Package: InSilicoVA 1.4.0

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, Tyler McCormick, Sam Clark

InSilicoVA_1.4.0.tar.gz
InSilicoVA_1.4.0.tar.gz(r-4.5-noble)InSilicoVA_1.4.0.tar.gz(r-4.4-noble)
InSilicoVA_1.4.0.tgz(r-4.4-emscripten)InSilicoVA_1.4.0.tgz(r-4.3-emscripten)
InSilicoVA.pdf |InSilicoVA.html✨
InSilicoVA/json (API)
NEWS

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

Peer review:

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

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT
Datasets:
  • 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
  • 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

openjdk

3.02 score 1 stars 1 packages 35 scripts 378 downloads 18 mentions 11 exports 40 dependencies

Last updated 2 years agofrom:bf10cca425. Checks:OK: 1 NOTE: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 30 2024
R-4.5-linuxNOTEDec 30 2024

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

Dependencies:cellrangerclicodacolorspacecpp11crayoncurlfansifarverggplot2gluegtablehmsInterVA5isobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigprettyunitsprogressR6RColorBrewerreadxlrematchrJavarlangscalestibbleutf8vctrsviridisLitewithr