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CFunctions_GSA_uHfix_vratio_M72.R
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CFunctions_GSA_uHfix_vratio_M72.R
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FitGo <- function(cntry, Vx, Fit, InitV, TimeScale, Plot, C) {
require(here)
setwd(here())
fit_env <- environment()
FitV <- c("psz1900", "rmort", "neta", "rmortTB", "CDRscale", "CDRscaleE", "alpha")
InitialV <- c("run", "dt", "prop")
if (length(InitV) == 3) {
for (i in 1:length(InitV)) {
assign(InitialV[i], InitV[i], envir = .GlobalEnv)
}
} else {
for (i in 1:2) {
assign(InitialV[i], as.numeric(InitV[i]), envir = .GlobalEnv)
}
assign(InitialV[3], as.numeric(InitV[3:6]), envir = .GlobalEnv)
}
assign("cntry", cntry, envir = .GlobalEnv)
assign("year1", TimeScale[1], envir = .GlobalEnv)
assign("yearend", TimeScale[2], envir = .GlobalEnv)
hchild <- fchild
hadult <- fadult
helderly <- felderly
chiyrs <- 15
aduyrs <- 50
yaduyrs <- 40
eldyrs <- (Mnage - chiyrs - aduyrs)
voldadu <- (vadult + velderly) / 2
noldadu <- (n + nelderly) / 2
roldadu <- (radult + relderly) / 2
CDRscaleO <- (CDRscale + CDRscaleE) / 2
vHadult <- vHratio * vadult
exit <- 0
p <- c((rep(pchild, l = chiyrs)), (rep(padult, l = aduyrs)), (rep(pelderly, l = eldyrs)))
f <- c((rep(fchild, l = chiyrs)), (rep(fadult, l = aduyrs)), (rep(felderly, l = eldyrs)))
h <- c((rep(hchild, l = chiyrs)), (rep(hadult, l = aduyrs)), (rep(helderly, l = eldyrs)))
v <- c((rep(vchild, l = chiyrs)), (rep(vadult, l = aduyrs)), (rep(velderly, l = eldyrs)))
r <- c((rep(rchild, l = chiyrs)), (rep(radult, l = yaduyrs)), (rep(roldadu, l = (aduyrs -
yaduyrs))), (rep(relderly, l = eldyrs)))
n <- c((rep(n, l = chiyrs)), (rep(n, l = yaduyrs)), (rep(noldadu, l = (aduyrs -
yaduyrs))), (rep(nelderly, l = eldyrs)))
fH <- c((rep(fHchild, l = chiyrs)), (rep(fHadult, l = (aduyrs + eldyrs))))
vH <- c((rep(vHchild, l = chiyrs)), (rep(vHadult, l = (aduyrs + eldyrs))))
pH <- c((rep(pHchild, l = chiyrs)), (rep(pHadult, l = (aduyrs + eldyrs))))
rH <- c((rep(rHchild, l = chiyrs)), (rep(rHadult, l = (aduyrs + eldyrs))))
hH <- fH
gH <- xH
g <- x
nH <- n
rmortH <- 0
times <- seq(year1, (yearend + (1 - dt)), dt)
steps <- length(times)
for (i in 1:length(Fit)) {
assign(FitV[i], Fit[i], envir = .GlobalEnv)
}
if (length(Fit) > 3) {
if (rmortTB < 0) {
ui <- rmortTB * (ui) + ui
uni <- rmortTB * (uni) + uni
} else {
ui <- rmortTB * (1 - ui) + ui
uni <- rmortTB * (1 - uni) + uni
}
}
if (length(Fit) > 3) {
if (rmortTBH < 0) {
uiH <- rmortTBH * (uiH) + uiH
uniH <- rmortTBH * (uniH) + uniH
} else {
uiH <- rmortTBH * (1 - uiH) + uiH
uniH <- rmortTBH * (1 - uniH) + uniH
}
}
if (length(Fit) > 3) {
if (alpha < 0) {
pH <- alpha * pH + pH
vH <- alpha * vH + vH
rH <- alpha * rH + rH
} else {
pH <- alpha * (1 - pH) + pH
vH <- alpha * (1 - vH) + vH
rH <- alpha * (1 - rH) + rH
}
}
uichild <- ui * uiscaleC
uiadult <- ui * uiscaleA
uielderly <- ui * uiscaleE
unichild <- uni * uiscaleC
uniadult <- uni * uiscaleA
unielderly <- uni * uiscaleE
uichildH <- uiH * uiscaleC
uiadultH <- uiH * uiscaleA
uielderlyH <- uiH * uiscaleE
unichildH <- uniH * uiscaleC
uniadultH <- uniH * uiscaleA
unielderlyH <- uniH * uiscaleE
ui <- c((rep(uichild, l = chiyrs)), (rep(uiadult, l = aduyrs)), (rep(uielderly,
l = eldyrs
)))
uni <- c((rep(unichild, l = chiyrs)), (rep(uniadult, l = aduyrs)), (rep(unielderly,
l = eldyrs
)))
uiH <- c((rep(uichildH, l = chiyrs)), (rep(uiadultH, l = aduyrs)), (rep(uielderlyH,
l = eldyrs
)))
uniH <- c((rep(unichildH, l = chiyrs)), (rep(uniadultH, l = aduyrs)), (rep(unielderlyH,
l = eldyrs
)))
is.nan.data.frame <- function(x) do.call(cbind, lapply(x, is.nan))
is.infinite.data.frame <- function(x) do.call(cbind, lapply(x, is.infinite))
if (length(Fit) < 5) {
CDRscale <- 0
}
if (length(Vx) > 1) {
assign("vaccine", Vx[1], envir = .GlobalEnv)
assign("coverage", Vx[2], envir = .GlobalEnv)
assign("coverageM", Vx[3], envir = .GlobalEnv)
assign("effI", Vx[4], envir = .GlobalEnv)
assign("effD", Vx[5], envir = .GlobalEnv)
assign("D", Vx[6], envir = .GlobalEnv)
assign("fmass", Vx[7], envir = .GlobalEnv)
assign("vxage", Vx[8], envir = .GlobalEnv)
assign("covH", Vx[9], envir = .GlobalEnv)
assign("VEH", Vx[10], envir = .GlobalEnv)
source("#VxGenGSA_M72.R")
} else {
