Model v1, with call to python

Analysis/ode.R

@@ -17,11 +17,11 @@ seirds.f <- function(t, y, k) {
   waning = k[7]
 
   # Saying infec rate of S in contact with E same as contact with I
-  dS <- epsilon - (beta*E + beta*I)*S + waning*R - mu*S
-  dE <- beta*S*E + beta*S*I - (delta+mu)*E
-  dI <- delta*E - mu*I - gamma_r*I
-  dR <- gamma_r*I - (waning+mu)*R
-  dD <- gamma_d*I
+  dS <- epsilon - (beta*E + beta*I)*S + waning*R - gamma_d*S
+  dE <- beta*S*E + beta*S*I - (delta+gamma_d)*E
+  dI <- delta*E - (1+gamma_d)*I
+  dR <- (1-mu)*I - (waning+gamma_d)*R
+  dD <- mu*I
   
   return(as.matrix(c(dS, dE, dI, dR, dD)))
 }
@@ -33,30 +33,23 @@ library(reticulate)
 #conda_install(envname = "r-reticulate", packages="pygraphviz")
 source_python('prep_model.py')
 
-# a) a=0.5, b=1, S(0)=0.9, I(0)=0.1, R(0)=0
-seirds.params <- c(0.7316455696202532,    # beta
-                   0.020253164556962026,  # delta
-                   0.09113924050632911,   # gamma_r
-                   0.002531645569620253,  # gamma_d
-                   0.0034602076124567475, # mu
-                   0.0,                   # epsilon
-                   0.0)                   # waning
+# Obtained from prep_model.py
+seirds.params <- c(beta,     # beta
+                   delta,    # delta
+                   gamma_r,  # gamma_r
+                   gamma_d,  # gamma_d
+                   mu,       # mu
+                   epsilon,  # epsilon
+                   omega)    # waning
 
-S <- 62
-E <- 8
-I <- 288
-R <- 36
-D <- 1
-
-N <- S+E+I+R+D
-S <- S/N
-E <- E/N
-I <- I/N
-R <- R/N
-D <- D/N
+S <- S/length(color_d)
+E <- E/length(color_d)
+I <- (I_R+I_D)/length(color_d)
+R <- R/length(color_d)
+D <- D/length(color_d)
 
 tmin <- 0
-tmax <- 7
+tmax <- 5
 
 library(pracma)
 seirds.ode.sol <- ode45(f = function(t,y){seirds.f(t,y,k=seirds.params)},
@@ -86,5 +79,6 @@ plot.seirds <- function(sol, method){
 }
 
 plot.seirds(seirds.ode.sol, "ODE45")
-
-print(seirds.ode.sol$y[tmax,1]+seirds.ode.sol$y[tmax,2]+seirds.ode.sol$y[tmax,3]+seirds.ode.sol$y[tmax,4]+seirds.ode.sol$y[tmax,5])
+ggsave("SERIDS.pdf")
+# Sanity check: Make sure sums to ~1.0
+sum(tail(seirds.ode.sol$y,1))

Analysis/prep_model.py

@@ -85,12 +85,13 @@ for node in A:
 
 # Params
 beta = (I_R+I_D)/len(A) # rate of infec (I/total?)
-delta = E/len(A) # symptom appearance rate (E/total?)
+#delta = E/len(A) # symptom appearance rate (E/total?)
+delta = 1 # incubation period
 gamma_r = R/len(A) # recov rate (R/total?)
 gamma_d = D/len(A) # death rate (D/total?)
 mu = D/(I_R+I_D) # fatality ratio (D/I)
 epsilon = ep_tmp/len(A) # infected import rate
-omega = 0 # waning immunity rate
+omega = 1 # waning immunity rate
 
 
 print("Model Compartments:")
@@ -109,3 +110,5 @@ print("gamma_r:", str(gamma_r))
 print("gamma_d:", str(gamma_d))
 print("mu:", str(mu))
 print("epsilon:", str(epsilon))
+print("omega:", str(omega))
+