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Get disease-specific map: distribution of cases by Member State

getMap.Rd

Function returning the disease-specific PNG map previously created and stored in a specific folder (see pathPNG argument) and that will be included in the epidemiological report at the bookmark location of the template report, depending of the type of map. Three type of maps can be included in the report:

  • Bookmark 'MAP_NB': Distribution of cases by country. An additional caption will be included at the location of the bookmark 'MAP_NB_CAPTION'.

  • Bookmark 'MAP_RATE': Distribution of cases per 100 000 population by country. An additional caption will be included at the location of the bookmark 'MAP_RATE_CAPTION'.

  • Bookmark 'MAP_ASR': Distribution of cases using age-strandardised rates per 100 000 population by country. An additional caption will be included at the location of the bookmark 'MAP_ASR_CAPTION'.

(see ECDC reports https://www.ecdc.europa.eu/en/publications-data/monitoring/all-annual-epidemiological-reports)

Usage

getMap(
  disease = "DENGUE",
  year = 2019,
  reportParameters = EpiReport::AERparams,
  index = 1,
  pathPNG = system.file("maps", package = "EpiReport"),
  doc
)

Arguments

disease

character string, disease code (default "DENGUE").

year

numeric, year to produce the map for (default 2019).

reportParameters

dataframe, dataset including the required parameters for the map and report production (default AERparams) (see specification of the dataset in the package vignette with browseVignettes(package = "EpiReport"))

index

integer, figure number

pathPNG

character string, full path to the folder containing the maps in PNG (default 'maps' folder included in the package system.file("maps", package = "EpiReport"))

doc

'Word' document (see 'officer' package) in which to add the maps at the bookmark location. If doc is missing, getMap returns a preview of the PNG image.

Value

'Word' doc an image preview

See also

Global function for the full epidemilogical report: getAER
Required Packages: body_replace_img_at_bkm
Internal functions: includeMap previewMap
Default datasets: AERparams

Examples

# --- Preview of the PNG map using the default Dengue dataset
getMap()

#> [1] "/home/runner/work/_temp/Library/EpiReport/maps/DENGUE_2019.ALL.COUNT.png"

# --- Plot using external PNG image
# --- Please see examples in the vignette
browseVignettes(package = "EpiReport")
#> No vignettes found by browseVignettes(package = "EpiReport")