d <- matrix(0, steps, Mnage)
dH <- matrix(0, steps, Mnage)
thetaS <- matrix(0, steps, Mnage)
thetaL <- matrix(0, steps, Mnage)
thetaR <- matrix(0, steps, Mnage)
thetaSH <- matrix(0, steps, Mnage)
thetaLH <- matrix(0, steps, Mnage)
thetaRH <- matrix(0, steps, Mnage)
vaccine <- 0
effI <- 0
effD <- 0
D <- 0
coverage <- 0
coverageM <- 0
fmass <- 0
vxage <- 0
VEH <- 0
covH <- 0
}
source("#InitGSA_vratio_M72.R")
for (k in year1:(yearend)) {
if (k <= 1950) {
yr <- 1950
} else {
yr <- k
}
mortdrop <- 1950
if (k <= mortdrop) {
if (rmort < 0) {
upop <- as.vector(rmort * (mort[1, 2:102]) + mort[1, 2:102])
} else {
upop <- as.vector(rmort * (1 - (mort[1, 2:102])) + mort[1, 2:102])
}
} else {
if (rmort < 0) {
upop <- as.vector(rmort * (mort[1 + yr - 1950, 2:102]) + mort[1 +
yr - 1950, 2:102])
} else {
upop <- as.vector(rmort * (1 - (mort[1 + yr - 1950, 2:102])) + mort[1 +
yr - 1950, 2:102])
}
}
if (k <= 1990) {
if (rmortH < 0) {
uHpop <- as.vector(rmortH * (mortH[1, 2:102]) + mortH[1, 2:102])
} else {
uHpop <- as.vector(rmortH * (1 - (mortH[1, 2:102])) + mortH[1, 2:102])
}
} else {
if (rmortH < 0) {
uHpop <- as.vector(rmortH * (mortH[1 + yr - 1990, 2:102]) + mortH[1 +
yr - 1990, 2:102])
} else {
uHpop <- as.vector(rmortH * (1 - (mortH[1 + yr - 1990, 2:102])) +
mortH[1 + yr - 1990, 2:102])
}
}
if (k <= 1990) {
CDR_yr <- 1990
} else {
CDR_yr <- k
}
if (k <= 1994) {
CoT_yr <- 1994
} else {
CoT_yr <- k
}
if (CDRscale < 0) {
CDRscaled <- rep(min(((CDRscale * cdr[1 + CDR_yr - 1990, ]) + cdr[1 +
CDR_yr - 1990, ]), 1), (chiyrs + yaduyrs))
} else {
CDRscaled <- rep(min((CDRscale * (1 - cdr[1 + CDR_yr - 1990, ]) + cdr[1 +
CDR_yr - 1990, ]), 1), (chiyrs + yaduyrs))
}
if (CDRscaleO < 0) {
CDRscaledO <- rep(min(((CDRscaleO * cdr[1 + CDR_yr - 1990, ]) + cdr[1 +
CDR_yr - 1990, ]), 1), (Mnage - (eldyrs + chiyrs + yaduyrs)))
} else {
CDRscaledO <- rep(min((CDRscaleO * (1 - cdr[1 + CDR_yr - 1990, ]) + cdr[1 +
CDR_yr - 1990, ]), 1), (Mnage - (eldyrs + chiyrs + yaduyrs)))
}
if (CDRscaleE < 0) {
CDRscaledE <- rep(min(((CDRscaleE * cdr[1 + CDR_yr - 1990, ]) + cdr[1 +
CDR_yr - 1990, ]), 1), eldyrs)
} else {
CDRscaledE <- rep(min((CDRscaleE * (1 - cdr[1 + CDR_yr - 1990, ]) + cdr[1 +
CDR_yr - 1990, ]), 1), eldyrs)
}
CDR <- c(CDRscaled, CDRscaledO, CDRscaledE)
if (k == 2010) {
CDR2010 <- CDR
}
CDRH <- CDR
CoT <- suctt[1 + CoT_yr - 1994]
if (k < 1990) {
ind <- 1
} else {
ind <- (k - 1990 + 2)
}
hiv <- hivall[ind, ]
artyr <- (art[CDR_yr - 1990 + 1, 1] / 100)
artyrc <- (art[CDR_yr - 1990 + 1, 2] / 100)
artredu <- 0.35
artreduC <- 0.3
uiHa[1:15] <- ((1 - artyrc) * uiH[1:15]) + (artyrc * (((uiH[1:15] - ui[1:15]) *
artreduC) + ui[1:15]))
uiHa[16:Mnage] <- ((1 - artyr) * uiH[16:Mnage]) + (artyr * (((uiH[16:Mnage] -
ui[16:Mnage]) * artredu) + ui[16:Mnage]))
uniHa[1:15] <- ((1 - artyrc) * uniH[1:15]) + (artyrc * (((uniH[1:15] - uni[1:15]) *
artreduC) + uni[1:15]))
uniHa[16:Mnage] <- ((1 - artyr) * uniH[16:Mnage]) + (artyr * (((uniH[16:Mnage] -
uni[16:Mnage]) * artredu) + uni[16:Mnage]))
pHa[1:15] <- ((1 - artyrc) * pH[1:15]) + (artyrc * (((pH[1:15] - p[1:15]) *
artreduC) + p[1:15]))
pHa[16:Mnage] <- ((1 - artyr) * pH[16:Mnage]) + (artyr * (((pH[16:Mnage] -
p[16:Mnage]) * artredu) + p[16:Mnage]))
vHa[1:15] <- ((1 - artyrc) * vH[1:15]) + (artyrc * (((vH[1:15] - v[1:15]) *
artreduC) + v[1:15]))
vHa[16:Mnage] <- ((1 - artyr) * vH[16:Mnage]) + (artyr * (((vH[16:Mnage] -
v[16:Mnage]) * artredu) + v[16:Mnage]))
rHa[1:15] <- ((1 - artyrc) * rH[1:15]) + (artyrc * (((rH[1:15] - r[1:15]) *
artreduC) + r[1:15]))
rHa[16:Mnage] <- ((1 - artyr) * rH[16:Mnage]) + (artyr * (((rH[16:Mnage] -
r[16:Mnage]) * artredu) + r[16:Mnage]))
xHa <- ((1 - artyr) * xH) + (artyr * (((xH - x) * artredu) + x))
gHa <- xHa
if (k <= 1950) {
yr <- 1950
} else {
yr <- k
}
fertdrop <- 1950
if (k < fertdrop) {
br <- bb[1]
if (k == year1) {
B <- round(br * psizeALL[1])
} else {
B <- round(br * psizeALL[((k - year1) * (1 / dt))])
}
} else {
B <- round(bb[1 + yr - 1950] * psizeALL[((k - year1) * (1 / dt))])
}
if (k < 1990) {
BH <- 0
} else {
brh <- H04rate[(k - 1990 + 1)]
BH <- round(brh * psizematrix[((k - year1) * (1 / dt)), 1])
}
if (k > year1) {
i <- ((1 / dt) * (k - year1) + 1)
start <- 1
lambda[i - 1, 1:Mnage] <- t(neta * (1 - exp(colSums(-(myneta[
