R/tspot.criteria.oxford.global.R

In mmparker/tbdiag: Functions for Tuberculosis Diagnostics Research

tspot.criteria.oxford.global <- function(tspot.obj){

    
    # Set up the results vector
    result <- rep(NA, times = length(tspot.obj$nil)) 

    # Identify the maximum of Panel A - Nil and Panel B - Nil
    panel.max <- pmax((tspot.obj$panel.a - tspot.obj$nil),
                      (tspot.obj$panel.b - tspot.obj$nil)
    )

    # For ease of reading criteria, set up a flag for each of the TSPOT
    # criteria
    # Nil is high
    high.nil <- tspot.obj$nil > 10

    # Antigen is in positive territory
    pos.spots <- panel.max >= 6

    # Mitogen is low
    low.mito <- tspot.obj$mito < 20


    # Positive
    result[pos.spots %in% TRUE &
           high.nil %in% FALSE &
           low.mito %in% c(TRUE, FALSE)] <- "Positive"


    # Negative
    result[pos.spots %in% FALSE &
           high.nil %in% FALSE &
           low.mito %in% FALSE] <- "Negative"


    # High nil
    result[pos.spots %in% c(TRUE, FALSE) &
           high.nil %in% TRUE &
           low.mito %in% c(TRUE, FALSE)] <- "Invalid - high nil"


    # Low mito
    result[pos.spots %in% FALSE &
           high.nil %in% FALSE &
           low.mito %in% TRUE] <- "Invalid - low mitogen"




    return(result)
}