I aim to provide working software for the methods I develop, and more recently to provide replication material for publications. This is a list of what's available so far. Except for the SUMMER package, I have led the teams creating this software, but in many cases, other individuals are primarily responsible for writing and maintaining it.

SVD-Comp Mortality Model

The R package implementing my SVD-Comp mortality model published in Demography is on CRAN as 'SVDMx'.

Verbal Autopsy

Software has been developed to implement InSilicoVA including R packages and universal executables delivered in a Docker container. This is openVA and has been developed by a team including Richard Li, Jason Thomas, Peter Choi, Tyler McCormick, and myself, with increasing help from Yue Chu.

For more information or help using the openVA tools, contact us using these email addresses:

• info@openva.net
• help@openva.net

pyOpenVA

To make the VA cause-coding algorithms fast and easily available using a familiar interface, we have created pyOpenVA. This is standard (i.e. non-research) software that installs using a traditional installer, does not require supporting software (e.g. R, Java, etc.) to be installed on your computer, and operates through a graphical user interface. pyOpenVA is written in Python and C++ so it is fast.

Key VA Software

• Main openVA site
• pyOpenVA - 'Assets' contains installers for Windows and MacOS
• openVA R Package
• openVA App
• Video for installation of openVA App
• Video for example analysis using openVA App
• All VA software on GitHub

Supporting VA Software

• InterVA4: Replicate and Analyse 'InterVA4'
• InterVA5: Replicate and Analyse 'InterVA5'
• InSilicoVA: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm
• CrossVA: Verbal Autopsy Data Transformation for InSilicoVA and InterVA5 Algorithms
• Tariff: Replicate Tariff Method for Verbal Autopsy
• OpenVA_Pipeline
• Model Verbal Autopsy (VA) Algorithms

Replication Material for SVD-Comp Mortality Model

• SVD-Component Mortality Model using Child or Child/Adult Mortality as Inputs

Replication Material for COVID-19 Prevalence Method

• Bayes Prevalence: Bayesian, model-based method to estimate prevalence of COVID-19 from survey with multiple imperfect tests

Small-area Estimates from Complex Survey Data

• SUMMER: Spatio-Temporal Under-Five Mortality Methods for Estimation

Miscellaneous

• Download and parse USA mortality data from usa.mortality.org
• Source code for this website
• General GitHub site

Structured Population Event History Register (SPEHR)

• Description
• Example Database 1
• Example Database 2
• Example Database 3
• Example Database 4

R Shiny Applications

• Excess Mortality Calculator: This was developed by Richard Li and Samuel Clark for Vital Strategies. The app estimates excess deaths from a variety of death count and population inputs using either simple or more sophisticated modeling approaches.