R/models.R

In aucarter/pr2ar: A set of functions for converting PfPR to attack-rate

#' Generic function for making the W matrix associated an input B function and
#' set of parameters
#'
#' @param PAR A set of model parameters
#' @param Bfn A function for building the matrix represention of the system of
#' equations that update the state vector
#' @export
makeV = function(PAR, Bfn) {
    PAR$A = 0
    Bfn(PAR)
}

#' Generic function for making the W matrix associated an input B function and
#' set of parameters
#'
#' @param PAR A set of model parameters
#' @param Bfn A function for building the matrix represention of the system of
#' equations that update the state vector
#' @export
makeW = function(PAR, Bfn) {
    V = makeV(PAR, Bfn)
    (Bfn(PAR) - V)/PAR$A
}

#' Generic function for making the D matrix that maps the state vector, Y, to
#' prevalence
#'
#' @param PAR A set of model parameters
#' @export
makeD <- function(PAR) {
    In = PAR$In
    Cn = PAR$Cn
    D = c(0)
    if (In > 1) {
        D = c(D, 0, rep(1, In * 2))
    } else {
        D = c(D, 1)
    }
    D = c(D, rep(0, Cn))
    return(D)
}

#' A function for making the matrix representation of the simple SIS model
#'
#' @param PAR A set of model parameters
#' @export
makeB <- function(PAR) {
    A = PAR$A
    Q = PAR$Q
    cbind(c(1 - A, A), c((1 - A) * (1 - Q), A * (1 - Q) + Q))

}

#' A function for making the matrix representation of the simple  model with
#' drugs added
#'
#' @param PAR A set of model parameters
#' @export
makeBdrugs <- function(PAR) {
    A = PAR$A
    Q = PAR$Q
    d = PAR$d
    rho = PAR$rho
    cbind(c((1 - d) * (1 - A), (1 - d) * (1 - rho) * A, d + (1 - d) * rho * A), c((1 - d) * (1 - A *
        rho) * (1 - Q), (1 - d) * (1 - A * rho) * Q, d + (1 - d) * rho * A), c(1 - d, 0, d))
}

#' A function for making the matrix representation of the age of infection (AoI)
#' with overwriting superinfection
#'
#' @param PAR A set of model parameters
#' @export
makeBage <- function(PAR) {
    A = PAR$A
    Q = PAR$Q
    In = PAR$In
    S = c(S = 1 - A, E0 = A, E = rep(0, In), I = rep(0, In))
    E0 = c(0, 0, A, rep(0, In - 1), (1 - A), rep(0, In - 1))
    M = cbind(S, E0)

    Ei = E0
    for (i in 1:In) M = cbind(M, Ei)

    for (i in 1:(In - 1)) {
        Ii = c((1 - A) * (1 - Q), A * (1 - Q), rep(0, i), A * Q, rep(0, In - i - 1), rep(0, i), (1 -
            A) * Q, rep(0, In - i - 1))
        M = cbind(M, Ii)
    }

    Im = c((1 - A) * (1 - Q), A * (1 - Q), rep(0, In - 1), A * Q, rep(0, In - 1), (1 - A) * Q)
    M = cbind(M, Im)

    M
}
#' A function for making the matrix representation of the age of infection (AoI)
#' with overwriting superinfection and drugs
#'
#' @param PAR A set of model parameters
#' @export
makeBdrugs_age = function(PAR) {
    A = PAR$A
    Q = PAR$Q
    rho = PAR$rho
    In = PAR$In
    Cn = PAR$Cn
    S = c(S = 1 - A, E0 = A, E = rep(0, In), I = rep(0, In), C = rep(0, Cn))
    E0 = c(0, 0, (1 - rho) * A, rep(0, In - 1), (1 - rho) * (1 - A), rep(0, In - 1), rho, rep(0, Cn -
        1))
    M = cbind(S, E0)

    Ei = E0
    for (i in 1:In) M = cbind(M, Ei)

    for (i in 1:(In - 1)) {
        Ii = c((1 - A) * (1 - Q), A * (1 - Q), rep(0, i), A * Q, rep(0, In - i - 1), rep(0, i), (1 -
            A) * Q, rep(0, In - i - 1), rep(0, Cn))
        M = cbind(M, Ii)
    }

    Im = c((1 - A) * (1 - Q), A * (1 - Q), rep(0, In - 1), A * Q, rep(0, In - 1), (1 - A) * Q, rep(0,
        Cn))
    M = cbind(M, Im)

    if (Cn == 2) {
        C1 = c(0, rep(0, 2 * In + 1), 0, 1)
        M = cbind(M, C1)
        C2 = c(1, rep(0, 2 * In + 1), 0, 0)
        M = cbind(M, C2)
    }
    M
}