|
| 1 | +# script to calculate next generation for some basic models |
| 2 | + |
| 3 | +library(epimdr2) |
| 4 | + |
| 5 | +##### SEIR model ########### |
| 6 | +# example from package vignette |
| 7 | +istates <- c("E", "I") |
| 8 | +flist <- c(dEdt = quote(beta * S * I / N), dIdt = quote(0)) |
| 9 | +Vm1 <- quote(mu * E + sigma * E) |
| 10 | +Vm2 <- quote(mu * I + alpha * I + gamma * I) |
| 11 | +Vp1 <- 0 |
| 12 | +Vp2 <- quote(sigma * E) |
| 13 | +V1 <- substitute(a - b, list(a = Vm1, b = Vp1)) |
| 14 | +V2 <- substitute(a - b, list(a = Vm2, b = Vp2)) |
| 15 | +vlist <- c(V1, V2) |
| 16 | +params <- list(mu = 0, alpha = 0, beta = 5, gamma = .8, sigma = 1.2, N = 1) |
| 17 | +df <- list(S = 1, E = 0, I = 0, R = 0) |
| 18 | +nextgenR0( |
| 19 | + Istates = istates, Flist = flist, |
| 20 | + Vlist = vlist, parameters = params, dfe = df |
| 21 | +) |
| 22 | +params$beta / params$gamma |
| 23 | + |
| 24 | +###### SIR Model with two risk groups (high and low) ######### |
| 25 | +# example from keeling and rohani |
| 26 | +istates <- c("IH", "IL") |
| 27 | +flist <- c( |
| 28 | + dIHdt = quote(bHH * SH * IH + bHL * SH * IL), |
| 29 | + dILdt = quote(bLH * SL * IH + bLL * SL * IL) |
| 30 | +) |
| 31 | +Vm1 <- quote(gamma * IH) |
| 32 | +Vm2 <- quote(gamma * IL) |
| 33 | +Vp1 <- 0 |
| 34 | +Vp2 <- 0 |
| 35 | +V1 <- substitute(a - b, list(a = Vm1, b = Vp1)) |
| 36 | +V2 <- substitute(a - b, list(a = Vm2, b = Vp2)) |
| 37 | +vlist <- c(V1, V2) |
| 38 | +params <- list( |
| 39 | + bHH = 10, bHL = 0.1, |
| 40 | + bLH = 0.1, bLL = 1, |
| 41 | + gamma = 1 |
| 42 | +) |
| 43 | +df <- list( |
| 44 | + SH = 0.2, SL = 0.8, |
| 45 | + IH = 0, IL = 0, |
| 46 | + RH = 0, RL = 0 |
| 47 | +) |
| 48 | +nextgenR0(Istates = istates, Flist = flist, Vlist = vlist, parameters = params, dfe = df) |
| 49 | + |
| 50 | +J <- matrix(c( |
| 51 | + params$bHH * df$SH - params$gamma, params$bHL * df$SH, |
| 52 | + params$bLH * df$SL, params$bLL * df$SL - params$gamma |
| 53 | +), nrow = 2) |
| 54 | +# when params$gamma = 1, R0= |
| 55 | +(params$bHH * df$SH + params$bLH * df$SL) * (1 - (norm(eigen(J)$vectors) - 1)) + |
| 56 | + (params$bHL * df$SH + params$bLL * df$SL) * (norm(eigen(J)$vectors) - 1) |
| 57 | +(params$bHH * df$SH + params$bLH * df$SL) * .9376 + |
| 58 | + (params$bHL * df$SH + params$bLL * df$SL) * .0624 |
| 59 | + |
| 60 | +####### SIR Model with 3 classes ###### |
| 61 | +# K, C, G: kids, core, general |
| 62 | +istates <- c("IK", "IC", "IG") |
| 63 | +flist <- c( |
| 64 | + dIKdt = quote(bKK * SK * IK + bKC * SK * IC + bKG * SK * IG), |
| 65 | + dICdt = quote(bCK * SC * IK + bCC * SC * IC + bCG * SC * IG), |
| 66 | + dIGdt = quote(bGK * SG * IK + bGC * SG * IC + bGG * SG * IG) |
| 67 | +) |
| 68 | +Vm1 <- quote(gamma * IK) |
| 69 | +Vm2 <- quote(gamma * IC) |
| 70 | +Vm3 <- quote(gamma * IG) |
| 71 | +Vp1 <- 0 |
| 72 | +Vp2 <- 0 |
| 73 | +Vp3 <- 0 |
| 74 | +V1 <- substitute(a - b, list(a = Vm1, b = Vp1)) |
| 75 | +V2 <- substitute(a - b, list(a = Vm2, b = Vp2)) |
| 76 | +V3 <- substitute(a - b, list(a = Vm3, b = Vp3)) |
| 77 | +vlist <- c(V1, V2, V3) |
| 78 | +params <- list( |
| 79 | + bKK = 10, bKC = 1, bKG = 1, |
| 80 | + bCK = 1, bCC = 10, bCG = 1, |
| 81 | + bGK = 1, bGC = 1, bGG = 1, |
| 82 | + gamma = 1 |
| 83 | +) |
| 84 | +df <- list( |
| 85 | + SK = 0.1, SC = 0.1, SG = 0.8, |
| 86 | + IK = 0, IC = 0, IG = 0, |
| 87 | + RK = 0, RC = 0, RG = 0 |
| 88 | +) |
| 89 | +nextgenR0(Istates = istates, Flist = flist, Vlist = vlist, parameters = params, dfe = df) |
0 commit comments