试图将我的思维包裹在矢量化中,尝试更快地进行模拟,我发现了这种非常基本的流行病模拟。代码来自书籍http://www.amazon.com/Introduction-Scientific-Programming-Simulation-Using/dp/1420068725/ref=sr_1_1?ie=UTF8&qid=1338069156&sr=8-1
#program spuRs/resources/scripts/SIRsim.r
SIRsim <- function(a, b, N, T) {
# Simulate an SIR epidemic
# a is infection rate, b is removal rate
# N initial susceptibles, 1 initial infected, simulation length T
# returns a matrix size (T+1)*3 with columns S, I, R respectively
S <- rep(0, T+1)
I <- rep(0, T+1)
R <- rep(0, T+1)
S[1] <- N
I[1] <- 1
R[1] <- 0
for (i in 1:T) {
S[i+1] <- rbinom(1, S[i], (1 - a)^I[i])
R[i+1] <- R[i] + rbinom(1, I[i], b)
I[i+1] <- N + 1 - R[i+1] - S[i+1]
}
return(matrix(c(S, I, R), ncol = 3))
}
模拟的核心是for
循环。我的问题是,由于代码从S[i+1]
和R[i+1]
值生成S[i]
和R[i]
值,是否可以使用apply函数对其进行矢量化?
非常感谢
答案 0 :(得分:5)
很难“迭代”迭代计算,但这是一个模拟和模拟很可能会运行多次。因此,通过添加参数M
(要执行的模拟次数),分配M x(T + 1)矩阵,然后填充连续列(次数)来写这个以同时进行所有模拟每个模拟。这些变化似乎非常直接(所以我可能犯了一个错误;我特别关注在rbinom
的第二和第三个参数中使用向量,尽管这与文档一致)
SIRsim <- function(a, b, N, T, M) {
## Simulate an SIR epidemic
## a is infection rate, b is removal rate
## N initial susceptibles, 1 initial infected, simulation length T
## M is the number of simulations to run
## returns a list of S, I, R matricies, each M simulation
## across T + 1 time points
S <- I <- R <- matrix(0, M, T + 1)
S[,1] <- N
I[,1] <- 1
for (i in seq_along(T)) {
S[,i+1] <- rbinom(M, S[,i], (1 - a)^I[,i])
R[,i+1] <- R[,i] + rbinom(M, I[,i], b)
I[,i+1] <- N + 1 - R[,i+1] - S[,i+1]
}
list(S=S, I=I, R=R)
}