SignalData

A dataset containing an export from the ECDC Atlas for salmonellosis and measles data.
This export is cleaned and ready for Signal Detection Analysis (see. cleanAtlasExport() )

datasets

Exploring time series for signal detection. It is specifically designed
to detect possible outbreaks using infectious disease surveillance data
at the European Union / European Economic Area or country level.
Automatic detection tools used are presented in the paper
"Monitoring count time series in R: aberration detection in public health surveillance",
by Salmon (2016) <doi:10.18637/jss.v070.i10>.
The package includes:
- Signal Detection tool, an interactive 'shiny' application
in which the user can import external data and perform basic signal detection analyses;
- An automated report in HTML format, presenting the results of the time series analysis in tables and graphs.
This report can also be stratified by population characteristics (see 'Population' variable).
This project was funded by the European Centre for Disease Prevention and Control.

Lore Merdrignac

EpiSignalDetection

Signal Detection Analysis

Joana Gomes Dias

Esther Kissling

Tommi Karki

Margot Einoder-Moreno

SignalData function

A data frame with 80,834 rows and 11 variables:<dl class="dl-horizontal">
 <dt>HealthTopic</dt><dd>Disease name e.g. Salmonellosis or Measles</dd>
 <dt>Population</dt><dd>Population characteristics e.g. All cases, Confirmed cases, Serotype AGONA,
 Serotype BAREILLY etc.</dd>
 <dt>Indicator</dt><dd>Indicator e.g. Hospitalised cases, Reported cases, Number of deaths, etc.</dd>
 <dt>Time</dt><dd>Time variable including both yearly data from 1999 to 2017, and monthly data from 1999-01 to 2018-02</dd>
 <dt>RegionName</dt><dd>Geographical level including country names e.g. Austria, Belgium, Bulgaria, etc.</dd>
 <dt>NumValue</dt><dd>Number of cases</dd>
 <dt>TimeUnit</dt><dd>Time unit corresponding to the format of the date in the 'Time' variable e.g. Year or Month</dd>
 <dt>TimeYear</dt><dd>Year of the date available in the 'Time' variable, regardless of the date format
 i.e. 1999 to 2018</dd>
 <dt>TimeMonth</dt><dd>Month of the date available in the 'Time' variable, regardless of the date format i.e. 1 to 12</dd>
 <dt>TimeWeek</dt><dd>Week of the date available in the 'Time' variable, regardless of the date format
 i.e. NA since this dataset does not include any weekly data</dd>
 <dt>TimeDate</dt><dd>Approximated date corresponding to the date available in the 'Time' variable (daily format)</dd>
</dl>

Format

Dataset for Signal Detection Analysis, reported cases, 1999-2018 (ECDC Atlas export) — SignalData

A data frame with 80,834 rows and 11 variables:<dl class='dl-horizontal'>
 <dt>HealthTopic</dt><dd>Disease name e.g. Salmonellosis or Measles</dd>
 <dt>Population</dt><dd>Population characteristics e.g. All cases, Confirmed cases, Serotype AGONA,
 Serotype BAREILLY etc.</dd>
 <dt>Indicator</dt><dd>Indicator e.g. Hospitalised cases, Reported cases, Number of deaths, etc.</dd>
 <dt>Time</dt><dd>Time variable including both yearly data from 1999 to 2017, and monthly data from 1999-01 to 2018-02</dd>
 <dt>RegionName</dt><dd>Geographical level including country names e.g. Austria, Belgium, Bulgaria, etc.</dd>
 <dt>NumValue</dt><dd>Number of cases</dd>
 <dt>TimeUnit</dt><dd>Time unit corresponding to the format of the date in the 'Time' variable e.g. Year or Month</dd>
 <dt>TimeYear</dt><dd>Year of the date available in the 'Time' variable, regardless of the date format
 i.e. 1999 to 2018</dd>
 <dt>TimeMonth</dt><dd>Month of the date available in the 'Time' variable, regardless of the date format i.e. 1 to 12</dd>
 <dt>TimeWeek</dt><dd>Week of the date available in the 'Time' variable, regardless of the date format
 i.e. NA since this dataset does not include any weekly data</dd>
 <dt>TimeDate</dt><dd>Approximated date corresponding to the date available in the 'Time' variable (daily format)</dd>
</dl>

SignalData: Dataset for Signal Detection Analysis, reported cases, 1999-2018 (ECDC Atlas export)

Description

Usage

Arguments

Format