1:4,
1:Mnage
]) * z * ((Imatrix[i - 1, 1:4]) / (psizematrix[i - 1, 1:4]))))))
AIDSdeaths[i, 1] <- B * uHpop[1] * dt
AIDSdeaths[i, 2:Mnage] <- agepopall[i - 1, 1:(Mnage - 1)] * uHpop[2:Mnage] *
dt
BKdeaths[i, 1] <- (B * upop[1] * dt) - AIDSdeaths[i, 1]
BKdeaths[i, 2:Mnage] <- (agepopall[i - 1, 1:(Mnage - 1)] * upop[2:Mnage] *
dt) - AIDSdeaths[i, 2:Mnage]
uH[1] <- (AIDSdeaths[i, 1] / BH) / dt
uH[2:Mnage] <- (AIDSdeaths[i, 2:Mnage] / agepopHIV[i - 1, 1:(Mnage -
1)]) / dt
u[1] <- (BKdeaths[i, 1] / B) / dt
u[2:Mnage] <- (BKdeaths[i, 2:Mnage] / agepopall[i - 1, 1:(Mnage - 1)]) / dt
uH[is.nan(uH)] <- 0
uH[is.infinite(uH)] <- 0
uH[is.na(uH)] <- 0
uH[uH < 0] <- 0
u[u < 0] <- 0
assign("u", u, envir = .GlobalEnv)
assign("lambda", lambda, envir = .GlobalEnv)
assign("BKdeaths", BKdeaths, envir = .GlobalEnv)
for (aaa in 1:Mnage) {
aaaa <- (u[aaa] + uH[aaa] + lambda[i - 1, aaa])
bbbb <- (u[aaa] + uH[aaa] + vHa[aaa] + (lambda[i - 1, aaa] * pHa[aaa] *
xHa))
cccc <- (u[aaa] + uH[aaa] + uiHa[aaa] + nH[aaa])
dddd <- (u[aaa] + uH[aaa] + uniHa[aaa] + nH[aaa] + w)
eeee <- (u[aaa] + uH[aaa] + rHa[aaa, 1] + (lambda[i - 1, aaa] *
gHa))
if (((is.nan(aaaa)) || (is.na(aaaa)) || (is.nan(bbbb)) || (is.na(bbbb)) ||
(is.nan(cccc)) || (is.na(cccc)) || (is.nan(dddd)) || (is.na(dddd)) ||
(is.nan(eeee)) || (is.na(eeee))) == TRUE) {
exit <- 1
print("nan")
} else {
if (((is.infinite(aaaa)) || (is.infinite(bbbb)) || (is.infinite(cccc)) ||
(is.infinite(dddd)) || (is.infinite(eeee))) == TRUE) {
exit <- 1
print("inf")
} else {
if ((((aaaa < 0) == TRUE) || ((bbbb < 0) == TRUE) || ((cccc <
0) == TRUE) || ((dddd < 0) == TRUE) || ((eeee < 0) == TRUE)) ==
TRUE) {
exit <- 1
print("neg")
} else {
if ((is.nan(u[aaa])) == TRUE) {
exit <- 1
print("nan2")
} else {
if ((is.nan(exit)) == TRUE) {
exit <- 1
print("nan3")
}
}
}
}
}
test <- 0
if (exit == 0) {
ifelse(((c(aaaa, bbbb, cccc, dddd, eeee) > 2)), test <- 1, print("proceed"))
}
if (test == 1) {
print("exit2")
uHuse <- (which.max(c(aaaa, bbbb, cccc, dddd, eeee)))
if (uHuse == 1) {
uH[aaa] <- ((1 / dt) - (u[aaa] + lambda[i - 1, aaa]))
}
if (uHuse == 2) {
uH[aaa] <- ((1 / dt) - (u[aaa] + (lambda[i - 1, aaa] * pHa[aaa] *
xHa) + vHa[aaa, 1]))
}
if (uHuse == 3) {
uH[aaa] <- ((1 / dt) - (u[aaa] + uiHa[aaa] + nH[aaa]))
}
if (uHuse == 4) {
uH[aaa] <- ((1 / dt) - (u[aaa] + uniHa[aaa] + nH[aaa] + w))
}
if (uHuse == 5) {
uH[aaa] <- ((1 / dt) - (u[aaa] + (lambda[i - 1, aaa] * gHa) +
rHa[aaa, 1]))
}
aaaa <- (u[aaa] + uH[aaa] + lambda[i - 1, aaa])
bbbb <- (u[aaa] + uH[aaa] + vHa[aaa] + (lambda[i - 1, aaa] *
pHa[aaa] * xHa))
cccc <- (u[aaa] + uH[aaa] + uiHa[aaa] + nH[aaa])
dddd <- (u[aaa] + uH[aaa] + uniHa[aaa] + nH[aaa] + w)
eeee <- (u[aaa] + uH[aaa] + rHa[aaa, 1] + (lambda[i - 1, aaa] *
gHa))
if ((((aaaa < 0) == TRUE) || ((bbbb < 0) == TRUE) || ((cccc <
0) == TRUE) || ((dddd < 0) == TRUE) || ((eeee < 0) == TRUE)) ==
TRUE) {
exit <- 1
}
}
}
upopstore[i, ] <- upop[1:Mnage]
uHpopstore[i, ] <- uHpop[1:Mnage]
ustore[i, ] <- u[1:Mnage]
uHstore[i, ] <- uH[1:Mnage]
j <- 1
S[i, j] <- B - BH
SH[i, j] <- BH
S[i, 2:Mnage] <- S[i - 1, 1:(Mnage - 1)] - (u[1:(Mnage - 1)] + lambda[i -
1, 1:(Mnage - 1)]) * S[i - 1, 1:(Mnage - 1)] * dt - hiv[1:(Mnage -
1)] * S[i - 1, 1:(Mnage - 1)]
L[i, 2:Mnage] <- L[i - 1, 1:(Mnage - 1)] + lambda[i - 1, 1:(Mnage -
1)] * (1 - p[1:(Mnage - 1)]) * (S[i - 1, 1:(Mnage - 1)] + g * R[i -
1, 1:(Mnage - 1)]) * dt - (v[1:(Mnage - 1)] + lambda[i - 1, 1:(Mnage -
1)] * p[1:(Mnage - 1)] * x + u[1:(Mnage - 1)]) * L[i - 1, 1:(Mnage -
1)] * dt - hiv[1:(Mnage - 1)] * L[i - 1, 1:(Mnage - 1)]
new_infect[i, 2:Mnage] <- lambda[i - 1, 1:(Mnage - 1)] * S[
i - 1,
1:(Mnage - 1)
] * dt + lambda[i - 1, 1:(Mnage - 1)] * (x * L[i -
1, 1:(Mnage - 1)] + g * R[i - 1, 1:(Mnage - 1)]) * dt
new_I_react[i, 2:Mnage] <- v[1:(Mnage - 1)] * f[1:(Mnage - 1)] * (L[i -
1, 1:(Mnage - 1)]) * dt + r[1:(Mnage - 1)] * h[1:(Mnage - 1)] *
R[i - 1, 1:(Mnage - 1)] * dt
new_NI_react[i, 2:Mnage] <- v[1:(Mnage - 1)] * (1 - f[1:(Mnage - 1)]) *
L[i - 1, 1:(Mnage - 1)] * dt + r[1:(Mnage - 1)] * (1 - h[1:(Mnage -
1)]) * R[i - 1, 1:(Mnage - 1)] * dt
new_actv_react[i, 2:Mnage] <- v[1:(Mnage - 1)] * (L[i - 1, 1:(Mnage -
1)]) * dt + r[1:(Mnage - 1)] * R[i - 1, 1:(Mnage - 1)] * dt
new_actv_inf[i, 2:Mnage] <- lambda[i - 1, 1:(Mnage - 1)] * p[1:(Mnage -
