getTopSymptoms {InterVA5}

Get the symptoms with the largest conditional probability (symptom | cause) for causes assigned by InterVA-5.

Description

The function takes an interVA5 object and the data used to assign the causes, and returns the the symptoms that contribute to the cause assignment (ranked in order of the conditional probabilities of observing a symptom, given the death is due to that particular cause).

Usage

getTopSymptoms(object, data, IDs = NULL, pretty = TRUE, includeAll = FALSE)

Arguments

object

An interVA5 object (i.e., the results returned from the InterVA5() function).

data

The input data that InterVA5 used to assign the causes of death.

IDs

A vector that contains the IDs for each death (note that all of IDs are contained in data$ID and object$ID).

pretty

A logical indicating if you want the results in an easy-to-read format (default is 'TRUE')

includeAll

A logical indicating if you want all of the symptoms included in the output (even those which are absent or have a value of missing/no) (default is 'FALSE' which only includes symptoms that are present).

Value

dist.cod

A list of results for each death (organized by ID). For each death, a list is returned that includes the death's ID, the cause, and a vector of strings listing a symptom, it if contributes to the cause assignment (if includeAll = TRUE), and the conditional probability of observing the symptom given that the death is due to this cause.

Author(s)

Jason Thomas, Zehang LI, Tyler McCormick, Sam Clark

See Also

InterVA5, getTopSymptoms

Examples

## Not run: 
data(RandomVA5)
sample.output <- InterVA5(RandomVA5, HIV = "h", Malaria = "v", write=FALSE)
topSymptoms <- getTopSymptoms(object = sample.output,
                              data = RandomVA5,
                              IDs = sample.output$ID[1],
                              pretty = TRUE,
                              includeAll = FALSE)

## End(Not run)