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icm.utils.R
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icm.utils.R
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#' @title Get Epidemic Output from icm Model
#'
#' @description This function provides all active model state sizes from
#' the network at the specified time step, output to a list of
#' vectors.
#'
#' @param dat Main \code{icm_dat} class data object passed through \code{icm}
#' simulations.
#' @param at Current time step.
#'
#' @inherit recovery.icm return
#'
#' @export
#' @keywords internal
#'
prevalence.icm <- function(dat, at) {
if (at == 1) {
dat$epi <- list()
dat$epi$s.num <- sum(dat$attr$active == 1 &
dat$attr$status == "s" &
dat$attr$group == 1)
dat$epi$i.num <- sum(dat$attr$active == 1 &
dat$attr$status == "i" &
dat$attr$group == 1)
dat$epi$num <- dat$epi$s.num + dat$epi$i.num
if (dat$control$type == "SIR") {
dat$epi$r.num <- sum(dat$attr$active == 1 &
dat$attr$status == "r" &
dat$attr$group == 1)
dat$epi$num <- dat$epi$s.num +
dat$epi$i.num +
dat$epi$r.num
}
} else {
dat$epi$s.num[at] <- sum(dat$attr$active == 1 &
dat$attr$status == "s" &
dat$attr$group == 1)
dat$epi$i.num[at] <- sum(dat$attr$active == 1 &
dat$attr$status == "i" &
dat$attr$group == 1)
dat$epi$num[at] <- dat$epi$s.num[at] + dat$epi$i.num[at]
if (dat$control$type == "SIR") {
dat$epi$r.num[at] <- sum(dat$attr$active == 1 &
dat$attr$status == "r" &
dat$attr$group == 1)
dat$epi$num[at] <- dat$epi$s.num[at] +
dat$epi$i.num[at] +
dat$epi$r.num[at]
}
}
return(dat)
}
#' @title Get Epidemic Output from icm Model
#'
#' @description This function provides all active model state sizes from
#' the network at the specified time step, output to a list of
#' vectors.
#'
#' @inheritParams prevalence.icm
#'
#' @inherit recovery.icm return
#'
#' @export
#' @keywords internal
#'
prevalence.icm.bip <- function(dat, at) {
if (at == 1) {
dat$epi <- list()
dat$epi$s.num <- sum(dat$attr$active == 1 &
dat$attr$status == "s" &
dat$attr$group == 1)
dat$epi$i.num <- sum(dat$attr$active == 1 &
dat$attr$status == "i" &
dat$attr$group == 1)
dat$epi$num <- dat$epi$s.num + dat$epi$i.num
dat$epi$s.num.g2 <- sum(dat$attr$active == 1 &
dat$attr$status == "s" &
dat$attr$group == 2)
dat$epi$i.num.g2 <- sum(dat$attr$active == 1 &
dat$attr$status == "i" &
dat$attr$group == 2)
dat$epi$num.g2 <- dat$epi$s.num.g2 + dat$epi$i.num.g2
if (dat$control$type == "SIR") {
dat$epi$r.num <- sum(dat$attr$active == 1 &
dat$attr$status == "r" &
dat$attr$group == 1)
dat$epi$num <- dat$epi$s.num +
dat$epi$i.num +
dat$epi$r.num
dat$epi$r.num.g2 <- sum(dat$attr$active == 1 &
dat$attr$status == "r" &
dat$attr$group == 2)
dat$epi$num.g2 <- dat$epi$s.num.g2 +
dat$epi$i.num.g2 +
dat$epi$r.num.g2
}
} else {
dat$epi$s.num[at] <- sum(dat$attr$active == 1 &
dat$attr$status == "s" &
dat$attr$group == 1)
dat$epi$i.num[at] <- sum(dat$attr$active == 1 &
dat$attr$status == "i" &
dat$attr$group == 1)
dat$epi$num[at] <- dat$epi$s.num[at] + dat$epi$i.num[at]
dat$epi$s.num.g2[at] <- sum(dat$attr$active == 1 &
dat$attr$status == "s" &
dat$attr$group == 2)
dat$epi$i.num.g2[at] <- sum(dat$attr$active == 1 &
dat$attr$status == "i" &
dat$attr$group == 2)
dat$epi$num.g2[at] <- dat$epi$s.num.g2[at] + dat$epi$i.num.g2[at]
if (dat$control$type == "SIR") {
dat$epi$r.num[at] <- sum(dat$attr$active == 1 &
dat$attr$status == "r" &
dat$attr$group == 1)
dat$epi$num[at] <- dat$epi$s.num[at] +
dat$epi$i.num[at] +
dat$epi$r.num[at]
dat$epi$r.num.g2[at] <- sum(dat$attr$active == 1 &
dat$attr$status == "r" &
dat$attr$group == 2)
dat$epi$num.g2[at] <- dat$epi$s.num.g2[at] +
dat$epi$i.num.g2[at] +
dat$epi$r.num.g2[at]
}
}
return(dat)
}