WHO Average Curves
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Update 0.3 has been released as of 2019-10-09. See below for details:
Better offline support
- Users can now save a copy of downloaded RespiMar data after downloading to their local disc.
- After downloading RespiMart data, press the ‘Save Copy’ button.
- This data can be reloaded for later use.
- To upload saved data, click the ‘Upload local RespiMart Data’ switch, and browse to your data.
Generate reports
- Users can now generate an html report of their average curve analysis.
- Use the ‘Download Report’ button on the Average Curve tab.
More parameters from RespiMart
- SARI deaths are now available.
- Where reported, sentinel and non-sentinel virological data is available.
- Percent or number of influenza positives by sentinel/non-sentinel sites is available.
- Composite parameters can be calculated using percentage positivity from sentinel/non-sentinel sites.
Return to previous analyses
- Users can save an analysis file in the ‘Make Average Curve’ tab.
- This analysis can be returned to using the new ‘Reload Analysis’ tab.
- If the original analysis was performed using RespiMart data, the data will automatically update.
- If the original analysis was performed with supplemental data, the user can update the previous analysis with new data.
Other updates
- In the overlaid seasons graph, the boundaries of each season can be seen with the ‘Show cut points’ option.
- Geometric means have been introduced to the average curve.
- These can be used to calculate thresholds or the curve.
- Dummy datasets have been integrated into the app – one for temperate countries, and one for tropical countries.
- Select ‘Dummy Dataset (Temperate)’ or ‘Dummy Dataset (Tropical)’ when downloading RespiMart data.
Information
The WHO average curves app is a tool developed to help users, at a national level, understand the seasonality and severity of influenza seasons at national levels. This app is intended to allow users to explore, transform, and upload/download data, before performing analysis.
This app is links with data from FluNet and fluID systems, which are hosted on the WHO RespiMart platform. FluNet and fluID data aggregated at country, area or territory level can be downloaded from RespiMart and used for analysis. Users can also upload and analyse their own data with the app. More information on FluNet and fluID global influenza surveillance data is available on the WHO website here.
Analysis performed on this app can be used to aid users in the Pandemic Influenza Severity Assessment (PISA) methodology. In the app, users can establish influenza severity thresholds, allowing them to judge the intensity of a given season. Specifically, this app can be used to define thresholds for the transmissibility and impact indicators. For more information on PISA, see the WHO PISA guidelines and training materials.
Two threshold setting approaches are currently outlined in the PISA documentation. The average curves methodology is available in this app, whereas the moving epidemic method (MEM) can be used here. This app can also be used to download FluNet and fluID data in formats accepted by MEM.
For detailed instructions on using this app, and for templates to format data, use the download button in the top-right corner.
Data Sources
Virological data collected in FluNet are provided by National Influenza Centres (NICs) of the Global Influenza Surveillance and Response System (GISRS) and other national influenza reference laboratories collaborating actively with GISRS (see https://www.who.int/tools/flunet ).
Information about the global influenza epidemiological data sharing platform fluID is available at https://www.who.int/teams/global-influenza-programme/surveillance-and-monitoring/fluid
We would like to thank the national epidemiological institutions, GISRS, and national influenza reference laboratories for their important contribution to global influenza surveillance.
WHO Average Curves App Version 0.4
This app was developed using R version 4.3.2 (2023-10-31) by the WHO Global Influenza Programme
The source code for this app, which can be run from a local installation of R, can be found here.
This app was developed with a set of R package dependencies.
Click here to Show Packages.R Package Dependencies:
Get Started
Data downloaded from FluNet and fluID is subject to WHO policies on use and sharing of data.
