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[英]R - deSolve package (ode function): change a matrix of parameters in SIR model according to time
[英]In R: FME/ deSolve - SIR fitting (time varying parameters)
我正在尝试做的事情:我有一个简单的 SIR model,具有随时间变化的传输速率测试版,我已经在 R 中实现了这个(感谢@tpetzoldt)。 我们有一个 N=10000 的人口,伽马也是固定的。
sir_1 <- function(f_beta, S0, I0, R0, times) {
# the differential equations
sir_equations <- function(time, variables, parameters) {
beta <- f_beta(time)
gamma <- f_gamma(time)
with(as.list(variables), {
dS <- -beta * I * S/10000
dI <- beta * I * S/10000 - 1/5 * I
dR <- 1/5 * I
return(list(c(dS, dI, dR), beta=beta))
})
}
# time dependent parameter functions
parameters_values <- list(
f_beta = f_beta
)
# the initial values of variables
initial_values <- c(S = S0, I = I0, R = R0)
out <- ode(initial_values, times, sir_equations, parameters)
}
times <- seq(0, 19)
f_beta <- approxfun(x=times, y=seq(0.901, 0.92, by=0.001), rule=2)
out <- as.data.frame(sir_1(f_beta=f_beta, S0 = 9990, I0 = 10, R0 = 0, times = times))
现在我有一些“真实”数据,使用 FME package 我想在每个时间步获得最佳 beta 参数
datareal <- cbind(time = times, I=c(10,32,120,230,480,567,1040,1743,2300,2619,3542,4039,4231,6378,
5356, 4987, 3421, 2789, 1789,1156))
sir_cost <- function (f_beta) {
outsir <- as.data.frame(sir_1(f_beta=f_beta, S0 = 9990, I0 = 10, R0 = 0, times = times))
costf <- modCost(model = outsir, obs = datareal)
}
p <- rep(0.8, 20)
Fit <- modFit(f = sir_cost, p = p)
Fit
$par
[1] 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8
我的问题:
非常感谢任何帮助。
我不认为估计每个时间步的 beta 是一个好主意。 这是问题所固有的,而不是deSolve或FME的错误。 如果应使用动态 model 来估计时间相关参数,我建议使用合适的 function 结更少,例如时间相关的线性、二次或样条,例如 3-5 而不是 20 结。 然后用approxfun
并将其插入。Model 拟合是一门艺术,因此请使用起始值和求解器。 还有,看书。
请注意,以下只是技术演示:
library("deSolve")
library("FME")
sir_1 <- function(f_beta, S0, I0, R0, times) {
# the differential equations
sir_equations <- function(time, variables, parameters) {
beta <- parameters$f_beta(time)
with(as.list(variables), {
dS <- -beta * I * S/10000
dI <- beta * I * S/10000 - 1/5 * I
dR <- 1/5 * I
return(list(c(dS, dI, dR), beta=beta))
})
}
initial_values <- c(S = S0, I = I0, R = R0)
parameters <- list(f_beta=f_beta)
out <- ode(initial_values, times, sir_equations, parameters)
}
times <- seq(0, 19)
# use method "constant" to leave beta constant over time step
f_beta <- approxfun(x=times, y=seq(0.901, 0.92, by=0.001), method="constant", rule=2)
out <- sir_1(f_beta=f_beta, S0 = 9990, I0 = 10, R0 = 0, times = times)
plot(out)
datareal <- cbind(time = times, I=c(10,32,120,230,480,567,1040,1743,2300,2619,3542,4039,4231,6378,
5356, 4987, 3421, 2789, 1789,1156))
plot(out, obs=datareal)
sir_cost <- function (p) {
f_beta <- approxfun(x=times, y=p, method="constant", rule=2)
outsir <- sir_1(f_beta=f_beta, S0 = 9990, I0 = 10, R0 = 0, times = times)
modCost(model = outsir, obs = datareal)
