getTableByMS function

Get disease-specific table: distribution of cases by Member State (GeoCode)

Get disease-specific table: distribution of cases by Member State (GeoCode)

Function returning the table ('flextable') that will be included in the epidemiological report at the bookmark location 'TABLE1'

of the template report. An additional caption will be included at the location of the bookmark 'TABLE1_CAPTION'.

(see Table 1 of the ECDC annual reports https://www.ecdc.europa.eu/en/all-topics-z/surveillance-and-disease-data/annual-epidemiological-reports-aers)

getTableByMS(
  x = EpiReport::DENGUE2019,
  disease = "DENGUE",
  year = 2019,
  reportParameters = EpiReport::AERparams,
  MSCode = EpiReport::MSCode,
  index = 1,
  doc
)

Arguments

  • x: dataframe, raw disease-specific dataset (see specification of the dataset in the package vignette with browseVignettes(package = "EpiReport")) (default DENGUE2019)
  • disease: character string, disease code (default "DENGUE"). Please make sure the disease code is included in the disease-specific dataset x in the HealthTopicCode variable.
  • year: numeric, year to produce the table for (default 2019). Please make sure the year is included in the disease-specific dataset x in the TimeCode variable.
  • reportParameters: dataframe, dataset including the required parameters for the report production (default AERparams) (see specification of the dataset in the package vignette with browseVignettes(package = "EpiReport"))
  • MSCode: dataframe, correspondence table of GeoCode names and codes (default MSCode) (see specification of the dataset in the package vignette with browseVignettes(package = "EpiReport"))
  • index: integer, figure number
  • doc: 'Word' document (see officer package) in which to add the table at the bookmark location. If doc is missing, getTable returns the flextable table object.

Returns

'Word' doc or flextable object (see 'flextable' package)

Details

The current version of the 'EpiReport' package includes three types of table (see detailed specification of the tables in the package vignette with browseVignettes(package = "EpiReport")):

  • COUNT -Table presenting the number of cases by Member State (GeoCode) over a 5-year period;
  • RATE -Table presenting the number of cases and rates by Member State (GeoCode) over a 5-year period;
  • ASR -Table presenting the number of cases and rates by Member State (GeoCode) over a 5-year period, including age-standardised rates for the most recent year.

Examples

# --- Draft the table using the default Dengue dataset
getTableByMS()

See Also

Global function for the full epidemiological report: getAER

Required Packages: flextable officer

Internal functions: shapeECDCFlexTable cleanECDCTable

Default datasets: AERparams MSCode

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