# install from the *develop* branch
devtools::install_github("f0nzie/rODE", ref = "develop")

install.packages("rODE")

library(rODE)
#> 
#> Attaching package: 'rODE'
#> The following object is masked from 'package:stats':
#> 
#>     step
importFromExamples("AdaptiveStep.R")
# running function
AdaptiveStepApp <- function(verbose = FALSE) {
    ode        <- new("Impulse")
    ode_solver <- RK45(ode)
    ode_solver <- init(ode_solver, 0.1)
    ode_solver <- setTolerance(ode_solver, 1.0e-4)
    i <- 1; rowVector <- vector("list")
    while (getState(ode)[1] < 12) {
        rowVector[[i]] <- list(s1 = getState(ode)[1],
                               s2 = getState(ode)[2],
                               t  = getState(ode)[3])
        ode_solver <- step(ode_solver)
        ode <- ode_solver@ode
        i <- i + 1
    }
    return(data.table::rbindlist(rowVector))
}
# run application
solution <- AdaptiveStepApp()
plot(solution)

# ++++++++++++++++++++++++++++++++++++++++++++++++  example: ComparisonRK45App.R
# Compares the solution by the RK45 ODE solver versus the analytical solution
# Example file: ComparisonRK45App.R
# ODE Solver:   Runge-Kutta 45
# Class:        RK45
library(rODE)
importFromExamples("ODETest.R")
 ComparisonRK45App <- function(verbose = FALSE) {
     ode <- new("ODETest")                     # create an `ODETest` object
     ode_solver <- RK45(ode)                   # select the ODE solver
     ode_solver <- setStepSize(ode_solver, 1)      # set the step
     ode_solver <- setTolerance(ode_solver, 1e-8)  # set the tolerance
     rowVector <- vector("list")
     time <-  0
     i    <- 1
     while (time < 50) {
         rowVector[[i]] <- list(t  = ode_solver@ode@state[2],
                                s1 = getState(ode_solver@ode)[1],
                                s2 = getState(ode_solver@ode)[2],
                                xs = getExactSolution(ode_solver@ode, time),
                                rc = getRateCounts(ode),
                                time = time)
         ode_solver <- step(ode_solver)       # advance one step
         stepSize <-  ode_solver@stepSize     # update the step size
         time <- time + stepSize
         state <- getState(ode_solver@ode)    # get the `state` vector
         i <- i + 1
     }
     return(data.table::rbindlist(rowVector))    # a data table with the results
 }
# show solution
solution <- ComparisonRK45App()                          # run the example
plot(solution)

# +++++++++++++++++++++++++++++++++++++++++++++++  example: FallingParticleApp.R
# Application that simulates the free fall of a ball using Euler ODE solver
library(rODE)
importFromExamples("FallingParticleODE.R")      # source the class
FallingParticleODEApp <- function(verbose = FALSE) {
    # initial values
    initial_y <- 10
    initial_v <- 0
    dt        <- 0.01
    ball   <- FallingParticleODE(initial_y, initial_v)
    solver <- Euler(ball)                        # set the ODE solver
    solver <- setStepSize(solver, dt)            # set the step
    rowVector <- vector("list")
    i <- 1
    # stop loop when the ball hits the ground, state[1] is the vertical position
    while (ball@state[1] > 0) {
        rowVector[[i]] <- list(t  = ball@state[3],
                               y  = ball@state[1],
                               vy = ball@state[2])
        solver <- step(solver)                   # move one step at a time
        ball <- solver@ode                       # update the ball state
        i <- i + 1
    }
    DT <- data.table::rbindlist(rowVector)
    return(DT)
}
# show solution
solution <- FallingParticleODEApp()
plot(solution)

#  +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ example KeplerApp.R
#  KeplerApp solves an inverse-square law model (Kepler model) using an adaptive
#  stepsize algorithm.
#  Application showing two planet orbiting
#  File in examples: KeplerApp.R
library(rODE)
importFromExamples("Kepler.R") # source the class Kepler
KeplerApp <- function(verbose = FALSE) {
    # set the orbit into a predefined state.
    r  <- c(2, 0)                                   # orbit radius
    v  <- c(0, 0.25)                                # velocity
    dt <- 0.1
    planet <- Kepler(r, v)
    solver <- RK45(planet)
    rowVector <- vector("list")
    i <- 1
    while (planet@state[5] <= 10) {
        rowVector[[i]] <- list(t  = planet@state[5],
                               planet1.r = planet@state[1],
                               p1anet1.v = planet@state[2],
                               planet2.r = planet@state[3],
                               p1anet2.v = planet@state[4])
        solver <- step(solver)
        planet <- solver@ode
        i <-  i + 1
    }
    DT <- data.table::rbindlist(rowVector)
    return(DT)
}
solution <- KeplerApp()
plot(solution)

