SUMMER - Small-Area-Estimation Unit/Area Models and Methods for Estimation in R

Provides methods for spatial and spatio-temporal smoothing of demographic and health indicators using survey data, with particular focus on estimating and projecting under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872>, Li et al. (2019) <doi:10.1371/journal.pone.0210645>, Wu et al. (DHS Spatial Analysis Reports No. 21, 2021), and Li et al. (2023) <doi:10.48550/arXiv.2007.05117>.

Last updated

bayesian-inferencesmall-area-estimationspace-time

10.53 score 26 stars 2 dependents 240 scripts 5.1k downloads

surveyPrev - Mapping the Prevalence of Binary Indicators using Survey Data in Small Areas

Provides a pipeline to perform small area estimation and prevalence mapping of binary indicators using health and demographic survey data, described in Dong et al. (2026) <doi:10.1093/jssam/smaf048>, Wakefield et al. (2025) <doi:10.48550/arXiv.2110.09576> and Wakefield et al. (2020) <doi:10.1111/insr.12400>.

Last updated

6.97 score 3 stars 52 scripts 183 downloads

openVA - Automated Method for Verbal Autopsy

Implements multiple existing open-source algorithms for coding cause of death from verbal autopsies. The methods implemented include 'InterVA4' by Byass et al (2012) <doi:10.3402/gha.v5i0.19281>, 'InterVA5' by Byass at al (2019) <doi:10.1186/s12916-019-1333-6>, 'InSilicoVA' by McCormick et al (2016) <doi:10.1080/01621459.2016.1152191>, 'NBC' by Miasnikof et al (2015) <doi:10.1186/s12916-015-0521-2>, and a replication of 'Tariff' method by James et al (2011) <doi:10.1186/1478-7954-9-31> and Serina, et al. (2015) <doi:10.1186/s12916-015-0527-9>. It also provides tools for data manipulation tasks commonly used in Verbal Autopsy analysis and implements easy graphical visualization of individual and population level statistics. The 'NBC' method is implemented by the 'nbc4va' package that can be installed from <https://github.com/rrwen/nbc4va>. Note that this package was not developed by authors affiliated with the Institute for Health Metrics and Evaluation and thus unintentional discrepancies may exist in the implementation of the 'Tariff' method.

Last updated

pipelineopenjdk

6.49 score 1 stars 1 dependents 57 scripts 308 downloads

InSilicoVA - Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm

Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm from McCormick et al. (2016) <DOI:10.1080/01621459.2016.1152191>. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.

Last updated

va-algorithmopenjdk

5.86 score 2 dependents 40 scripts 234 downloads

InterVA4 - Replicate and Analyse 'InterVA4'

Provides an R version of the 'InterVA4' software (<http://www.interva.net>) for coding cause of death from verbal autopsies. It also provides simple graphical representation of individual and population level statistics.

Last updated

va-algorithm

4.59 score 2 dependents 13 scripts 204 downloads

Tariff - Replicate Tariff Method for Verbal Autopsy

Implement the Tariff algorithm for coding cause-of-death from verbal autopsies. The Tariff method was originally proposed in James et al (2011) <DOI:10.1186/1478-7954-9-31> and later refined as Tariff 2.0 in Serina, et al. (2015) <DOI:10.1186/s12916-015-0527-9>. Note that this package was not developed by authors affiliated with the Institute for Health Metrics and Evaluation and thus unintentional discrepancies may exist between the this implementation and the implementation available from IHME.

Last updated

2.78 score 2 dependents 7 scripts 192 downloads