InSilicoVA: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm

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Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA4' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.

Author
Zehang Li, Tyler McCormick, Sam Clark
Date of publication
2016-03-29 18:59:29
Maintainer
Zehang Li <lizehang@uw.edu>
License
GPL-2
Version
1.1.2

View on CRAN

Man pages

causetext
Translation list of COD codes
condprob
Conditional probability table used by InterVA-4
condprobnum
Conditional probability values used by InterVA-4
csmf.diag
Convergence test for fitted InSilico model
extract.prob
Obtain conditional probabilities from training data
get.indiv
Get individual COD probabilities from InSilicoVA Model Fits
indivplot
plot aggregated COD distribution
insilico
Implement InSilicoVA methods
insilico.fit
Implement InSilicoVA methods with more flexible customization
insilico.train
Modified InSilicoVA methods with training data
InsilicoVA-package
Perform InSilicoVA algorithm and provide graphical...
physician_debias
Implement physician debias algorithm
plot.insilico
plot CSMF from a "insilico" object
probbase
Conditional probability of InterVA4
RandomPhysician
100 records of Sample Input together with two simulated...
RandomVA1
100 records of Sample Input
SampleCategory
Correspondence between InterVA causes and the physician coded...
SamplePhysician
100 records of Sample debiased physician codes
stackplot
plot grouped CSMF from a "insilico" object
summary.insilico
Summarizing InSilicoVA Model Fits
updateIndiv
Update individual COD probabilities from InSilicoVA Model...

Files in this package

InSilicoVA
InSilicoVA/inst
InSilicoVA/inst/java
InSilicoVA/inst/java/Insilico.jar
InSilicoVA/NAMESPACE
InSilicoVA/data
InSilicoVA/data/RandomVA1.rda
InSilicoVA/data/probbase.rda
InSilicoVA/data/condprobnum.rda
InSilicoVA/data/RandomVA2.rda
InSilicoVA/data/SamplePhysician.rda
InSilicoVA/data/condprob.rda
InSilicoVA/data/SampleCategory.rda
InSilicoVA/data/causetext.rda
InSilicoVA/data/RandomPhysician.rda
InSilicoVA/R
InSilicoVA/R/report.r
InSilicoVA/R/indivplot.r
InSilicoVA/R/diag.r
InSilicoVA/R/plot.r
InSilicoVA/R/print_insilico.r
InSilicoVA/R/onLoad.r
InSilicoVA/R/insilico_train.r
InSilicoVA/R/extct_prob.r
InSilicoVA/R/phy_debias.r
InSilicoVA/R/get_indiv.r
InSilicoVA/R/insilico_core.r
InSilicoVA/R/groupplot.r
InSilicoVA/R/print_insilico_summary.r
InSilicoVA/R/insilico_standard.r
InSilicoVA/R/zzz.R
InSilicoVA/MD5
InSilicoVA/java
InSilicoVA/java/Insilico
InSilicoVA/java/Insilico/src
InSilicoVA/java/Insilico/src/MathUtil.java
InSilicoVA/java/Insilico/src/ProgressPopup.java
InSilicoVA/java/Insilico/src/InsilicoSampler.java
InSilicoVA/java/Insilico/src/ProgressBar.java
InSilicoVA/DESCRIPTION
InSilicoVA/man
InSilicoVA/man/updateIndiv.Rd
InSilicoVA/man/SamplePhysician.Rd
InSilicoVA/man/RandomVA1.Rd
InSilicoVA/man/InsilicoVA-package.Rd
InSilicoVA/man/causetext.Rd
InSilicoVA/man/extract.prob.Rd
InSilicoVA/man/summary.insilico.Rd
InSilicoVA/man/RandomPhysician.Rd
InSilicoVA/man/condprob.Rd
InSilicoVA/man/SampleCategory.Rd
InSilicoVA/man/insilico.Rd
InSilicoVA/man/get.indiv.Rd
InSilicoVA/man/physician_debias.Rd
InSilicoVA/man/insilico.fit.Rd
InSilicoVA/man/plot.insilico.Rd
InSilicoVA/man/RandomVA2.rd
InSilicoVA/man/stackplot.Rd
InSilicoVA/man/indivplot.Rd
InSilicoVA/man/csmf.diag.Rd
InSilicoVA/man/condprobnum.Rd
InSilicoVA/man/probbase.Rd
InSilicoVA/man/insilico.train.Rd