EpiReport (version 1.0.4)

getSeason: Get disease-specific seasonality graph: distribution of cases by month

Description

Function returning the plot describing the seasonality of the disease that will be included in the epidemiological report at the bookmark location 'TS_SEASON' of the template report.

The graph includes the distribution of cases at EU/EEA level, by month, over the past five years, with:

• The number of cases by month in the reference year (green solid line)

• The mean number of cases by month in the four previous years (grey dashed line)

• The minimum number of cases by month in the four previous years (grey area)

• The maximum number of cases by month in the four previous years (grey area)

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

Usage

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

Value

'Word' doc or a ggplot2 object

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 graph 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 graph and 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 graph at the bookmark location. If doc is missing, getSeason returns the ggplot2 object.

See Also

Global function for the full epidemilogical report: getAER
Required Packages: ggplot body_replace_text_at_bkm
Internal functions: plotSeasonality
Default datasets: AERparams MSCode

Examples

# --- Plot using the default dataset
getSeason()

# --- Plot using external dataset
# --- Please see examples in the vignette
browseVignettes(package = "EpiReport")