R/InterVA5_1.0-package.R

In InterVA5: Replicate and Analyse 'InterVA5'

#' Translation list of COD codes
#'
#' This is the translation of COD abbreviation codes into their corresponding
#' full names.
#'
#'
#' @name causetextV5
#' @docType data
#' @format A data frame with the translation of codes to their names for 3
#' pregnancy statuses, 61 CODs (both the version of COD only and COD with group code),
#' and 6 circumstances of mortality (COMCAT).
#' @keywords datasets
#' @examples
#'
#' data(causetextV5)
#'
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#' Perform InterVA5 algorithm and provide graphical summarization of COD
#' distribution.
#'
#' Computes individual cause of death and population cause-specific mortality
#' fractions using the InterVA5 algorithm. Provides a simple graphical
#' representation of the result.
#'
#' To get the most up-to-date version of the package, as well as the past
#' versions, please check the github repository at:
#' \url{https://github.com/verbal-autopsy-software/InterVA5}
#'
#' \tabular{ll}{ Package: \tab InterVA5\cr Type: \tab Package\cr Version: \tab
#' 1.0\cr Date: \tab 2018-02-01\cr License: \tab GPL-3\cr }
#'
#' @name InterVA5-package
#' @docType package
#' @author Jason Thomas, Zehang Li, Tyler McCormick, Sam Clark
#'
#' Maintainer: Jason Thomas <jarathomas@@gmail.com>
#' @references http://www.byass.uk/interva/
#' @keywords InterVA
#'
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#' Conditional probability of InterVA5 (version 17 -- Sept. 9th, 2018)
#'
#' This is the table of conditional probabilities of symptoms given CODs, along with
#' prior probabilities in the first row. The
#' values are from InterVA-5
#'
#'
#' @name probbaseV5
#' @docType data
#' @format A data frame with 354 observations on 87 variables. The first row contains
#' observations corresponding to prior probabilities; while the subsequent observations
#' (rows 2 - 354) are the conditional probabilities.
#' @keywords datasets
#' @examples
#' 
#' data(probbaseV5)
#'
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#' Version 14 of the conditional probability of InterVA5
#'
#' This is version 14 (February 15th, 2018) of the table of conditional probabilities of symptoms given CODs, along with
#' prior probabilities in the first row. The
#' values are from InterVA-5
#'
#'
#' @name probbaseV5_14
#' @docType data
#' @format A data frame with 354 observations on 87 variables. The first row contains
#' observations corresponding to prior probabilities; while the subsequent observations
#' (rows 2 - 354) are the conditional probabilities.
#' @keywords datasets
#' @examples
#' 
#' data(probbaseV5_14)
#'
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#' Version 17 of the conditional probability of InterVA5
#'
#' This is version 17 (Sept. 9th, 2018) of the table of conditional probabilities of symptoms given CODs, along with
#' prior probabilities in the first row. The
#' values are from InterVA-5
#'
#'
#' @name probbaseV5_17
#' @docType data
#' @format A data frame with 354 observations on 87 variables. The first row contains
#' observations corresponding to prior probabilities; while the subsequent observations
#' (rows 2 - 354) are the conditional probabilities.
#' @keywords datasets
#' @examples
#' 
#' data(probbaseV5_17)
#'
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#' Version 18 of the conditional probability of InterVA5
#'
#' This is version 18 (April 3, 2020) of the table of conditional probabilities of symptoms given CODs, along with
#' prior probabilities in the first row. The
#' values are from InterVA-5
#'
#'
#' @name probbaseV5_18
#' @docType data
#' @format A data frame with 354 observations on 87 variables. The first row contains
#' observations corresponding to prior probabilities; while the subsequent observations
#' (rows 2 - 354) are the conditional probabilities.
#' @keywords datasets
#' @examples
#' 
#' data(probbaseV5_18)
#'
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#' Version 19 of the conditional probability of InterVA5
#'
#' This is version 19 (July 20, 2021) of the table of conditional probabilities of symptoms given CODs, along with
#' prior probabilities in the first row. The
#' values differ from the last version (v18) of InterVA-5 (interva.net) by setting
#' Pr(abortion-related death | i309 = 1) = "N"
#' Pr(abortion-related death | i310 = 1) = "N"
#' (the previous values were "E").
#'
#'
#' @name probbaseV5_19
#' @docType data
#' @format A data frame with 354 observations on 87 variables. The first row contains
#' observations corresponding to prior probabilities; while the subsequent observations
#' (rows 2 - 354) are the conditional probabilities.
#' @keywords datasets
#' @examples
#' 
#' data(probbaseV5_19)
#'
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#' 200 records of Sample Input
#'
#' This is a dataset consisting of 200 arbitrary sample input deaths in the
#' acceptable format of InterVA5. Any dataset that needs to be analyzed by this
#' package should be in the same format. The order of the input fields must
#' not be changed.
#'
#'
#' @name RandomVA5
#' @docType data
#' @format 200 arbitrary input records.
#' @keywords datasets
#' @examples
#'
#' data(RandomVA5)
#'
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