getTrend {EpiReport}

Get disease-specific trend plot: trend and number of cases by month

Description

Function returning the plot describing the trend of the disease over time that will be included in the epidemiological report at the bookmark location 'TS_TREND' on the template report.

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

• The number of cases by month over the 5-year period (grey solid line)

• The 12-month moving average of the number of cases by month (green solid line)

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

Usage

getTrend(
  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 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, getTrend returns the ggplot2 object.

Value

'Word' doc or a ggplot2 preview

See Also

Global function for the full epidemilogical report: getAER
Required Packages: ggplot2 officer
Internal functions: plotTS12MAvg
Default datasets: AERparams MSCode

Examples

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

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