1)] * S[i - 1, 1:(Mnage - 1)] * dt + lambda[i - 1, 1:(Mnage - 1)] *
p[1:(Mnage - 1)] * x * (L[i - 1, 1:(Mnage - 1)]) * dt + lambda[i -
1, 1:(Mnage - 1)] * p[1:(Mnage - 1)] * g * R[i - 1, 1:(Mnage -
1)] * dt
new_I[i, 2:Mnage] <- lambda[i - 1, 1:(Mnage - 1)] * p[1:(Mnage - 1)] *
f[1:(Mnage - 1)] * (S[i - 1, 1:(Mnage - 1)] + g * R[i - 1, 1:(Mnage -
1)]) * dt + (v[1:(Mnage - 1)] + lambda[i - 1, 1:(Mnage - 1)] *
p[1:(Mnage - 1)] * x) * f[1:(Mnage - 1)] * L[i - 1, 1:(Mnage -
1)] * dt + r[1:(Mnage - 1)] * h[1:(Mnage - 1)] * R[i - 1, 1:(Mnage -
1)] * dt + w * NI[i - 1, 1:(Mnage - 1)] * dt
new_I_noconv[i, 2:Mnage] <- lambda[i - 1, 1:(Mnage - 1)] * p[1:(Mnage -
1)] * f[1:(Mnage - 1)] * (S[i - 1, 1:(Mnage - 1)] + g * R[
i - 1,
1:(Mnage - 1)
]) * dt + (v[1:(Mnage - 1)] + lambda[i - 1, 1:(Mnage -
1)] * p[1:(Mnage - 1)] * x) * f[1:(Mnage - 1)] * L[i - 1, 1:(Mnage -
1)] * dt + r[1:(Mnage - 1)] * h[1:(Mnage - 1)] * R[i - 1, 1:(Mnage -
1)] * dt
new_NI[i, 2:Mnage] <- lambda[i - 1, 1:(Mnage - 1)] * p[1:(Mnage -
1)] * (1 - f[1:(Mnage - 1)]) * (S[i - 1, 1:(Mnage - 1)] + g * R[i -
1, 1:(Mnage - 1)]) * dt + (v[1:(Mnage - 1)] + lambda[i - 1, 1:(Mnage -
1)] * p[1:(Mnage - 1)] * x) * (1 - f[1:(Mnage - 1)]) * L[
i - 1,
1:(Mnage - 1)
] * dt + r[1:(Mnage - 1)] * (1 - h[1:(Mnage - 1)]) *
R[i - 1, 1:(Mnage - 1)] * dt
new_actv[i, 2:Mnage] <- lambda[i - 1, 1:(Mnage - 1)] * p[1:(Mnage -
1)] * S[i - 1, 1:(Mnage - 1)] * dt + (v[1:(Mnage - 1)] + lambda[i -
1, 1:(Mnage - 1)] * p[1:(Mnage - 1)] * x) * L[i - 1, 1:(Mnage -
1)] * dt + (r[1:(Mnage - 1)] + lambda[i - 1, 1:(Mnage - 1)] * p[1:(Mnage -
1)] * g) * R[i - 1, 1:(Mnage - 1)] * dt
new_actv_chk[i, 2:Mnage] <- new_actv_react[i, 2:Mnage] + new_actv_inf[
i,
2:Mnage
]
new_notif[i, 2:Mnage] <- CDR[2:(Mnage)] * (new_I[i, 2:Mnage] + e *
new_NI[i, 2:Mnage])
R[i, 2:Mnage] <- R[i - 1, 1:(Mnage - 1)] + n[1:(Mnage - 1)] * (I[i -
1, 1:(Mnage - 1)] + NI[i - 1, 1:(Mnage - 1)]) * dt + CDR[2:(Mnage)] *
CoT * (new_I[i, 2:Mnage] + e * new_NI[i, 2:Mnage]) - (r[1:(Mnage -
1)] + g * lambda[i - 1, 1:(Mnage - 1)] + u[1:(Mnage - 1)]) * R[i -
1, 1:(Mnage - 1)] * dt - hiv[1:(Mnage - 1)] * R[i - 1, 1:(Mnage -
1)]
I[i, 2:Mnage] <- I[i - 1, 1:(Mnage - 1)] + (1 - CDR[2:(Mnage)] * CoT) *
(new_I[i, 2:Mnage]) - (n[1:(Mnage - 1)] + u[1:(Mnage - 1)] + ui[1:(Mnage -
1)]) * I[i - 1, 1:(Mnage - 1)] * dt - hiv[1:(Mnage - 1)] * I[i -
1, 1:(Mnage - 1)]
NI[i, 2:Mnage] <- NI[i - 1, 1:(Mnage - 1)] + ((1 - CDR[2:(Mnage)] *
CoT * e) * new_NI[i, 2:Mnage]) - (n[1:(Mnage - 1)] + u[1:(Mnage -
1)] + uni[1:(Mnage - 1)] + w) * NI[i - 1, 1:(Mnage - 1)] * dt -
hiv[1:(Mnage - 1)] * NI[i - 1, 1:(Mnage - 1)]
SH[i, 2:Mnage] <- SH[i - 1, 1:(Mnage - 1)] - (u[1:(Mnage - 1)] + uH[1:(Mnage -
1)] + lambda[i - 1, 1:(Mnage - 1)]) * SH[i - 1, 1:(Mnage - 1)] *
dt + hiv[1:(Mnage - 1)] * S[i - 1, 1:(Mnage - 1)]
LH[i, 2:Mnage] <- LH[i - 1, 1:(Mnage - 1)] + lambda[i - 1, 1:(Mnage -
1)] * (1 - pHa[1:(Mnage - 1)]) * (SH[i - 1, 1:(Mnage - 1)] + gHa *
RH[i - 1, 1:(Mnage - 1)]) * dt - (vHa[1:(Mnage - 1)] + lambda[i -
1, 1:(Mnage - 1)] * pHa[1:(Mnage - 1)] * xHa + u[1:(Mnage - 1)] +
uH[1:(Mnage - 1)]) * LH[i - 1, 1:(Mnage - 1)] * dt + hiv[1:(Mnage -
1)] * L[i - 1, 1:(Mnage - 1)]
new_IH_react[i, 2:Mnage] <- vHa[1:(Mnage - 1)] * fH[1:(Mnage - 1)] *
(LH[i - 1, 1:(Mnage - 1)]) * dt + rHa[1:(Mnage - 1)] * hH[1:(Mnage -
1)] * RH[i - 1, 1:(Mnage - 1)] * dt
new_NIH_react[i, 2:Mnage] <- vHa[1:(Mnage - 1)] * (1 - fH[1:(Mnage -
1)]) * LH[i - 1, 1:(Mnage - 1)] * dt + rHa[1:(Mnage - 1)] * (1 -
hH[1:(Mnage - 1)]) * RH[i - 1, 1:(Mnage - 1)] * dt
new_actvH_react[i, 2:Mnage] <- vHa[1:(Mnage - 1)] * (LH[i - 1, 1:(Mnage -
1)]) * dt + rHa[1:(Mnage - 1)] * RH[i - 1, 1:(Mnage - 1)] * dt
new_IH[i, 2:Mnage] <- lambda[i - 1, 1:(Mnage - 1)] * pHa[1:(Mnage -
1)] * fH[1:(Mnage - 1)] * (SH[i - 1, 1:(Mnage - 1)] + gHa * RH[i -
1, 1:(Mnage - 1)]) * dt + (vHa[1:(Mnage - 1)] + lambda[i - 1, 1:(Mnage -
1)] * pHa[1:(Mnage - 1)] * xHa) * fH[1:(Mnage - 1)] * LH[
i - 1,
1:(Mnage - 1)
] * dt + rHa[1:(Mnage - 1)] * hH[1:(Mnage - 1)] *
RH[i - 1, 1:(Mnage - 1)] * dt + w * NIH[i - 1, 1:(Mnage - 1)] *
dt
new_IH_noconv[i, 2:Mnage] <- lambda[i - 1, 1:(Mnage - 1)] * pHa[1:(Mnage -
1)] * fH[1:(Mnage - 1)] * (SH[i - 1, 1:(Mnage - 1)] + gHa * RH[i -
