openVA (version 1.1.2)

getTopCOD: 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)

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)

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

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)
if (FALSE) {
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)
}