update COVIDM to NCEM calculation

[pearsonca]

omicronSA/R/ngm_ratio.R

Lines 59 to 90 in 33d4ecb

	#' @param dIp, a vector of times + probabilities for the duration of this event
	#' @param dIs, same
	#' @param dIa, same
	#' @param mixmatrix, the mixing matrices
	#' @param mwweights, their relative weights
	#' @param fIs, the relative contribution of Is
	#' @param fIp, same
	#' @param fIa, same
	#' @param uval, vector of susceptibility modifiers, by age
	#' @param yval, vector of asymptomatic fractions, by age
	#' @param u_multiplier, the multiplier to modify effective susceptibility
	#' @param durmultiplier, the relative multiplier to reduce durations of infectiousness
	#'
	#' @return the eigenvalue of the ODE transmission / transition matrix
	ngmR <- function(
	dIp = delay_gamma(1.5, 4.0, t_max = 15, t_step = 0.25)$p,
	dIs = delay_gamma(3.5, 4.0, t_max = 15, t_step = 0.25)$p,
	dIa = delay_gamma(5.0, 4.0, t_max = 15, t_step = 0.25)$p,
	mixmatrix, mweights,
	fIs = 1, fIp = 1, fIa = 0.5,
	uval, yval,
	u_multiplier = 1, durmultiplier = 1
	) {
	durIp <- mean_dur(dIp, 0.25)*durmultiplier
	durIs <- mean_dur(dIs, 0.25)*durmultiplier
	durIa <- mean_dur(dIa, 0.25)*durmultiplier
	mixing <- Reduce(`+`, mapply(function(c, m) c*m, mixmatrix, mweights, SIMPLIFY = FALSE))
	ngm = uval * u_multiplier * t(t(mixing) * (
	yval * (fIp * durIp + fIs * durIs) +(1 - yval) * fIa * durIa))
	Re(eigen(ngm)$values[1])
	}

The relevant lines to update for eigenvalue / NGM calculations.