getTableByMS: Get disease-specific table: distribution of cases by Member...
In EpiReport: Epidemiological Report

Description Usage Arguments Details Value See Also Examples

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
)

`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.

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.

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

Global function for the full epidemiological report: getAER
Required Packages: flextable officer
Internal functions: shapeECDCFlexTable cleanECDCTable
Default datasets: AERparams MSCode