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Last data update: 2014.03.03

R: Get individual COD probabilities from InSilicoVA Model Fits

get.indiv

R Documentation

Get individual COD probabilities from InSilicoVA Model Fits

Description

This function calculates individual probabilities for each death and provide posterior credible intervals for each estimates. The default set up is to calculate the 95

Usage

get.indiv(object, data = NULL, CI = 0.95, is.aggregate = FALSE,
  by = NULL, java_option = "-Xmx1g", ...)

Arguments

`object`	Fitted `"insilico"` object.
`data`	data for the fitted `"insilico"` object. The first column of the data should be the ID that matches the `"insilico"` fitted model.
`CI`	Credible interval for posterior estimates.
`is.aggregate`	logical indicator for constructing aggregated distribution rather than individual distributions.
`by`	list of column names to group by.
`java_option`	Option to initialize java JVM. Default to “-Xmx1g”, which sets the maximum heap size to be 1GB.
`...`	Not used.

Value

`mean`	individual mean COD distribution matrix.
`median`	individual median COD distribution matrix.
`lower`	individual lower bound for each COD probability.
`upper`	individual upper bound for each COD probability.

Author(s)

Zehang Li, Tyler McCormick, Sam Clark

Maintainer: Zehang Li <lizehang@uw.edu>

References

Tyler H. McCormick, Zehang R. Li, Clara Calvert, Amelia C. Crampin, Kathleen Kahn and Samuel J. Clark Probabilistic cause-of-death assignment using verbal autopsies, arXiv preprint arXiv:1411.3042 http://arxiv.org/abs/1411.3042 (2014)

Examples

## Not run: 
data(RandomVA1)
fit1<- insilico(RandomVA1, subpop = NULL,
                Nsim = 1000, burnin = 500, thin = 10 , seed = 1,
                auto.length = FALSE)
summary(fit1, id = "d199")

# Calculate aggregated COD distributions
agg.csmf <- get.indiv(data = RandomVA2, fit1, CI = 0.95,
                     is.aggregate = TRUE, by = NULL)
head(agg.csmf)

agg.by.sex.age <- get.indiv(data = RandomVA2, fit1, CI = 0.95,
                            is.aggregate = TRUE, by = list("sex", "age"))
							   head(agg.by.sex.age$mean)

## End(Not run)