = input)

#-- Running the report based on the EpiSignalDetection::SignalData dataset
#-- and store the HTML output 'test.html' in the folder 'C:/R/'
runEpiSDReport(input = input, outputfile = "C:/R/test.html")

#-- Running the report based on external data
input <- list(
file = list(datapath = "C:/Users/Downloads/ECDC_surveillance_data_Pertussis.csv"),
disease = "Pertussis",
country = "Greece",
indicator = "Reported cases",
stratification = "All cases",
unit = "Month",
daterange = c("2011-12-01", "2016-12-01"),
algo = "FarringtonFlexible",
testingperiod = 3
)

runEpiSDReport(input = input, stratified = TRUE)

## End(Not run)