.. image:: https://travis-ci.com/ihmeuw/SmartVA-Analyze.svg?branch=master :target: https://travis-ci.com/ihmeuw/SmartVA-Analyze

SmartVA-Analyze is an application that implements the Tariff 2.0 Method <http://www.healthdata.org/research-article/improving-performance-tariff-method-assigning-causes-death-verbal-autopsies/>_ for computer certification of verbal autopsies.

More information and the SmartVA-Analyze application can be found here: http://www.healthdata.org/verbal-autopsy/tools

The latest development version of the SmartVA-Analyze application can be found in releases. <https://github.com/ihmeuw/SmartVA-Analyze/releases>_ The application is available as a Windows graphical user interface (GUI), Windows command-line interface (CLI), and Linux binary.

The latest stable version of the SmartVA-Analyze application can be found here: http://www.healthdata.org/verbal-autopsy/tools

The SmartVA-Analyze application requires an input csv in the format of the PHMRC Full Questionnaire <http://www.healthdata.org/verbal-autopsy/tools/>, PHMRC Shortened (SmartVA) Questionnaire <http://www.healthdata.org/verbal-autopsy/tools/>, WHO 2016 Questionnaire <https://www.who.int/healthinfo/statistics/verbalautopsystandards/en/> or WHO 2022 Questionnaire <https://www.who.int/healthinfo/statistics/verbalautopsystandards/en/>.. The simplest workflow is to collect verbal autopsy data with ODK Collect <https://docs.opendatakit.org/collect-intro/> and export the questionaire data via ODK Aggregate <https://docs.opendatakit.org/aggregate-intro/> or ODK Briefcase <https://docs.opendatakit.org/briefcase-intro/>_.

Requirements

To compile the source code of SmartVA-Analyze, the following applications must be installed:

* `Anaconda <https://www.anaconda.com/download/>`_

* `Docker <https://www.docker.com/get-started>`_

Build Instructions

To build the SmartVA-Analyze application as seen in releases <https://github.com/ihmeuw/SmartVA-Analyze/releases>_, run one of the following commands:

Windows: build_script.bat

macOS, Linux: $ sh build_script.sh

Environment Instructions

To create your python environment, either create a conda environment or use the Docker image.

Windows::

    $ conda create -n smartva python=2.7.13 wxpython=4.*
    $ conda activate smartva
    $ pip install -r requirements.txt -r requirements-dev.txt -r requirements-win.txt

macOS, Linux::

    $ conda create -n smartva python=2.7.13 wxpython=4.*
    $ conda activate smartva
    $ pip install -r requirements.txt -r requirements-dev.txt

    or

    $ docker build -t smartva-build-linux -f ./pkg/docker/linux-build/Dockerfile ./pkg/docker
    $ docker build -t smartva-dev -f pkg/docker/dev/Dockerfile .
    $ docker run -it --rm -v `pwd`:/home/smartva/smartva smartva-dev

Run Instructions

To test your python environment, run the following command to show the available options.

$ python app.py --help

::

Usage: app.py [OPTIONS] INPUT OUTPUT

Options:
  --country TEXT                  Data origin country abbreviation. "LIST"
                                  displays all. Default is "Unknown".
  --hiv BOOLEAN                   Data is from an HIV region. Default is True.
  --malaria BOOLEAN               Data is from a Malaria region. Default is
                                  True.
  --hce BOOLEAN                   Use Health Care Experience (HCE) variables.
                                  Default is True.
  --freetext BOOLEAN              Use "free text" variables. Default is True.
  --figures BOOLEAN               Generate charts and figures output. Default
                                  is True.
  --language [english|chinese|spanish]
                                  Language used for output files.
  --version                       Show the version and exit.
  --legacy-format                 Output files in a format that matches
                                  SmartVA v1.2
  --help                          Show this message and exit.

Example

::

    $ mkdir ./test/example/output
    $ python app.py "./test/example/input/PHMRC_short_example.csv" "./test/example/output" --hiv=False
    $ python app.py "./test/example/input/WHO_2016_1_5_1_example.csv" "./test/example/output" --language=chinese --country=CHN

Test Instructions

All tests are run using pytest:

$ python -m pytest