1, 1:(Mnage - 1)]) * dt + (vHa[1:(Mnage - 1)] + lambda[i - 1, 1:(Mnage -
1)] * pHa[1:(Mnage - 1)] * xHa) * fH[1:(Mnage - 1)] * LH[
i - 1,
1:(Mnage - 1)
] * dt + rHa[1:(Mnage - 1)] * hH[1:(Mnage - 1)] *
RH[i - 1, 1:(Mnage - 1)] * dt
new_NIH[i, 2:Mnage] <- lambda[i - 1, 1:(Mnage - 1)] * pHa[1:(Mnage -
1)] * (1 - fH[1:(Mnage - 1)]) * (SH[i - 1, 1:(Mnage - 1)] + gHa *
RH[i - 1, 1:(Mnage - 1)]) * dt + (vHa[1:(Mnage - 1)] + lambda[i -
1, 1:(Mnage - 1)] * pHa[1:(Mnage - 1)] * xHa) * (1 - fH[1:(Mnage -
1)]) * LH[i - 1, 1:(Mnage - 1)] * dt + rHa[1:(Mnage - 1)] * (1 -
hH[1:(Mnage - 1)]) * RH[i - 1, 1:(Mnage - 1)] * dt
new_actvH[i, 2:Mnage] <- lambda[i - 1, 1:(Mnage - 1)] * pHa[1:(Mnage -
1)] * SH[i - 1, 1:(Mnage - 1)] * dt + (vHa[1:(Mnage - 1)] + lambda[i -
1, 1:(Mnage - 1)] * pHa[1:(Mnage - 1)] * xHa) * LH[i - 1, 1:(Mnage -
1)] * dt + (rHa[1:(Mnage - 1)] + lambda[i - 1, 1:(Mnage - 1)] *
pHa[1:(Mnage - 1)] * gHa) * RH[i - 1, 1:(Mnage - 1)] * dt
new_notifH[i, 2:Mnage] <- CDRH[2:(Mnage)] * (new_IH[i, 2:Mnage] +
e * new_NIH[i, 2:Mnage])
RH[i, 2:Mnage] <- RH[i - 1, 1:(Mnage - 1)] + nH[1:(Mnage - 1)] * (IH[i -
1, 1:(Mnage - 1)] + NIH[i - 1, 1:(Mnage - 1)]) * dt + CDRH[2:(Mnage)] *
CoT * (new_IH[i, 2:Mnage] + e * new_NIH[i, 2:Mnage]) - (rHa[1:(Mnage -
1)] + gHa * lambda[i - 1, 1:(Mnage - 1)] + u[1:(Mnage - 1)] + uH[1:(Mnage -
1)]) * RH[i - 1, 1:(Mnage - 1)] * dt + hiv[1:(Mnage - 1)] * R[i -
1, 1:(Mnage - 1)]
IH[i, 2:Mnage] <- IH[i - 1, 1:(Mnage - 1)] + (1 - CDRH[2:(Mnage)] *
CoT) * (new_IH[i, 2:Mnage]) - (nH[1:(Mnage - 1)] + u[1:(Mnage -
1)] + uH[1:(Mnage - 1)] + uiHa[1:(Mnage - 1)]) * IH[i - 1, 1:(Mnage -
1)] * dt + hiv[1:(Mnage - 1)] * I[i - 1, 1:(Mnage - 1)]
NIH[i, 2:Mnage] <- NIH[i - 1, 1:(Mnage - 1)] + ((1 - CDRH[2:(Mnage)] *
CoT * e) * new_NIH[i, 2:Mnage]) - (nH[1:(Mnage - 1)] + u[1:(Mnage -
1)] + uH[1:(Mnage - 1)] + uniHa[1:(Mnage - 1)] + w) * NIH[
i - 1,
1:(Mnage - 1)
] * dt + hiv[1:(Mnage - 1)] * NI[i - 1, 1:(Mnage -
1)]
Sv[i, 1] <- 0
Lv[i, 1] <- 0
Rv[i, 1] <- 0
Iv[i, 1] <- 0
NIv[i, 1] <- 0
new_Iv[i, 1] <- 0
new_NIv[i, 1] <- 0
new_Iv_noconv[i, 1] <- 0
new_notifv[i, 1] <- 0
SvH[i, 1] <- 0
LvH[i, 1] <- 0
RvH[i, 1] <- 0
IvH[i, 1] <- 0
NIvH[i, 1] <- 0
new_IvH[i, 1] <- 0
new_NIvH[i, 1] <- 0
new_IvH_noconv[i, 1] <- 0
new_notifvH[i, 1] <- 0
Sv[i, 2:Mnage] <- Sv[i - 1, 1:(Mnage - 1)] - (u[1:(Mnage - 1)] + ((1 -
effI) * lambda[i - 1, 1:(Mnage - 1)])) * Sv[i - 1, 1:(Mnage - 1)] *
dt - hiv[1:(Mnage - 1)] * Sv[i - 1, 1:(Mnage - 1)]
Lv[i, 2:Mnage] <- Lv[i - 1, 1:(Mnage - 1)] + ((1 - effI) * lambda[i -
1, 1:(Mnage - 1)]) * (1 - ((1 - effD) * p[1:(Mnage - 1)])) * (Sv[i -
1, 1:(Mnage - 1)] + g * Rv[i - 1, 1:(Mnage - 1)]) * dt - ((1 -
effD) * v[1:(Mnage - 1)] + ((1 - effI) * lambda[i - 1, 1:(Mnage -
1)]) * ((1 - effD) * p[1:(Mnage - 1)]) * x + u[1:(Mnage - 1)]) *
Lv[i - 1, 1:(Mnage - 1)] * dt - hiv[1:(Mnage - 1)] * Lv[
i - 1,
1:(Mnage - 1)
]
new_Iv[i, 2:Mnage] <- ((1 - effI) * lambda[i - 1, 1:(Mnage - 1)]) *
((1 - effD) * p[1:(Mnage - 1)]) * f[1:(Mnage - 1)] * (Sv[
i - 1,
1:(Mnage - 1)
] + g * Rv[i - 1, 1:((Mnage - 1))]) * dt + ((1 - effD) *
v[1:(Mnage - 1)] + ((1 - effI) * lambda[i - 1, 1:(Mnage - 1)]) *
((1 - effD) * p[1:(Mnage - 1)]) * x) * f[1:(Mnage - 1)] * Lv[i -
1, 1:(Mnage - 1)] * dt + (1 - effD) * r[1:(Mnage - 1)] * h[1:(Mnage -
1)] * Rv[i - 1, 1:(Mnage - 1)] * dt + w * NIv[i - 1, 1:(Mnage -
1)] * dt
new_Iv_noconv[i, 2:Mnage] <- ((1 - effI) * lambda[i - 1, 1:(Mnage -
1)]) * ((1 - effD) * p[1:(Mnage - 1)]) * f[1:(Mnage - 1)] * (Sv[i -
1, 1:(Mnage - 1)] + g * Rv[i - 1, 1:(Mnage - 1)]) * dt + ((1 -
effD) * v[1:(Mnage - 1)] + ((1 - effI) * lambda[i - 1, 1:(Mnage -
1)]) * ((1 - effD) * p[1:(Mnage - 1)]) * x) * f[1:(Mnage - 1)] *
Lv[i - 1, 1:(Mnage - 1)] * dt + (1 - effD) * r[1:(Mnage - 1)] *
h[1:(Mnage - 1)] * Rv[i - 1, 1:(Mnage - 1)] * dt
new_NIv[i, 2:Mnage] <- ((1 - effI) * lambda[i - 1, 1:(Mnage - 1)]) *
((1 - effD) * p[1:(Mnage - 1)]) * (1 - f[1:(Mnage - 1)]) * (Sv[i -
1, 1:(Mnage - 1)] + g * Rv[i - 1, 1:(Mnage - 1)]) * dt + ((1 -
effD) * v[1:(Mnage - 1)] + ((1 - effI) * lambda[i - 1, 1:(Mnage -
1)]) * ((1 - effD) * p[1:(Mnage - 1)]) * x) * (1 - f[1:(Mnage -
1)]) * Lv[i - 1, 1:(Mnage - 1)] * dt + (1 - effD) * r[1:(Mnage -
1)] * (1 - h[1:(Mnage - 1)]) * Rv[i - 1, 1:(Mnage - 1)] * dt
