#' AIDS survival probability curve
#' @param n Number of days to calculate.
#' @returns
#' A vector where the ith element is the probability that an
#' individual infected with HIV i days ago has not progressed to AIDS.
#' @references
#' Ron Brookmeyer and James J Goedert. Censoring in an epidemic with an appli-cation to hemophilia-associated aids.Biometrics, pages 325–335, 1989.
#'
#' @export
aids_survival <- function(n = 365 * 5) {
aids_surv <-
1 - sapply(1:n, function(x)
stats::pweibull(x / 365, 2.516, 1 / 0.086))
}
#' False Recency Rate (FRR) for the LAg-Avidity
#' @returns
#' A vector of length 2. The first element is the proportion of untreated, non-elite controller, non-AIDS individuals infected more
#' than 2 years ago that test as recent on the LAg-Avidity assay. The second is the standard
#' error of the proportion.
#' @export
lag_avidity_frr <- function() {
c(proportion = 2 / 362,
std_error = sqrt((2 / 362) * (1 - 2 / 362) / 362))
}
#' Survival curve for testing recent
#' @param n Number of days to calculate.
#' @details
#' A reanalysis of Duong et. al. (2015). See Fellows (2021) for details
#' @returns
#' A vector where the ith element is the probability that an untreated non-elite controller
#' individual infected i days ago tests recent on the LAg-Avidity assay.
#' @references
#' Yen T Duong, Reshma Kassanjee, Alex Welte, Meade Morgan, Anindya De, TrudyDobbs, Erin Rottinghaus, John Nkengasong, Marcel E Curlin, Chonticha Kitti-nunvorakoon, et al. Recalibration of the limiting antigen avidity eia to deter-mine mean duration of recent infection in divergent hiv-1 subtypes.PloS one,10(2):e0114947, 2015.
#' @export
lag_avidity_survival <- function(n=365*5){
s <- structure(c(0.963137666201887, 0.962021320449555, 0.96087261491624,
0.959690736193394, 0.958474858081183, 0.957224141853411, 0.955937736557767,
0.954614779353037, 0.953254395884926, 0.95185570070215, 0.950417797714457,
0.948939780694213, 0.947420733823218, 0.945859732286333, 0.944255842913532,
0.942608124871917, 0.940915630409195, 0.939177405650066, 0.937392491446896,
0.93555992428597, 0.933678737250535, 0.931747961041729, 0.929766625058384,
0.927733758536558, 0.925648391749513, 0.923509557268677, 0.921316291285994,
0.919067634997825, 0.916762636050418, 0.914400350046692, 0.911979842113892,
0.909500188531381, 0.906960478417606, 0.904359815474973, 0.901697319791072,
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), .Dim = 1825L)
if(n > length(s))
stop("n is larger than 5 * 365")
s[1:n]
}
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