# ++++++++++++++++++++++++++++++++++++++++++++++++++  example: KeplerEnergyApp.R
# Demostration of the use of the Verlet ODE solver
#
library(rODE)
importFromExamples("KeplerEnergy.R") # source the class Kepler
KeplerEnergyApp <- function(verbose = FALSE) {
    # initial values
    x   <- 1
    vx  <- 0
    y   <- 0
    vy  <- 2 * pi
    dt  <- 0.01
    tol <- 1e-3
    particle <- KeplerEnergy()
    particle <- init(particle, c(x, vx, y, vy, 0))
    odeSolver <- Verlet(particle)
    odeSolver <- init(odeSolver, dt)
    particle@odeSolver <- odeSolver
    initialEnergy <- getEnergy(particle)
    rowVector <- vector("list")
    i <- 1
    while (getTime(particle) <= 1.20) {
        rowVector[[i]] <- list(t  = particle@state[5],
                               x  = particle@state[1],
                               vx = particle@state[2],
                               y  = particle@state[3],
                               vy = particle@state[4],
                               E  = getEnergy(particle))
        particle <- doStep(particle)
        energy <- getEnergy(particle)
        i <- i + 1
    }
    DT <- data.table::rbindlist(rowVector)
    return(DT)
}
solution <- KeplerEnergyApp()
plot(solution)

library(rODE)
importFromExamples("Logistic.R") # source the class Logistic
# Run the application
LogisticApp <- function(verbose = FALSE) {
    x  <- 0.1
    vx <- 0
    r  <- 2        # Malthusian parameter (rate of maximum population growth)
    K  <- 10.0     # carrying capacity of the environment
    dt <- 0.01; tol  <- 1e-3; tmax <- 10
    population <- Logistic()
    population <- init(population, c(x, vx, 0), r, K)
    odeSolver <- Verlet(population)
    odeSolver <- init(odeSolver, dt)
    population@odeSolver <- odeSolver
    rowVector <- vector("list")
    i <- 1
    while (getTime(population) <= tmax) {
        rowVector[[i]] <- list(t  = getTime(population),
                               s1 = population@state[1],
                               s2 = population@state[2])
        population <- doStep(population)
        i <- i + 1
    }
    DT <- data.table::rbindlist(rowVector)
    return(DT)
}
# show solution
solution <- LogisticApp()
plot(solution)

# ++++++++++++++++++++++++++++++++++++++++++++++++++      example: PendulumApp.R
# Simulation of a pendulum using the EulerRichardson ODE solver
library(rODE)
suppressPackageStartupMessages(library(ggplot2))
importFromExamples("Pendulum.R")      # source the class
PendulumApp <- function(verbose = FALSE) {
    # initial values
    theta    <- 0.2
    thetaDot <- 0
    dt       <- 0.1
    ode <- new("ODE")
    pendulum <- Pendulum()
    pendulum@state[3] <- 0      # set time to zero, t = 0
    pendulum <- setState(pendulum, theta, thetaDot)
    pendulum <- setStepSize(pendulum, dt = dt) # using stepSize in RK4
    pendulum@odeSolver <- setStepSize(pendulum@odeSolver, dt) # set new step size
    rowvec <- vector("list")
    i <- 1
    while (pendulum@state[3] <= 40)    {
        rowvec[[i]] <- list(t     = pendulum@state[3],    # time
                            theta = pendulum@state[1],    # angle
                            thetadot = pendulum@state[2]) # derivative of angle
        pendulum <- step(pendulum)
        i <- i + 1
    }
    DT <- data.table::rbindlist(rowvec)
    return(DT)
}
# show solution
solution <- PendulumApp()
plot(solution)

# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++  example: PlanetApp.R
# Simulation of Earth orbiting around the SUn using the Euler ODE solver
library(rODE)
importFromExamples("Planet.R")      # source the class
PlanetApp <- function(verbose = FALSE) {
    # x =  1, AU or Astronomical Units. Length of semimajor axis or the orbit
    # of the Earth around the Sun.
    x <- 1; vx <- 0; y <- 0; vy <- 6.28; t <- 0
    state <- c(x, vx, y, vy, t)
    dt <-  0.01
    planet <- Planet()
    planet@odeSolver <- setStepSize(planet@odeSolver, dt)
    planet <- init(planet, initState = state)
    rowvec <- vector("list")
    i <- 1
    # run infinite loop. stop with ESCAPE.
    while (planet@state[5] <= 90) {     # Earth orbit is 365 days around the sun
        rowvec[[i]] <- list(t  = planet@state[5],     # just doing 3 months
                            x  = planet@state[1],     # to speed up for CRAN
                            vx = planet@state[2],
                            y  = planet@state[3],
                            vy = planet@state[4])
        for (j in 1:5) {                 # advances time
            planet <- doStep(planet)
        }
        i <- i + 1
    }
    DT <- data.table::rbindlist(rowvec)
    return(DT)
}
# run the application
solution <- PlanetApp()
select_rows <- seq(1, nrow(solution), 10)      # do not overplot
solution <- solution[select_rows,]
plot(solution)

# +++++++++++++++++++++++++++++++++++++++++++++++++ application: ProjectileApp.R
#                                                      test Projectile with RK4
#                                                      originally uses Euler
library(rODE)
importFromExamples("Projectile.R")      # source the class
ProjectileApp <- function(verbose = FALSE) {
    # initial values
    x <- 0; vx <- 10; y <- 0; vy <- 10
    state <- c(x, vx, y, vy, 0)                        # state vector
    dt <- 0.01
    projectile <- Projectile()
    projectile <- setState(projectile, x, vx, y, vy)
    projectile@odeSolver <- init(projectile@odeSolver, 0.123)
    projectile@odeSolver <- setStepSize(projectile@odeSolver, dt)
    rowV <- vector("list")
    i <- 1
    while (projectile@state[3] >= 0)    {
        rowV[[i]] <- list(t  = projectile@state[5],
                          x  = projectile@state[1],
                          vx = projectile@state[2],
                          y  = projectile@state[3],     # vertical position
                          vy = projectile@state[4])
        projectile <- step(projectile)
        i <- i + 1
    }
    DT <- data.table::rbindlist(rowV)
    return(DT)
}
solution <- ProjectileApp()
plot(solution)

# +++++++++++++++++++++++++++++++++++++++++++++++++++ application: ReactionApp.R
# ReactionApp solves an autocatalytic oscillating chemical
# reaction (Brusselator model) using
# a fourth-order Runge-Kutta algorithm.
library(rODE)
importFromExamples("Reaction.R")      # source the class
ReactionApp <- function(verbose = FALSE) {
    X  <- 1; Y <- 5;
    dt <- 0.1
    reaction <- Reaction(c(X, Y, 0))
    solver <- RK4(reaction)
    rowvec <- vector("list")
    i <- 1
    while (solver@ode@state[3] < 100) {             # stop at t = 100
        rowvec[[i]] <- list(t = solver@ode@state[3],
                            X = solver@ode@state[1],
                            Y = solver@ode@state[2])
        solver <- step(solver)
        i <-  i + 1
    }
    DT <- data.table::rbindlist(rowvec)
    return(DT)
}
solution <- ReactionApp()
plot(solution)

# +++++++++++++++++++++++++++++++++++++++++++++++ application: RigidBodyNXFApp.R
# example of a nonstiff system is the system of equations describing
# the motion of a rigid body without external forces.
library(rODE)
importFromExamples("RigidBody.R")
# run the application
RigidBodyNXFApp <- function(verbose = FALSE) {
    # load the R class that sets up the solver for this application
    y1 <- 0   # initial y1 value
    y2 <- 1    # initial y2 value
    y3 <- 1    # initial y3 value
    dt <- 0.01 # delta time for step
    body <- RigidBodyNXF(y1, y2, y3)
    solver <- Euler(body)
    solver <- setStepSize(solver, dt)
    rowVector <- vector("list")
    i <- 1
    # stop loop when the body hits the ground
    while (body@state[4] <= 12) {
        rowVector[[i]] <- list(t  = body@state[4],
                               y1 = body@state[1],
                               y2 = body@state[2],
                               y3 = body@state[3])
        solver <- step(solver)
        body <- solver@ode
        i <- i + 1
    }
    DT <- data.table::rbindlist(rowVector)
    return(DT)
}
# get the data table from the app
solution <- RigidBodyNXFApp()
plot(solution)