new_notifv[i, 2:Mnage] <- CDR[2:(Mnage)] * (new_Iv[i, 2:Mnage] + e *
new_NIv[i, 2:Mnage])
new_actvv[i, 2:Mnage] <- ((1 - effI) * lambda[i - 1, 1:(Mnage - 1)]) *
((1 - effD) * p[1:(Mnage - 1)]) * Sv[i - 1, 1:(Mnage - 1)] * dt +
(((1 - effD) * v[1:(Mnage - 1)]) + ((1 - effI) * lambda[
i - 1,
1:(Mnage - 1)
]) * ((1 - effD) * p[1:(Mnage - 1)]) * x) * Lv[i -
1, 1:(Mnage - 1)] * dt + (((1 - effD) * r[1:(Mnage - 1)]) + ((1 -
effI) * lambda[i - 1, 1:(Mnage - 1)]) * ((1 - effD) * p[1:(Mnage -
1)]) * g) * Rv[i - 1, 1:(Mnage - 1)] * dt
Rv[i, 2:Mnage] <- Rv[i - 1, 1:(Mnage - 1)] + n[1:(Mnage - 1)] * (Iv[i -
1, 1:(Mnage - 1)] + NIv[i - 1, 1:(Mnage - 1)]) * dt + CDR[2:(Mnage)] *
CoT * (new_Iv[i, 2:Mnage] + e * new_NIv[i, 2:Mnage]) - ((1 - effD) *
r[1:(Mnage - 1)] + g * (1 - effI) * lambda[i - 1, 1:(Mnage - 1)] +
u[1:(Mnage - 1)]) * Rv[i - 1, 1:(Mnage - 1)] * dt - hiv[1:(Mnage -
1)] * Rv[i - 1, 1:(Mnage - 1)]
Iv[i, 2:Mnage] <- Iv[i - 1, 1:(Mnage - 1)] + (1 - CDR[2:(Mnage)] *
CoT) * new_Iv[i, 2:Mnage] - (n[1:(Mnage - 1)] + u[1:((Mnage - 1))] +
ui[1:(Mnage - 1)]) * Iv[i - 1, 1:(Mnage - 1)] * dt - hiv[1:(Mnage -
1)] * Iv[i - 1, 1:(Mnage - 1)]
NIv[i, 2:Mnage] <- NIv[i - 1, 1:(Mnage - 1)] + (1 - CDR[2:(Mnage)] *
CoT * e) * new_NIv[i, 2:Mnage] - (n[1:(Mnage - 1)] + u[1:(Mnage -
1)] + uni[1:(Mnage - 1)] + w) * NIv[i - 1, 1:(Mnage - 1)] * dt -
hiv[1:(Mnage - 1)] * NIv[i - 1, 1:(Mnage - 1)]
SvH[i, 2:Mnage] <- SvH[i - 1, 1:(Mnage - 1)] - (u[1:(Mnage - 1)] +
uH[1:(Mnage - 1)] + ((1 - (effI * VEH)) * lambda[i - 1, 1:(Mnage -
1)])) * SvH[i - 1, 1:(Mnage - 1)] * dt + hiv[1:(Mnage - 1)] * Sv[i -
1, 1:(Mnage - 1)]
LvH[i, 2:Mnage] <- LvH[i - 1, 1:(Mnage - 1)] + ((1 - (effI * VEH)) *
lambda[i - 1, 1:(Mnage - 1)]) * (1 - ((1 - (effD * VEH)) * pHa[1:(Mnage -
1)])) * (SvH[i - 1, 1:(Mnage - 1)] + gHa * RvH[i - 1, 1:(Mnage -
1)]) * dt - ((1 - (effD * VEH)) * vHa[1:(Mnage - 1)] + ((1 - (effI *
VEH)) * lambda[i - 1, 1:(Mnage - 1)]) * ((1 - (effD * VEH)) * pHa[1:(Mnage -
1)]) * xHa + u[1:(Mnage - 1)] + uH[1:(Mnage - 1)]) * LvH[
i - 1,
1:(Mnage - 1)
] * dt + hiv[1:(Mnage - 1)] * Lv[i - 1, 1:(Mnage -
1)]
new_IvH[i, 2:Mnage] <- ((1 - (effI * VEH)) * lambda[i - 1, 1:(Mnage -
1)]) * ((1 - (effD * VEH)) * pHa[1:(Mnage - 1)]) * fH[1:(Mnage -
1)] * (SvH[i - 1, 1:(Mnage - 1)] + gHa * RvH[i - 1, 1:((Mnage -
1))]) * dt + ((1 - (effD * VEH)) * vHa[1:(Mnage - 1)] + ((1 - (effI *
VEH)) * lambda[i - 1, 1:(Mnage - 1)]) * ((1 - (effD * VEH)) * pHa[1:(Mnage -
1)]) * xHa) * fH[1:(Mnage - 1)] * LvH[i - 1, 1:(Mnage - 1)] * dt +
(1 - (effD * VEH)) * rHa[1:(Mnage - 1)] * hH[1:(Mnage - 1)] * RvH[i -
1, 1:(Mnage - 1)] * dt + w * NIvH[i - 1, 1:(Mnage - 1)] * dt
new_IvH_noconv[i, 2:Mnage] <- ((1 - (effI * VEH)) * lambda[
i - 1,
1:(Mnage - 1)
]) * ((1 - (effD * VEH)) * pHa[1:(Mnage - 1)]) * fH[1:(Mnage -
1)] * (SvH[i - 1, 1:(Mnage - 1)] + gHa * RvH[i - 1, 1:(Mnage -
1)]) * dt + ((1 - (effD * VEH)) * vHa[1:(Mnage - 1)] + ((1 - (effI *
VEH)) * lambda[i - 1, 1:(Mnage - 1)]) * ((1 - (effD * VEH)) * pHa[1:(Mnage -
1)]) * xHa) * fH[1:(Mnage - 1)] * LvH[i - 1, 1:(Mnage - 1)] * dt +
(1 - (effD * VEH)) * rHa[1:(Mnage - 1)] * hH[1:(Mnage - 1)] * RvH[i -
1, 1:(Mnage - 1)] * dt
new_NIvH[i, 2:Mnage] <- ((1 - (effI * VEH)) * lambda[i - 1, 1:(Mnage -
1)]) * ((1 - (effD * VEH)) * pHa[1:(Mnage - 1)]) * (1 - fH[1:(Mnage -
1)]) * (SvH[i - 1, 1:(Mnage - 1)] + gHa * RvH[i - 1, 1:(Mnage -
1)]) * dt + ((1 - (effD * VEH)) * vHa[1:(Mnage - 1)] + ((1 - (effI *
VEH)) * lambda[i - 1, 1:(Mnage - 1)]) * ((1 - (effD * VEH)) * pHa[1:(Mnage -
1)]) * xHa) * (1 - fH[1:(Mnage - 1)]) * LvH[i - 1, 1:(Mnage - 1)] *
dt + (1 - (effD * VEH)) * rHa[1:(Mnage - 1)] * (1 - hH[1:(Mnage -
1)]) * RvH[i - 1, 1:(Mnage - 1)] * dt
new_notifvH[i, 2:Mnage] <- CDRH[2:(Mnage)] * (new_IvH[i, 2:Mnage] +
e * new_NIvH[i, 2:Mnage])
new_actvvH[i, 2:Mnage] <- ((1 - (effI * VEH)) * lambda[i - 1, 1:(Mnage -
1)]) * ((1 - (effD * VEH)) * pHa[1:(Mnage - 1)]) * SvH[i - 1, 1:(Mnage -
1)] * dt + (((1 - (effD * VEH)) * vHa[1:(Mnage - 1)]) + ((1 - (effI *
VEH)) * lambda[i - 1, 1:(Mnage - 1)]) * ((1 - (effD * VEH)) * pHa[1:(Mnage -
1)]) * xHa) * LvH[i - 1, 1:(Mnage - 1)] * dt + (((1 - (effD * VEH)) *
rHa[1:(Mnage - 1)]) + ((1 - (effI * VEH)) * lambda[i - 1, 1:(Mnage -
