stan_lines: stan_lines

In imadmali/stanode: R wrapper for modeling ODEs in Stan

Description

Workhorse function that inputs in the ODE system as an R function (and associated state variables and parameters) and outputs the analogous function in terms of Stan syntax.

Usage

stan_lines(func, state, pars, times)

Arguments

func	A function (currently if-else statements are not supported).
state	A named vector of the initial conditions of the state variables.
pars	A named vector of the parameter values.
times	A sequence of time steps.

Details

See stan_ode for details on function arguments.

Value

A a string vector whose elements are equations of the R ODE system translated into Stan syntax.

See Also

stan_ode_generate.

Examples

## Not run: 
# EXAMPLE 1

f1 <- function(y, t, p) {
 with(as.list(c(y,parms)), {
  dy1 <- y2
  dy2 <- -y1 - theta1 * y2
  return(c(list(dy1 = dy1, dy2 = dy2)))
 })
}
stan_lines(f1, state = c("y1" = 2, "y2" = 5),
           pars = c("theta1" = 0.5),
           times = seq(1,10,by=0.01))

# EXAMPLE 2

f2 <- function(y, t, p) {
  dy1 <- theta1 * y1 + y2 * y3
  dy2 <- theta2 * (y2 - y3)
  dy3 <- -y1*y2 + (theta3)^2*y2 - y3
  return(c(dy1=dy1, dy2=dy2, dy3=dy3))
}
stan_lines(f2, state = c("y1" = 2, "y2" = 5, "y3" = 8),
           pars = c("theta1" = 0.5, "theta2" = 0.2, "theta3" = 0.8),
           times = seq(1,10,by=0.01))

# EXAMPLE 3

f3 <- function(y, t, p) {
  dy1 <- ((y1 + theta1)^2 + y2^2)^(3/2)
  dy2 <- ((y1 - theta2)^2 + y2^2)^(3/2)
  dy3 <- y1 + 2*dy2 - theta2 * ((y1 + theta1)/dy1) - theta1 * ((y1 - theta2)/ dy2)
  dy4 <- y2 - 2*dy1 - theta2 * (y2/dy1) - theta1 * (y2/dy2)
  return(c(dy1=dy1, dy2=dy2, dy3=dy3, dy4=dy4))
}
stan_lines(f3, state = c("y1" = 2, "y2" = 5),
           pars = c("theta1" = 0.5, "theta2" = 0.2),
           times = seq(1,10,by=0.01))

## End(Not run)

imadmali/stanode documentation built on May 3, 2019, 11:48 p.m.