CODEWITHSUNDEEP
rmapply
Hansong
Hansong

Reputation: 21

How to apply two list of numbers into a function using mapply?

I'm trying to use two different set of lists as an input of a function using mapply, but I'm not sure how to. With the current code I have, it gives out an unexpected error. Did I use the mapply in a wrong way?

Here is a sample of the code:

t_index <- c("2022-01-01","2022-01-08","2022-01-15","2022-01-22","2022-01-29","2022-02-05","2022-02-12","2022-02-19",
             "2022-02-26","2022-03-12","2022-03-26","2022-04-09","2022-04-23","2022-05-07","2022-05-21","2022-06-11")

t_index_day <- filter(flu2, Date %in% t_index)
t_index_day <- t_index_day$day

# SIR model
sir_1 <- function(alpha, beta, gamma, delta, S0, E0, I0, R0, D0, N, times) {
  require(deSolve) # for the "ode" function
  # the differential equations:
  sir_equations <- function(time, variables, parameters) {
    with(as.list(c(variables, parameters)), {
      dS <- -beta * I * S/N
      dE <- beta* I * S/N - (alpha*E)
      dI <-  alpha*E - (gamma*I) - (delta*I)
      dR <-  gamma * I 
      dD <-  delta * I  
      return(list(c(dS, dE,dI, dR, dD)))
    })
  }
  # the parameters values:
  parameters_values <- c(alpha = alpha,beta  = beta, gamma = gamma, delta = delta)
  # the initial values of variables:===
  initial_values <- c(S = S0, E=E0, I = I0, R = R0, D = D0)
  # solving
  out <- ode(initial_values, times, sir_equations, parameters_values)
  # returning the output:
  as.data.frame(out)
}


# sum of squares equation function for first
ss <- function(alpha,beta, gamma, delta, time, num, data = flu2, N = 50000000) {
  print (num)
  data = data[time[num]:time[num+1],]
  E0 <-data$cases[1]*(alpha)
  I0 <- data$cases[1]
  R0 <- data$cases[1]*(gamma)
  D0 <- data$deaths[1]
  times <- data$day
  predictions <- sir_1(alpha = alpha,beta = beta, gamma = gamma, delta = delta,   # parameters
                       S0 = N - 639083, # cumulative case until now
                       E0 = E0,
                       I0 = I0, 
                       R0 = R0,
                       D0 = D0,
                       N = N, 
                       times = times)                # time points
  sum((predictions$I[-1] - data$cases[-1])^2)
}

loop <- as.integer(1:(length(t_index)-1))
beta_val <- seq(from = 0.1, to = 0.43, le = 300) 
delta_val <- seq(from = 1/10000, to = 1/100, le = 300)

for (i in loop){
  if (i == 1){
    ss_val <- mapply(ss,beta_val, delta_val,alpha = 1/5, gamma = 1/7,time = t_index_day, num = i,data = flu2)
    print(ss_val)

Error code:

error code

Upvotes: 1

Views: 68

Answers (1)

Hansong
Hansong

Reputation: 21

Then problem was with mapply trying to get all inputs as a part of a list, while I only wanted beta_val and delta_val as a part and the rest as a whole.

To solve this problem I changed the definition of the function ss:

ss <- function(alpha,beta, gamma, delta, time = t_index_day, num, data = flu2, N = 50000000) {
  print (num)
  data = data[time[num]:time[num+1],]
  E0 <-data$cases[1]*(alpha)
  I0 <- data$cases[1]
  R0 <- data$cases[1]*(gamma)
  D0 <- data$deaths[1]
  times <- data$day
  predictions <- sir_1(alpha = alpha,beta = beta, gamma = gamma, delta = delta,   # parameters
                       S0 = N - 639083, # cumulative case until now
                       E0 = E0,
                       I0 = I0, 
                       R0 = R0,
                       D0 = D0,
                       N = N, 
                       times = times)                # time points
  sum((predictions$I[-1] - data$cases[-1])^2)
}

Upvotes: 1

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