1)]) * ((1 - (effD * VEH)) * pHa[1:(Mnage - 1)]) * gHa) * RvH[i -
1, 1:(Mnage - 1)] * dt
RvH[i, 2:Mnage] <- RvH[i - 1, 1:(Mnage - 1)] + nH[1:(Mnage - 1)] *
(IvH[i - 1, 1:(Mnage - 1)] + NIvH[i - 1, 1:(Mnage - 1)]) * dt +
CDRH[2:(Mnage)] * CoT * (new_IvH[i, 2:Mnage] + e * new_NIvH[
i,
2:Mnage
]) - ((1 - (effD * VEH)) * rHa[1:(Mnage - 1)] + gHa *
(1 - (effI * VEH)) * lambda[i - 1, 1:(Mnage - 1)] + u[1:(Mnage -
1)] + uH[1:(Mnage - 1)]) * RvH[i - 1, 1:(Mnage - 1)] * dt + hiv[1:(Mnage -
1)] * Rv[i - 1, 1:(Mnage - 1)]
IvH[i, 2:Mnage] <- IvH[i - 1, 1:(Mnage - 1)] + (1 - CDRH[2:(Mnage)] *
CoT) * new_IvH[i, 2:Mnage] - (nH[1:(Mnage - 1)] + u[1:(Mnage -
1)] + uH[1:(Mnage - 1)] + uiHa[1:(Mnage - 1)]) * IvH[i - 1, 1:(Mnage -
1)] * dt + hiv[1:(Mnage - 1)] * Iv[i - 1, 1:(Mnage - 1)]
NIvH[i, 2:Mnage] <- NIvH[i - 1, 1:(Mnage - 1)] + (1 - CDRH[2:(Mnage)] *
CoT * e) * new_NIvH[i, 2:Mnage] - (nH[1:(Mnage - 1)] + u[1:(Mnage -
1)] + uH[1:(Mnage - 1)] + uniHa[1:(Mnage - 1)] + w) * NIvH[i -
1, 1:(Mnage - 1)] * dt + hiv[1:(Mnage - 1)] * NIv[i - 1, 1:(Mnage -
1)]
S2 <- S[i, ] + Sv[i, ] * (d[i, ] * (1 - thetaS[i, ])) - thetaS[i, ] * S[i, ]
L2 <- L[i, ] + Lv[i, ] * (d[i, ] * (1 - thetaL[i, ])) - thetaL[i, ] * L[i, ]
R2 <- R[i, ] + Rv[i, ] * (d[i, ] * (1 - thetaR[i, ])) - thetaR[i, ] * R[i, ]
I2 <- I[i, ] + Iv[i, ] * d[i, ]
NI2 <- NI[i, ] + NIv[i, ] * d[i, ]
Sv2 <- Sv[i, ] - Sv[i, ] * (d[i, ] * (1 - thetaS[i, ])) + thetaS[i, ] * S[i, ]
Lv2 <- Lv[i, ] - Lv[i, ] * (d[i, ] * (1 - thetaL[i, ])) + thetaL[i, ] * L[i, ]
Rv2 <- Rv[i, ] - Rv[i, ] * (d[i, ] * (1 - thetaR[i, ])) + thetaR[i, ] * R[i, ]
Iv2 <- Iv[i, ] - Iv[i, ] * (d[i, ])
NIv2 <- NIv[i, ] - NIv[i, ] * (d[i, ])
SH2 <- SH[i, ] + SvH[i, ] * (dH[i, ] * (1 - thetaSH[i, ])) - thetaSH[i, ] * SH[i, ]
LH2 <- LH[i, ] + LvH[i, ] * (dH[i, ] * (1 - thetaLH[i, ])) - thetaLH[i, ] * LH[i, ]
RH2 <- RH[i, ] + RvH[i, ] * (dH[i, ] * (1 - thetaRH[i, ])) - thetaRH[i, ] * RH[i, ]
IH2 <- IH[i, ] + IvH[i, ] * dH[i, ]
NIH2 <- NIH[i, ] + NIvH[i, ] * dH[i, ]
SvH2 <- SvH[i, ] - SvH[i, ] * (dH[i, ] * (1 - thetaSH[i, ])) + thetaSH[i, ] * SH[i, ]
LvH2 <- LvH[i, ] - LvH[i, ] * (dH[i, ] * (1 - thetaLH[i, ])) + thetaLH[i, ] * LH[i, ]
RvH2 <- RvH[i, ] - RvH[i, ] * (dH[i, ] * (1 - thetaRH[i, ])) + thetaRH[i, ] * RH[i, ]
IvH2 <- IvH[i, ] - IvH[i, ] * (dH[i, ])
NIvH2 <- NIvH[i, ] - NIvH[i, ] * (dH[i, ])
if (vaccine == 1) {
num_vac[i, ] <- (S[i, ] + L[i, ] + R[i, ] + Sv[i, ] + Lv[i, ] +
Rv[i, ] + SH[i, ] + LH[i, ] + RH[i, ] + SvH[i, ] + LvH[i, ] +
RvH[i, ]) * thetaV2[i, ]
}
if (vaccine == 2) {
num_vac[i, ] <- (S[i, ] + L[i, ] + R[i, ] + Sv[i, ] + Lv[i, ] +
Rv[i, ] + SH[i, ] + LH[i, ] + RH[i, ] + SvH[i, ] + LvH[i, ] +
RvH[i, ]) * thetaV2[i, ]
}
if (vaccine == 3) {
num_vac[i, ] <- (S[i, ] + L[i, ] + R[i, ] + Sv[i, ] + Lv[i, ] +
Rv[i, ] + SH[i, ] + LH[i, ] + RH[i, ] + SvH[i, ] + LvH[i, ] +
RvH[i, ]) * thetaV2[i, ]
}
S[i, ] <- S2
L[i, ] <- L2
R[i, ] <- R2
I[i, ] <- I2
NI[i, ] <- NI2
Sv[i, ] <- Sv2
Lv[i, ] <- Lv2
Rv[i, ] <- Rv2
Iv[i, ] <- Iv2
NIv[i, ] <- NIv2
SH[i, ] <- SH2
LH[i, ] <- LH2
RH[i, ] <- RH2
IH[i, ] <- IH2
NIH[i, ] <- NIH2
SvH[i, ] <- SvH2
LvH[i, ] <- LvH2
RvH[i, ] <- RvH2
IvH[i, ] <- IvH2
NIvH[i, ] <- NIvH2
psize[i] <- sum(
S[i, ], L[i, ], R[i, ], I[i, ], NI[i, ], Sv[i, ],
Lv[i, ], Rv[i, ], Iv[i, ], NIv[i, ]
)
psizeH[i] <- sum(SH[i, ], LH[i, ], RH[i, ], IH[i, ], NIH[i, ], SvH[i, ], LvH[i, ], RvH[i, ], IvH[i, ], NIvH[i, ])
psizeALL[i] <- sum(S[i, ], L[i, ], R[i, ], I[i, ], NI[i, ], Sv[i, ], Lv[i, ], Rv[i, ], Iv[i, ], NIv[i, ], SH[i, ], LH[i, ], RH[i, ], IH[i, ], NIH[i, ], SvH[i, ], LvH[i, ], RvH[i, ], IvH[i, ], NIvH[i, ])
psize014[i] <- sum(
S[i, 1:15], L[i, 1:15], R[i, 1:15], I[i, 1:15],
NI[i, 1:15], Sv[i, 1:15], Lv[i, 1:15], Iv[i, 1:15], NIv[i, 1:15],
Rv[i, 1:15]
)
psize1554[i] <- sum(
S[i, 16:55], L[i, 16:55], R[i, 16:55], I[i, 16:55],
NI[i, 16:55], Sv[i, 16:55], Lv[i, 16:55], Iv[i, 16:55], NIv[
i,
16:55
], Rv[i, 16:55]
)
psize5564[i] <- sum(
S[i, 56:65], L[i, 56:65], R[i, 56:65], I[i, 56:65],
NI[i, 56:65], Sv[i, 56:65], Lv[i, 56:65], Iv[i, 56:65], NIv[
i,
56:65
], Rv[i, 56:65]
)
psize65plus[i] <- sum(
S[i, 66:Mnage], L[i, 66:Mnage], R[i, 66:Mnage],
I[i, 66:Mnage], NI[i, 66:Mnage], Sv[i, 66:Mnage], Lv[i, 66:Mnage],
Rv[i, 66:Mnage], Iv[i, 66:Mnage], NIv[i, 66:Mnage]
)
psize55plus[i] <- sum(