}
# Play with start values!!!
p <- rep(0.8, 20)
# e.g.: consider random start values
set.seed(123)
p <- runif(20, min=0.8, max=1.2)
# try other solvers, especially such with true box constraints
Fit <- modFit(f = sir_cost, p = p,
lower=rep(0.2, 20), upper=rep(5, 20), # box constraints
method="Port")
summary(Fit) # system is singular (that is what we expected)
# use another solver. Note: it takes a while
Fit <- modFit(f = sir_cost, p = p,
lower=rep(0.2, 20), upper=rep(5, 20), # box constraints
method="L-BFGS-B")
# goes in a surprisingly good direction
Fit$par
f_beta <- approxfun(x=times, y=Fit$par, method="constant", rule=2)
out2 <- sir_1(f_beta=f_beta, S0 = 9990, I0 = 10, R0 = 0, times = times)
# compare with data
plot(out, out2, obs=datareal)
# but see how unstable beta is
plot(out2)
为 model 安装与时间相关的参数可能是个好主意,但如果有理由这样做,我建议限制参数的数量并使用一种平滑的 function。
以下示例显示了如何为此目的使用样条曲线,但当然也可以(并且可能更可取)使用具有某些机械意义的 function。
作为副作用,也可以识别伽马而不是先验地修复它。 尽管如此,这仍然是一个技术演示,但我将科学问题悬而未决,即依赖时间的 beta 是否有意义。
library("FME")
sir_1 <- function(f_beta, gamma, S0, I0, R0, times) {
# the differential equations
sir_equations <- function(time, variables, parameters) {
beta <- parameters$f_beta(time)
gamma <- parameters$gamma
with(as.list(variables), {
dS <- -beta * I * S / 10000
dI <- beta * I * S / 10000 - gamma * I
dR <- gamma * I
# return vector of derivatives, and beta as auxiliary variable
return(list(c(dS, dI, dR), beta = beta))
})
}
initial_values <- c(S = S0, I = I0, R = R0)
# pass constant parameter and parameter function together as a list
parameters <- list(
f_beta = f_beta,
gamma = gamma
)
ode(initial_values, times, sir_equations, parameters)
}
times <- seq(0, 19)
datareal <- data.frame(
time = times,
I = c(10, 32, 120, 230, 480, 567, 1040, 1743, 2300,
2619, 3542, 4039, 4231, 6378,
5356, 4987, 3421, 2789, 1789, 1156)
)
## define parameter as a vector: gamma and beta
t_beta <- c(0, 12, 16, 19) # consider more or less knots
n_beta <- length(t_beta)
y_beta <- rep(1, n_beta)
p <- c(gamma = 1/5, y_beta) # combine all parameters in one vector
## a small helper function for parameter selection
select <- function(p, which, exclude = FALSE) {
parnames <- names(p)
p[(which == parnames) != exclude]
}
## check the helper function
select(p, "gamma")
select(p, "gamma", excl=TRUE)
## cost function, see ?modCost help page
sir_cost <- function (p) {
gamma <- select(p, "gamma")
y_beta <- select(p, "gamma", exclude = TRUE)
f_beta <- splinefun(x = t_beta, y = y_beta)
outsir <- sir_1(f_beta = f_beta, gamma = gamma,
S0 = 9990, I0 = 10, R0 = 0, times = times)
modCost(model = outsir, obs = datareal)
}
## model calibration, see ?modFit
Fit <- modFit(f = sir_cost, p = p,
# lower bound to avoid negative values of beta
lower = c(gamma = 0, rep(0.0, n_beta)),
# note: high sensitivity wrt. upper bound
upper = c(gamma=1, rep(2.0, n_beta)),
# an algorithm that supports box constraints
method = "Port")
## all parameters were identifiable
summary(Fit)
## smaller time steps to obtain a curves
times <- seq(0, 19, 0.1)
## split components of fitted parameters
gamma <- select(Fit$par, "gamma")
y_beta <- select(Fit$par, "gamma", exclude = TRUE)
out2 <- sir_1(f_beta = splinefun(x = t_beta, y = y_beta), gamma,
S0 = 9990, I0 = 10, R0 = 0, times = times)
## show fitted curves and compare simulation with data
## see ?plot.deSolve help page
plot(out2, obs = datareal, which = c("S", "R", "I", "beta"),
las = 1, obspar = list(pch = 16, col = "red"))
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