library(rODE)
importFromExamples("SHO.R")
# SHOApp.R
SHOApp <- function(...) {
    x <- 1.0; v <- 0; k <- 1.0; dt <- 0.01; tolerance <- 1e-3
    sho    <- SHO(x, v, k)
    solver_factory <- ODESolverFactory()
    solver <- createODESolver(solver_factory, sho, "DormandPrince45")
    # solver <- DormandPrince45(sho)                    # this can also be used
    solver <- setTolerance(solver, tolerance)
    solver <- init(solver, dt)
    i <- 1; rowVector <- vector("list")
    while (sho@state[3] <= 500) {
        rowVector[[i]] <- list(x = sho@state[1],
                               v = sho@state[2],
                               t = sho@state[3])
        solver <- step(solver)
        sho    <- solver@ode
        i <- i + 1
    }
    return(data.table::rbindlist(rowVector))
}
solution <- SHOApp()
plot(solution)

# ++++++++++++++++++++++++++++++++++++++++++++++++++application:  SpringRK4App.R
# Simulation of a spring considering no friction
library(rODE)
importFromExamples("SpringRK4.R")
# run application
SpringRK4App <- function(verbose = FALSE) {
    theta    <- 0
    thetaDot <- -0.2
    tmax     <- 22; dt <- 0.1
    ode <- new("ODE")
    spring <- SpringRK4()
    spring@state[3] <- 0      # set time to zero, t = 0
    spring <- setState(spring, theta, thetaDot)
    spring <- setStepSize(spring, dt = dt) # using stepSize in RK4
    spring@odeSolver <- setStepSize(spring@odeSolver, dt) # set new step size
    rowvec <- vector("list")
    i <- 1
    while (spring@state[3] <= tmax)    {
        rowvec[[i]] <- list(t  = spring@state[3],      # angle
                            y1 = spring@state[1],      # derivative of the angle
                            y2 = spring@state[2])      # time
        i <- i + 1
        spring <- step(spring)
    }
    DT <- data.table::rbindlist(rowvec)
    return(DT)
}
# show solution
solution <- SpringRK4App()
plot(solution)

# ++++++++++++++++++++++++++++++++++++++++++++++++   application: VanderPolApp.R
# Solution of the Van der Pol equation
#
library(rODE)
importFromExamples("VanderPol.R")
# run the application
VanderpolApp <- function(verbose = FALSE) {
    # set the orbit into a predefined state.
    y1 <- 2; y2 <- 0; dt <- 0.1;
    rigid_body <- VanderPol(y1, y2)
    solver <- RK45(rigid_body)
    rowVector <- vector("list")
    i <- 1
    while (rigid_body@state[3] <= 20) {
        rowVector[[i]] <- list(t  = rigid_body@state[3],
                               y1 = rigid_body@state[1],
                               y2 = rigid_body@state[2])
        solver <- step(solver)
        rigid_body <- solver@ode
        i <-  i + 1
    }
    DT <- data.table::rbindlist(rowVector)
    return(DT)
}
# show solution
solution <- VanderpolApp()
plot(solution)

# +++++++++++++++++++++++++++++++++++++     example: VanderpolMuTimeControlApp.R
# This is a modification of the original Vanderpol.R script
# In this version, we will add tha ability of setting mu and time lapse.
# This example is also shown in the Matlab help guide
library(rODE)
importFromExamples("VanderpolMuTimeControl.R")
# run the application
VanderpolMuTimeControlApp <- function(verbose = FALSE) {
    # set the orbit into a predefined state.
    y1 <- 2; y2 <- 0; mu <- 10; tmax <- mu * 3; dt <- 0.01
    rigid_body <- VanderPol(y1, y2, mu)
    solver <- RK45(rigid_body)
    rowVector <- vector("list")
    i <- 1
    while (rigid_body@state[3] <= tmax) {
        rowVector[[i]] <- list(t  = rigid_body@state[3],
                               y1 = rigid_body@state[1],
                               y2 = rigid_body@state[2]
                               )
        solver <- step(solver)
        rigid_body <- solver@ode
        i <-  i + 1
    }
    DT <- data.table::rbindlist(rowVector)
    return(DT)
}
# show solution
solution <- VanderpolMuTimeControlApp()
plot(solution)