S[i, 56:Mnage], L[i, 56:Mnage], R[i, 56:Mnage],
I[i, 56:Mnage], NI[i, 56:Mnage], Sv[i, 56:Mnage], Lv[i, 56:Mnage],
Rv[i, 56:Mnage], Iv[i, 56:Mnage], NIv[i, 56:Mnage]
)
psize55minus[i] <- sum(
S[i, 1:55], L[i, 1:55], R[i, 1:55], I[i, 1:55],
NI[i, 1:55], Sv[i, 1:55], Lv[i, 1:55], Rv[i, 1:55], Iv[i, 1:55],
NIv[i, 1:55]
)
psizeVX[i] <- sum(Sv[i, ], Lv[i, ], Rv[i, ], Iv[i, ], NIv[i, ])
psizeVX9[i] <- sum(Sv[i, 10], Lv[i, 10], Iv[i, 10], NIv[i, 10], Rv[
i,
10
])
psizeVX9100[i] <- sum(
Sv[i, 10:101], Lv[i, 10:101], Iv[i, 10:101],
NIv[i, 10:101], Rv[i, 10:101]
)
psizeNOVX[i] <- sum(S[i, ], L[i, ], R[i, ], I[i, ], NI[i, ])
psizeNOVX9[i] <- sum(S[i, 10], L[i, 10], I[i, 10], NI[i, 10], R[
i,
10
])
psizeNOVX9100[i] <- sum(
S[i, 10:101], L[i, 10:101], I[i, 10:101],
NI[i, 10:101], R[i, 10:101]
)
psize1559[i] <- sum(
S[i, 16:60], L[i, 16:60], R[i, 16:60], I[i, 16:60],
NI[i, 16:60], Sv[i, 16:60], Lv[i, 16:60], Rv[i, 16:60], Iv[i, 16:60],
NIv[i, 16:60]
)
psize1529[i] <- sum(
S[i, 16:30], L[i, 16:30], R[i, 16:30], I[i, 16:30],
NI[i, 16:30], Sv[i, 16:30], Lv[i, 16:30], Rv[i, 16:30], Iv[i, 16:30],
NIv[i, 16:30]
)
psize3044[i] <- sum(
S[i, 31:45], L[i, 31:45], R[i, 31:45], I[i, 31:45],
NI[i, 31:45], Sv[i, 31:45], Lv[i, 31:45], Rv[i, 31:45], Iv[i, 31:45],
NIv[i, 31:45]
)
psize4559[i] <- sum(
S[i, 46:60], L[i, 46:60], R[i, 46:60], I[i, 46:60],
NI[i, 46:60], Sv[i, 46:60], Lv[i, 46:60], Rv[i, 46:60], Iv[i, 46:60],
NIv[i, 46:60]
)
psize60plus[i] <- sum(
S[i, 61:Mnage], L[i, 61:Mnage], R[i, 61:Mnage],
I[i, 61:Mnage], NI[i, 61:Mnage], Sv[i, 61:Mnage], Lv[i, 61:Mnage],
Rv[i, 61:Mnage], Iv[i, 61:Mnage], NIv[i, 61:Mnage]
)
psize0509[i] <- sum(
S[i, 6:10], L[i, 6:10], R[i, 6:10], I[i, 6:10],
NI[i, 6:10], Sv[i, 6:10], Lv[i, 6:10], Rv[i, 6:10], Iv[i, 6:10],
NIv[i, 6:10]
)
psize1019[i] <- sum(
S[i, 11:20], L[i, 11:20], R[i, 11:20], I[i, 11:20],
NI[i, 11:20], Sv[i, 11:20], Lv[i, 11:20], Rv[i, 11:20], Iv[i, 11:20],
NIv[i, 11:20]
)
psize2029[i] <- sum(
S[i, 21:30], L[i, 21:30], R[i, 21:30], I[i, 21:30],
NI[i, 21:30], Sv[i, 21:30], Lv[i, 21:30], Rv[i, 21:30], Iv[i, 21:30],
NIv[i, 21:30]
)
psize3039[i] <- sum(
S[i, 31:40], L[i, 31:40], R[i, 31:40], I[i, 31:40],
NI[i, 31:40], Sv[i, 31:40], Lv[i, 31:40], Rv[i, 31:40], Iv[i, 31:40],
NIv[i, 31:40]
)
psize4049[i] <- sum(
S[i, 41:50], L[i, 41:50], R[i, 41:50], I[i, 41:50],
NI[i, 41:50], Sv[i, 41:50], Lv[i, 41:50], Rv[i, 41:50], Iv[i, 41:50],
NIv[i, 41:50]
)
psize5059[i] <- sum(
S[i, 51:60], L[i, 51:60], R[i, 51:60], I[i, 51:60],
NI[i, 51:60], Sv[i, 51:60], Lv[i, 51:60], Rv[i, 51:60], Iv[i, 51:60],
NIv[i, 51:60]
)
psize6069[i] <- sum(
S[i, 61:70], L[i, 61:70], R[i, 61:70], I[i, 61:70],
NI[i, 61:70], Sv[i, 61:70], Lv[i, 61:70], Rv[i, 61:70], Iv[i, 61:70],
NIv[i, 61:70]
)
psize70plus[i] <- sum(
S[i, 71:Mnage], L[i, 71:Mnage], R[i, 71:Mnage],
I[i, 71:Mnage], NI[i, 71:Mnage], Sv[i, 71:Mnage], Lv[i, 71:Mnage],
Rv[i, 71:Mnage], Iv[i, 71:Mnage], NIv[i, 71:Mnage]
)
psize5574[i] <- sum(
S[i, 56:75], L[i, 56:75], R[i, 56:75], I[i, 56:75],
NI[i, 56:75], Sv[i, 56:75], Lv[i, 56:75], Rv[i, 56:75], Iv[i, 56:75],
NIv[i, 56:75]
)
psize75plus[i] <- sum(
S[i, 76:Mnage], L[i, 76:Mnage], R[i, 76:Mnage],
I[i, 76:Mnage], NI[i, 76:Mnage], Sv[i, 76:Mnage], Lv[i, 76:Mnage],
Rv[i, 76:Mnage], Iv[i, 76:Mnage], NIv[i, 76:Mnage]
)
psize1524[i] <- sum(
S[i, 16:25], L[i, 16:25], R[i, 16:25], I[i, 16:25],
NI[i, 16:25], Sv[i, 16:25], Lv[i, 16:25], Rv[i, 16:25], Iv[i, 16:25],
NIv[i, 16:25]
)
psize2554[i] <- sum(
S[i, 26:55], L[i, 26:55], R[i, 26:55], I[i, 26:55],
NI[i, 26:55], Sv[i, 26:55], Lv[i, 26:55], Rv[i, 26:55], Iv[i, 26:55],
NIv[i, 26:55]
)
psize15plus[i] <- sum(
S[i, 16:Mnage], L[i, 16:Mnage], R[i, 16:Mnage],
I[i, 16:Mnage], NI[i, 16:Mnage], Sv[i, 16:Mnage], Lv[i, 16:Mnage],
Rv[i, 16:Mnage], Iv[i, 16:Mnage], NIv[i, 16:Mnage]
)
psize1549[i] <- psize1559[i] - psize5059[i]
agepopall[i, 1:Mnage] <- S[i, 1:Mnage] + L[i, 1:Mnage] + R[i, 1:Mnage] +
I[i, 1:Mnage] + NI[i, 1:Mnage] + Sv[i, 1:Mnage] + Lv[i, 1:Mnage] +
Rv[i, 1:Mnage] + Iv[i, 1:Mnage] + NIv[i, 1:Mnage] + SH[i, 1:Mnage] +
LH[i, 1:Mnage] + RH[i, 1:Mnage] + IH[i, 1:Mnage] + NIH[i, 1:Mnage] +
SvH[i, 1:Mnage] + LvH[i, 1:Mnage] + RvH[i, 1:Mnage] + IvH[i, 1:Mnage] +
NIvH[i, 1:Mnage]
psize04H[i] <- sum(
SH[i, 1:5], LH[i, 1:5], RH[i, 1:5], IH[i, 1:5],