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#' @title Recovery: netsim Module
#'
#' @description This function simulates recovery from the infected state
#' either to a distinct recovered state (SIR model type) or back
#' to a susceptible state (SIS model type), for use in
#' \code{\link{netsim}}.
#'
#' @param dat Main \code{netsim_dat} object containing a \code{networkDynamic}
#' object and other initialization information passed from
#' \code{\link{netsim}}.
#' @param at Current time step.
#'
#' @return The updated \code{netsim_dat} main list object.
#'
#' @export
#' @keywords internal
#'
recovery.net <- function(dat, at) {
## Only run with SIR/SIS
type <- get_control(dat, "type", override.null.error = TRUE)
type <- if (is.null(type)) "None" else type
if (!(type %in% c("SIR", "SIS"))) {
return(dat)
}
# Variables ---------------------------------------------------------------
active <- get_attr(dat, "active")
status <- get_attr(dat, "status")
infTime <- get_attr(dat, "infTime")
recovState <- ifelse(type == "SIR", "r", "s")
rec.rate <- get_param(dat, "rec.rate")
nRecov <- 0
idsElig <- which(active == 1 & status == "i")
nElig <- length(idsElig)
# Time-Varying Recovery Rate ----------------------------------------------
infDur <- at - infTime[active == 1 & status == "i"]
infDur[infDur == 0] <- 1
lrec.rate <- length(rec.rate)
if (lrec.rate == 1) {
ratesElig <- rec.rate
} else {
ratesElig <- ifelse(infDur <= lrec.rate, rec.rate[infDur],
rec.rate[lrec.rate])
}
# Process -----------------------------------------------------------------
if (nElig > 0) {
vecRecov <- which(rbinom(nElig, 1, ratesElig) == 1)
if (length(vecRecov) > 0) {
idsRecov <- idsElig[vecRecov]
nRecov <- length(idsRecov)
status[idsRecov] <- recovState
}
}
dat <- set_attr(dat, "status", status)
# Output ------------------------------------------------------------------
outName <- ifelse(type == "SIR", "ir.flow", "is.flow")
dat <- set_epi(dat, outName, at, nRecov)
return(dat)
}
#' @title Recovery: netsim Module
#'
#' @description This function simulates recovery from the infected state
#' either to a distinct recovered state (SIR model type) or back
#' to a susceptible state (SIS model type), for use in
#' \code{\link{netsim}}.
#'
#' @inheritParams recovery.net
#'
#' @inherit recovery.net return
#'
#' @export
#' @keywords internal
#'
recovery.2g.net <- function(dat, at) {
## Only run with SIR/SIS
type <- get_control(dat, "type", override.null.error = TRUE)
type <- if (is.null(type)) "None" else type
if (!(type %in% c("SIR", "SIS"))) {
return(dat)
}
# Variables ---------------------------------------------------------------
active <- get_attr(dat, "active")
status <- get_attr(dat, "status")
infTime <- get_attr(dat, "infTime")
group <- get_attr(dat, "group")
recovState <- ifelse(type == "SIR", "r", "s")
rec.rate <- get_param(dat, "rec.rate")
rec.rate.g2 <- get_param(dat, "rec.rate.g2")
nRecov <- nRecovG2 <- 0
idsElig <- which(active == 1 & status == "i")
nElig <- length(idsElig)
# Time-Varying Recovery Rate ----------------------------------------------
infDur <- at - infTime[active == 1 & status == "i"]
infDur[infDur == 0] <- 1
lrec.rate <- length(rec.rate)
if (lrec.rate == 1) {
gElig <- group[idsElig]
rates <- c(rec.rate, rec.rate.g2)
ratesElig <- rates[gElig]
} else {
gElig <- group[idsElig]
if (is.null(rec.rate.g2)) {
rates <- ifelse(infDur <= lrec.rate, rec.rate[infDur],
rec.rate[lrec.rate])
} else {
rates <- rep(NA, length(infDur))
rates[gElig == 1] <- ifelse(infDur[gElig == 1] <= lrec.rate,
rec.rate[infDur[gElig == 1]],
rec.rate[lrec.rate])
rates[gElig == 2] <- ifelse(infDur[gElig == 2] <= length(rec.rate.g2),
rec.rate.g2[infDur[gElig == 2]],
rec.rate.g2[length(rec.rate.g2)])
}
ratesElig <- rates
}
# Process -----------------------------------------------------------------
if (nElig > 0) {
vecRecov <- which(rbinom(nElig, 1, ratesElig) == 1)
if (length(vecRecov) > 0) {
idsRecov <- idsElig[vecRecov]
nRecov <- sum(group[idsRecov] == 1)
nRecovG2 <- sum(group[idsRecov] == 2)
status[idsRecov] <- recovState
}
}
dat <- set_attr(dat, "status", status)
# Output ------------------------------------------------------------------
outName <- ifelse(type == "SIR", "ir.flow", "is.flow")
outName[2] <- paste0(outName, ".g2")
dat <- set_epi(dat, outName[1], at, nRecov)
dat <- set_epi(dat, outName[2], at, nRecovG2)
return(dat)
}
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