getTopCOD: Extract the most likely cause(s) of death

In openVA: Automated Method for Verbal Autopsy

Extract the most likely cause(s) of death

Description

Extract the most likely cause(s) of death

Usage

getTopCOD(x, interVA.rule = TRUE, n = 1, include.prob = FALSE)

Arguments

x	a fitted object from codeVA.
interVA.rule	Logical indicator for interVA object only. If TRUE and (the parameter) n <= 3, then the InterVA thresholds are used to determine the top causes.
n	Number of top causes to include (if n > 3, then the parameter interVA.rule is treated as FALSE).
include.prob	Logical indicator for including the probabilities (for insilico) or indicator of how likely the cause is (for interVA) in the results

Value

a data frame of ID, most likely cause assignment(s), and corresponding probability (for insilico) or indicator of how likely the cause is (for interVA)

See Also

Other output extraction: getCCC(), getCSMF_accuracy(), getCSMF(), getIndivProb()

Examples

data(RandomVA1)
# for illustration, only use interVA on 100 deaths
fit <- codeVA(RandomVA1[1:100, ], data.type = "WHO", model = "InterVA", 
                  version = "4.02", HIV = "h", Malaria = "l", write=FALSE)
getTopCOD(fit)
## Not run: 
library(openVA)

# InterVA4 Example
data(SampleInput)
fit_interva <- codeVA(SampleInput, data.type = "WHO2012", model = "InterVA",
                      version = "4.03", HIV = "l", Malaria = "l", write = FALSE)
getTopCOD(fit_interva, n = 1)
getTopCOD(fit_interva, n = 3)
getTopCOD(fit_interva, n = 3, include.prob = TRUE)
getTopCOD(fit_interva, interVA.rule = FALSE, n = 3)
getTopCOD(fit_interva, n = 5)
getTopCOD(fit_interva, n = 5, include.prob = TRUE)

# InterVA5 & Example
data(RandomVA5)
fit_interva5 <- codeVA(RandomVA5[1:50,], data.type = "WHO2016", model = "InterVA",
                       version = "5", HIV = "l", Malaria = "l", write = FALSE)
getTopCOD(fit_interva5, n = 1)
getTopCOD(fit_interva5, n = 3)
getTopCOD(fit_interva5, n = 3, include.prob = TRUE)
getTopCOD(fit_interva5, interVA.rule = FALSE, n = 3)
getTopCOD(fit_interva5, n = 5)
getTopCOD(fit_interva5, n = 5, include.prob = TRUE)

# InSilicoVA Example
data(RandomVA5)
fit_insilico <- codeVA(RandomVA5[1:100,], data.type = "WHO2016", 
                       auto.length = FALSE)
getTopCOD(fit_insilico, n = 1)
getTopCOD(fit_insilico, n = 3)
getTopCOD(fit_insilico, n = 3, include.prob = TRUE)


# Tariff Example (only top cause is returned)
data(RandomVA3)
test <- RandomVA3[1:200, ]
train <- RandomVA3[201:400, ]
allcauses <- unique(train$cause)
fit_tariff <- tariff(causes.train = "cause", symps.train = train, 
                     symps.test = test, causes.table = allcauses)
getTopCOD(fit_tariff, n = 1)

# NBC Example
library(nbc4va)
data(nbc4vaData)
train <- nbc4vaData[1:50, ]
test <- nbc4vaData[51:100, ]
fit_nbc <- nbc(train, test, known=TRUE)
getTopCOD(fit_nbc, n = 1)
getTopCOD(fit_nbc, n = 3)
getTopCOD(fit_nbc, n = 3, include.prob = TRUE)

## End(Not run)

openVA documentation built on May 29, 2024, 6:04 a.m.