© Copyright World Health Organization (WHO), 2024. All Rights Reserved.Download RespiMart Data
Download Status:
*Downloaded data is prioritised over local
Upload Supplementary Data
Supplemental Data Status:
- Select multiple files at once to upload a set of parameters
- When uploading data in MS Excel formats, parameters are named after the sheet name
- When uploading data in .csv format, parameters are named after the file name
Consolidate
Select FluNet & FluID Parameters
Select Composite Parameters
Configure Composites
Select measures of percentage positivity to use when calculating composite indicators
Select Uploaded Parameters
Select Age Group Parameters
Visualise and Download
Upload Analysis Files
Analysis Preparation
About this tab:
This tab allows users to return to existing analyses. If performing an analysis for the first time, ignore this tab. To save an existing analysis, press the 'Save Analysis' button on the average curves menu, after you have set thresholds. When returning to an analsis, data downloaded from RespiMart will be automatically updated, and data.
Parameter Summary
Ideally, at least 5 years of data should be used to set thresholds
Historical Data Series
The denominator for percent influenza positivity is, by availabilty, influenza positives + negatives, then samples processed, and finally samples recieved.
Choose Parameter
Options
Select Parameter
Basic Options
Smoothing Interval (weeks)
Advanced Options
Remove Data
Dataset
Dataset Details
Overview of MEM
The Moving Epidemic Method (MEM) is a tool developed in the Health Sentinel Network of Castilla y León (Spain) to help in the routine influenza surveillance in health systems. It gives a better understanding of the annual influenza epidemics and allows the weekly assessment of the epidemic status and intensity.
Although in its conception it was originally created to be used with influenza data and health sentinel networks, MEM has been tested with different respiratory infectious diseases and surveillance systems so nowadays it could be used with any parameter which present a seasonal accumulation of cases that can be considered an epidemic.
MEM development started in 2001 and the first record appeared in 2003 in the Options for the Control of Influenza V. It was presented to the baselines working group of the European Influenza Surveillance Scheme (EISS) in the 12th EISS Annual Meeting (Malaga, Spain, 2007), with whom started a collaboration that continued when, in 2008, was established the European Influenza Surveillance Network.
In 2009 MEM is referenced in an official European document: the Who European guidance for influenza surveillance in humans. A year later MEM was implemented in The European Surveillance System (TESSy), of the European Centre for Disease Prevention and Control (ECDC), and in 2012, after a year piloting, in the EuroFlu regional influenza surveillance platform, of the World Health Organization Regional Office for Europe (WHO-E).
As a result of the collaboration with ECDC and WHO-E, two papers have been published, one related to the establishment of epidemic thresholds and other to the comparison of intensity levels in Europe.
In the WHO Pandemic and Epidemic Influenza Severity Assessment (PISA) guidance, MEM is recommended, alongside the average curves method, as way in which to set intensity and epidemic thresholds.
Using the MEM app in parallel with this one is recommended; users should identify which methodology gives the most suitable thresholds. Your currently selected data can be downloaded below, in formats that can be used by the MEM app.
The web version of the MEM app is available hereVisualise and Download Data
Options
Visualise
Overlaid Seasons
Plot
Options
Basic Options
Wave 1 Weeks
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Wave 2 Weeks
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Threshold Options
Cumulative values are intended for use with epidemiological parameters, and not percentage influenza positivity
Characterise Seasonality
Information
The functions below are intended to guide the estimation of a country’s seasonality. Please not that these functions are experimental, and should be used as suggestions in determining seasonality, rather than strict guidance. Seasonality calculation works as follows:
- An epidemic threshold is set – this is the median by default
- Historical epidemics are found by identifying time periods where the epidemic threshold was crossed for n weeks. The number of weeks for n is set by changing the Minimum epidemic duration below.
- The number of seasons per year is derived by dividing the number of detected epidemics by the number of historical seasons.
- The weeks in which the detected epidemics occur are shown in the histogram/density curve below.
- If less than 1.5 epidemics per year are detected, a one wave average curve model will be suggested. Historically, if more epidemics weeks coincide with weeks 45 and 18 than between weeks 16 and 40, a shifted year is suggested, and vice versa.
- If greater than 1.5 epidemics per year are detected, a two wave average curve is suggested. In this case, minima of the epidemic density curve are used to find two times of the year when influenza activity is low – each year is split between these two points, creating intervals known as wave 1 and wave 2.