Package: EpiSignalDetection 0.1.1
Joana Gomes Dias
EpiSignalDetection: Signal Detection Analysis
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 et al. (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.
Authors:
EpiSignalDetection_0.1.1.tar.gz
EpiSignalDetection_0.1.1.zip(r-4.5)EpiSignalDetection_0.1.1.zip(r-4.4)EpiSignalDetection_0.1.1.zip(r-4.3)
EpiSignalDetection_0.1.1.tgz(r-4.4-any)EpiSignalDetection_0.1.1.tgz(r-4.3-any)
EpiSignalDetection_0.1.1.tar.gz(r-4.5-noble)EpiSignalDetection_0.1.1.tar.gz(r-4.4-noble)
EpiSignalDetection_0.1.1.tgz(r-4.4-emscripten)EpiSignalDetection_0.1.1.tgz(r-4.3-emscripten)
EpiSignalDetection.pdf |EpiSignalDetection.html✨
EpiSignalDetection/json (API)
NEWS
| # Install 'EpiSignalDetection' in R: |
| install.packages('EpiSignalDetection', repos = c('https://eu-ecdc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/eu-ecdc/episignaldetection/issues
- AlgoParam - List of datasets containing the Farrington Flexible and GLRNB default parameters by time unit
- SignalData - Dataset for Signal Detection Analysis, reported cases, 1999-2018
Last updated 6 years agofrom:d214a275b9. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 04 2024 |
| R-4.5-win | NOTE | Sep 04 2024 |
| R-4.5-linux | NOTE | Sep 04 2024 |
| R-4.4-win | NOTE | Sep 04 2024 |
| R-4.4-mac | NOTE | Sep 04 2024 |
| R-4.3-win | NOTE | Sep 04 2024 |
| R-4.3-mac | NOTE | Sep 04 2024 |
Exports:aggAtlasExportalgoSDcleanAtlasExportfilterAtlasExportimportAtlasExportplotSDrunEpiSDApprunEpiSDReportstsSDstudyPeriod
Dependencies:base64encbslibcachemclicolorspacecommonmarkcrayoncrosstalkdeldirdigestdplyrDTevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttpuvisobandISOweekjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepanderpillarpkgconfigpolyclippolyCubpromisesR6rappdirsRColorBrewerRcpprlangrmarkdownsassscalesshinysourcetoolsspspatstat.dataspatstat.geomspatstat.univarspatstat.utilsstringistringrsurveillancetibbletidyselecttinytexutf8vctrsviridisLitewithrxfunxtableyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Aggregate filtered final Atlas export | aggAtlasExport |
| List of datasets containing the Farrington Flexible and GLRNB default parameters by time unit | AlgoParam |
| Build algo object | algoSD |
| Clean the Atlas export dataframe | cleanAtlasExport |
| Filter clean Atlas export | filterAtlasExport |
| Import ECDC Atlas export file (csv) | importAtlasExport |
| Plot the Signal Detection time series | plotSD |
| Run the EpiSignalDectection 'shiny' application | runEpiSDApp |
| Run the EpiSignalDetection report (HTML markdown) | runEpiSDReport |
| Dataset for Signal Detection Analysis, reported cases, 1999-2018 (ECDC Atlas export) | SignalData |
| Build sts object | stsSD |
| Compute the study period | studyPeriod |
