Package: InSilicoVA 1.4.2

Zehang Richard Li

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.

Authors:Zehang Richard Li [aut, cre], Tyler McCormick [aut], Sam Clark [aut]

InSilicoVA_1.4.2.tar.gz
InSilicoVA_1.4.2.tar.gz(r-4.7-any)InSilicoVA_1.4.2.tar.gz(r-4.6-any)
InSilicoVA_1.4.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
InSilicoVA/json (API)
NEWS

# Install 'InSilicoVA' in R:
install.packages('InSilicoVA', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/verbal-autopsy-software/insilicova/issues

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT
Datasets:
  • causetext - Translation list of COD codes
  • condprob - Conditional probability table used by InterVA-4
  • condprobnum - Conditional probability values used by InterVA-4
  • probbase - Conditional probability of InterVA4
  • probbase3 - Conditional probability of InterVA4.03
  • RandomPhysician - 100 records of Sample Input together with two simulated physician codes
  • RandomVA1 - 1000 records of Sample Input
  • RandomVA2 - 100 records of Sample Input
  • SampleCategory - Correspondence between InterVA causes and the physician coded cause categories
  • SamplePhysician - 100 records of Sample debiased physician codes

On CRAN:

Conda:

openjdk

3.38 score 1 stars 2 packages 40 scripts 229 downloads 18 mentions 11 exports 34 dependencies

Last updated from:89e4d32186. Checks:4 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK151
source / vignettesOK198
linux-release-x86_64OK155
wasm-releaseOK131

Exports:csmf.diagextract.probget.indivindivplotinsilicoinsilico.fitinsilico.trainmapICDphysician_debiasstackplotupdateIndiv

Dependencies:cellrangerclicodacpp11crayoncurlfarverggplot2gluegtablehmsInterVA5isobandlabelinglatticelifecyclemagrittrpillarpkgconfigprettyunitsprogressR6RColorBrewerreadxlrematchrJavarlangS7scalestibbleutf8vctrsviridisLitewithr