tariff: Replicate Tariff methods

In Tariff: Replicate Tariff Method for Verbal Autopsy

Description

This function implements Tariff method.

Usage

tariff(causes.train, symps.train, symps.test, causes.table = NULL,
  use.rank = TRUE, nboot.rank = 1, use.sig = TRUE, nboot.sig = 500,
  use.top = FALSE, ntop = 40, ...)

Arguments

causes.train	character vector of causes, or the column name of cause in the training data
symps.train	N.train by S matrix
symps.test	N.test by S matrix
causes.table	list of causes in the data
use.rank	logical indicator for whether using ranks instead of scores
nboot.rank	number of re-sampling for baseline rank comparison. Default to 1, which resamples training data to have a uniform cause distribution of the same size. Set this to 0 removes bootstrapping the training dataset.
use.sig	logical indicator for whether using significant Tariff only
nboot.sig	number of re-sampling for testing significance.
use.top	logical indicator for whether the tariff matrix should be cleaned to have only top symptoms
ntop	number of top tariff kept for each cause
...	not used

Value

score	matrix of score for each cause within each death
causes.train	vector of most likely causes in training data
causes.test	vector of most likely causes in testing data
csmf	vector of CSMF
causes.table	cause list used for output, i.e., list of existing causes in the training data
use.rank	logical indicator for whether using ranks instead of scores

Author(s)

Zehang Li, Tyler McCormick, Sam Clark

Maintainer: Zehang Li <[e-mail]>

References

James, S. L., Flaxman, A. D., Murray, C. J., & Population Health Metrics Research Consortium. (2011). Performance of the Tariff Method: validation of a simple additive algorithm for analysis of verbal autopsies. Population Health Metrics, 9(1), 1-16.

Serina, P., Riley, I., Stewart, A., James, S. L., Flaxman, A. D., Lozano, R., ... & Ahuja, R. (2015). Improving performance of the Tariff Method for assigning causes of death to verbal autopsies. BMC medicine, 13(1), 1.

Tyler H. McCormick, Zehang R. Li, Clara Calvert, Amelia C. Crampin, Kathleen Kahn and Samuel J. Clark(2016) Probabilistic cause-of-death assignment using verbal autopsies, http://arxiv.org/abs/1411.3042 To appear, Journal of the American Statistical Association

Examples

data("RandomVA3")
test <- RandomVA3[1:200, ]
train <- RandomVA3[201:400, ]
allcauses <- unique(train$cause)
fit <- tariff(causes.train = "cause", symps.train = train, 
				symps.test = test, causes.table = allcauses)
correct <- which(fit$causes.test[,2] == test$cause)
accuracy <- length(correct) / dim(test)[1]

Tariff documentation built on May 2, 2019, 3:35 p.m.