scratch code

Author: paigemiller

.lintr

@@ -1,2 +1,5 @@
-linters: linters_with_defaults(object_usage_linter = NULL)
+linters: linters_with_defaults(
+    object_usage_linter = NULL,
+    object_name_lintr = NULL
+    )
 encoding: "UTF-8"

scratch/test-ngm.R

@@ -0,0 +1,89 @@
+# script to calculate next generation for some basic models
+
+library(epimdr2)
+
+##### SEIR model ###########
+# example from package vignette
+istates <- c("E", "I")
+flist <- c(dEdt = quote(beta * S * I / N), dIdt = quote(0))
+Vm1 <- quote(mu * E + sigma * E)
+Vm2 <- quote(mu * I + alpha * I + gamma * I)
+Vp1 <- 0
+Vp2 <- quote(sigma * E)
+V1 <- substitute(a - b, list(a = Vm1, b = Vp1))
+V2 <- substitute(a - b, list(a = Vm2, b = Vp2))
+vlist <- c(V1, V2)
+params <- list(mu = 0, alpha = 0, beta = 5, gamma = .8, sigma = 1.2, N = 1)
+df <- list(S = 1, E = 0, I = 0, R = 0)
+nextgenR0(
+    Istates = istates, Flist = flist,
+    Vlist = vlist, parameters = params, dfe = df
+)
+params$beta / params$gamma
+
+###### SIR Model with two risk groups (high and low) #########
+# example from keeling and rohani
+istates <- c("IH", "IL")
+flist <- c(
+    dIHdt = quote(bHH * SH * IH + bHL * SH * IL),
+    dILdt = quote(bLH * SL * IH + bLL * SL * IL)
+)
+Vm1 <- quote(gamma * IH)
+Vm2 <- quote(gamma * IL)
+Vp1 <- 0
+Vp2 <- 0
+V1 <- substitute(a - b, list(a = Vm1, b = Vp1))
+V2 <- substitute(a - b, list(a = Vm2, b = Vp2))
+vlist <- c(V1, V2)
+params <- list(
+    bHH = 10, bHL = 0.1,
+    bLH = 0.1, bLL = 1,
+    gamma = 1
+)
+df <- list(
+    SH = 0.2, SL = 0.8,
+    IH = 0, IL = 0,
+    RH = 0, RL = 0
+)
+nextgenR0(Istates = istates, Flist = flist, Vlist = vlist, parameters = params, dfe = df)
+
+J <- matrix(c(
+    params$bHH * df$SH - params$gamma, params$bHL * df$SH,
+    params$bLH * df$SL, params$bLL * df$SL - params$gamma
+), nrow = 2)
+# when params$gamma = 1, R0=
+(params$bHH * df$SH + params$bLH * df$SL) * (1 - (norm(eigen(J)$vectors) - 1)) +
+    (params$bHL * df$SH + params$bLL * df$SL) * (norm(eigen(J)$vectors) - 1)
+(params$bHH * df$SH + params$bLH * df$SL) * .9376 +
+    (params$bHL * df$SH + params$bLL * df$SL) * .0624
+
+####### SIR Model with 3 classes ######
+# K, C, G: kids, core, general
+istates <- c("IK", "IC", "IG")
+flist <- c(
+    dIKdt = quote(bKK * SK * IK + bKC * SK * IC + bKG * SK * IG),
+    dICdt = quote(bCK * SC * IK + bCC * SC * IC + bCG * SC * IG),
+    dIGdt = quote(bGK * SG * IK + bGC * SG * IC + bGG * SG * IG)
+)
+Vm1 <- quote(gamma * IK)
+Vm2 <- quote(gamma * IC)
+Vm3 <- quote(gamma * IG)
+Vp1 <- 0
+Vp2 <- 0
+Vp3 <- 0
+V1 <- substitute(a - b, list(a = Vm1, b = Vp1))
+V2 <- substitute(a - b, list(a = Vm2, b = Vp2))
+V3 <- substitute(a - b, list(a = Vm3, b = Vp3))
+vlist <- c(V1, V2, V3)
+params <- list(
+    bKK = 10, bKC = 1, bKG = 1,
+    bCK = 1, bCC = 10, bCG = 1,
+    bGK = 1, bGC = 1, bGG = 1,
+    gamma = 1
+)
+df <- list(
+    SK = 0.1, SC = 0.1, SG = 0.8,
+    IK = 0, IC = 0, IG = 0,
+    RK = 0, RC = 0, RG = 0
+)
+nextgenR0(Istates = istates, Flist = flist, Vlist = vlist, parameters = params, dfe = df)