90 lines
2.6 KiB
R
90 lines
2.6 KiB
R
## Set Working Directory to file directory - RStudio approach
|
|
setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
|
|
|
|
seirds.f <- function(t, y, k) {
|
|
S <- y[1]
|
|
E <- y[2]
|
|
I <- y[3]
|
|
R <- y[4]
|
|
D <- y[5]
|
|
|
|
beta = k[1]
|
|
delta = k[2]
|
|
gamma_r = k[3]
|
|
gamma_d = k[4]
|
|
mu = k[5]
|
|
epsilon = k[6]
|
|
waning = k[7]
|
|
|
|
# Saying infec rate of S in contact with E same as contact with I
|
|
dS <- epsilon - (beta*E + beta*I)*S + waning*R - mu*S
|
|
dE <- beta*S*E + beta*S*I - (delta+mu)*E
|
|
dI <- delta*E - mu*I - gamma_r*I
|
|
dR <- gamma_r*I - (waning+mu)*R
|
|
dD <- gamma_d*I
|
|
|
|
return(as.matrix(c(dS, dE, dI, dR, dD)))
|
|
}
|
|
|
|
library(reticulate)
|
|
#conda_install(envname = "r-reticulate", packages="networkx")
|
|
#conda_install(envname = "r-reticulate", packages="matplotlib")
|
|
#conda_install(envname = "r-reticulate", packages="pydot")
|
|
#conda_install(envname = "r-reticulate", packages="pygraphviz")
|
|
source_python('prep_model.py')
|
|
|
|
# a) a=0.5, b=1, S(0)=0.9, I(0)=0.1, R(0)=0
|
|
seirds.params <- c(0.7316455696202532, # beta
|
|
0.020253164556962026, # delta
|
|
0.09113924050632911, # gamma_r
|
|
0.002531645569620253, # gamma_d
|
|
0.0034602076124567475, # mu
|
|
0.0, # epsilon
|
|
0.0) # waning
|
|
|
|
S <- 62
|
|
E <- 8
|
|
I <- 288
|
|
R <- 36
|
|
D <- 1
|
|
|
|
N <- S+E+I+R+D
|
|
S <- S/N
|
|
E <- E/N
|
|
I <- I/N
|
|
R <- R/N
|
|
D <- D/N
|
|
|
|
tmin <- 0
|
|
tmax <- 7
|
|
|
|
library(pracma)
|
|
seirds.ode.sol <- ode45(f = function(t,y){seirds.f(t,y,k=seirds.params)},
|
|
y = c(S, E, I, R, D),
|
|
t0 = tmin, tfinal = tmax)
|
|
|
|
# plot
|
|
library(reshape2)
|
|
library(ggplot2)
|
|
plot.seirds <- function(sol, method){
|
|
# - pred/prey columns melted to 1 column called "value"
|
|
sol.melted <- melt(data.frame(time=sol$t,
|
|
S=sol$y[,1],
|
|
E=sol$y[,2],
|
|
I=sol$y[,3],
|
|
R=sol$y[,4],
|
|
D=sol$y[,5]),
|
|
id = "time") # melt based on time
|
|
# New column created with variable names, called “variable”
|
|
colnames(sol.melted)[2] <- "Group" # used in legend
|
|
g <- ggplot(data = sol.melted,
|
|
aes(x = time, y = value, color = Group))
|
|
g <- g + geom_point(size=2)
|
|
g <- g + xlab("time") + ylab("Population")
|
|
g <- g + ggtitle(paste("SEIRDS Model Using", method))
|
|
show(g)
|
|
}
|
|
|
|
plot.seirds(seirds.ode.sol, "ODE45")
|
|
|
|
print(seirds.ode.sol$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]) |