HIV estimates accuracy tool
HIV remains one of the most important public health concerns in the European Union and European Economic Area. Accurate data are therefore crucial to appropriately direct and evaluate public health response.
The HIV estimates accuracy tool is a new end-user application that uses statistical methods to calculate adjusted estimates from HIV surveillance data taking into account the issues of missing data and reporting delay. The tool accepts case-based surveillance data for HIV containing a minimum required set of variables.
The tool can be accessed through the following options:
1. For restricted users, the HIV estimates accuracy tool is a web tool available online through Shinyapps:
For new users:
To access the tool, send an e-mail to HIV.Modelling@ecdc.europa.eu with the subject: ’Registration for HIV estimates accuracy tool + Full Name’. An invitation e-mail will be sent back with a link to sign in to Shinyapps using one of the following three methods:
- Shinyapps.io authentication (recommended)
- Google authorization
- GitHub authorization
After signing up, you will receive a second email from Shinyapps to log in to the tool using your credentials.
For returning users:
2. For experienced R users, a CRAN-like repository is set up for installing the tool as an R package in R GUI or RStudio.
The tool can be installed using standard R commands executed in R console:
- Type the following command:
> install.packages("hivEstimatesAccuracy", repo = "http://www.nextpagesoft.net/hiv-estimates-accuracy/repo/")
- and press Enter. This downloads and installs latest version of the tool and all its dependencies.
- Once R is done with installing, the tool will run with the following command:
- The user can update the tool with the following command:
> update.packages(repo = "http://www.nextpagesoft.net/hiv-estimates-accuracy/repo")
3. An offline Windows x64 deployment package with R environment embedded
The last option for local deployment of the tool is to use a deployment package, which includes all required software and R packages.
- Download the deployment package (201 MB download size).
- Unpack the file to a folder.
- After unpacking, a new folder will appear called ’hivEstimatesAccuracy’. Double-click on the ’hivEstimatesAccuracy.bat’ file. This will open the tool in the default web browser. Close the browser window when finished with the file.
This offline package can only run on 64-bit versions of Microsoft Windows 7, 8, and 10.
Data integrity verification
MD5 checksum: 325460fc68e349f1943d06a6b35cc7ed
SHA1 checksum: a66a20772f30ba7bbc33132f3a36b9b84310c6cd
For option 2, both R engine and Pandoc must be installed, with LaTeX preferably installed as well. Option 3 (an offline Windows x64 deployment package) includes the required software and does not require additional prerequisites.
a) R engine performs all calculations
b) Pandoc converts Markdown documents (report sources) to HTML, LaTeX and/or Word. It is delivered with RStudio, so if one is already using RStudio, there is no need to install it separately.
Missing data are a well recognised problem within surveillance systems. When values for certain variables are missing and cases with missing values are excluded from analysis, it may lead to biased and potentially less precise estimates. Reporting delay, the time from case diagnosis to notification, can lead to problems when analysing the most recent years given that information on certain cases or variables may not have been collected yet due to national reporting process characteristics. These phenomena are common in disease surveillance and also apply to HIV.
The tool performs multiple imputations for the missing values of a set of variables (age, gender and CD4 count) using joint multivariate normal models and extensions or full conditional specification (also known as multiple imputation by chained equations). Additionally, the tool allows for correction of delays in reporting through reverse time hazard estimation. The adjustments may be used separately or in combination.
The outputs include results in the form of a report containing tables and graphs, and datasets in various file formats, in which the corrections have been incorporated and are ready for further analysis.
The tool accepts case-based surveillance data for HIV containing a minimum required set of variables. The support files types are rds., txt, csv, xls and xlsx (uncompressed and ZIP archives).
Several attributes/variables are required by the tool to run the adjustments. The upload file must contain all these attribute/variable names. Different variable names are accepted, but the variables must be coded in a specific way.
A complete instruction manual explains the basics of the ECDC HIV estimates accuracy tool and includes technical and methodological details on how to use the tool and calculate estimates. The manual can also be consulted to interpret tool outputs and aid in the selection of certain parameters.
ECDC accepts no responsibility or liability whatsoever (including but not limited to any direct or consequential loss or damage it might occur to you and/or any other third party) arising out of or in connection with the installation and/or usage of this software.
Copyright © European Centre for Disease Prevention and Control, 2018.
European Centre for Disease Prevention and Control. HIV estimates accuracy tool [Internet, software application]. Stockholm: EC DC; 2018. Available from: https://ecdc.europa.eu/en/publications-data/hiv-estimates-accuracy-tool
Rosinska Magdalena, Pantazis Nikos, Janiec Janusz, Pharris Anastasia, Amato-Gauci Andrew J, Quinten Chantal, ECDC HIV/AIDS Surveillance Network. Potential adjustment methodology for missing data and reporting delay in the HIV Surveillance System, European Union/European Economic Area, 2015. EuroSurveillance 2018; 23(23).
For technical support and reporting problems please contact: HIV.Modelling@ecdc.europa.eu.
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