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

getTrend

R Documentation

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

Examples