deploy.pbpk: Deploy an Ordinary Differential Equation (ODE) model on...

In KinkyDesign/jaqpotr: Deploys R models as web services on the Jaqpot platform

Deploy an Ordinary Differential Equation (ODE) model on Jaqpot.

Description

Uploads an ODE model on Jaqpot that can be solved using the ode function of package 'deSolve'.

Usage

deploy.pbpk(
  user.input,
  out.vars,
  create.params,
  create.inits,
  create.events,
  custom.func,
  ode.fun,
  method = "lsodes",
  url = "https://api.jaqpot.org/",
  envFile = NULL
)

Arguments

user.input	A list with keys the names of the inputs that the end-user will be asked to complete on the Jaqpot User Interface (UI) and values expemplary input values.
out.vars	A vector containing the names of the state variables of the ODEs to be printed on the UI. The names should be a subset of the names of the state variables of the ODE system.
create.params	A function that receives a list of inputs (with key being the name and value the corresponding value) and with inner tranformations converts them to an appropriate parameter vector that is used by the create.inits, create.events and ode.fun. The function should return a list.
create.inits	A function that receives the list returned by create.params and uses it to create the initial conditions of the ODE system. The function should return a named vector.
create.events	A function that receives the list returned by create.params and uses it to create the events to be forced on the ODE system. The function should return a list.
custom.func	A custom function that the user can call from within the ode.fun
ode.fun	The ODE system in a function format that is appropriate for use in the 'deSolve' package solvers.
method	A string declaring the ODE solver to be used. The user should see all available options from 'deSolve' package
url	The base path of Jaqpot services. This argument is optional and needs to be changed only if an alternative Jaqpot installation is used.
...	Extra arguments to be passed down to the solver.

Details

The user should provide the inputs that the end-user will provide on the Jaqpot User Interface (UI) and the state variables of the ODE system that are to be printed on the UI upon execution of the ODE system. In addition, the user should provide five functions. The first function transforms the user input according to the needs of the ODE model, the second creates the initial conditions of the ODEs, the third creates the events that are forced on the system, the fourth enables the use of custom functions inside the ODEs and the last is the ODEs, with syntax compatible with package 'deSolve'. The functions are used in a nested style (see examples). Note that the names of independent and dependent features (i.e. user.input) cannot be further modified via the Jaqpot UI, so the user should choose them with caution.

Value

The id of the uploaded model.

Examples

## Not run: 

##########################################
# Function for creating parameter vector #
##########################################

create.params <- function(input){
  with( as.list(input),{

    ############################
    # Physiological parameters #
    ############################
   # tissue weights (in g)
    W_tot <- weight # ;body weight, experimental data - g
    W_lu <-1.2 # weight of lungs, experimental data - g
    W_li <- 10.03 # weight of liver, experimental data - g

    W_blood <- 0.065 * W_tot
    W_rob <- W_tot - (W_blood + W_li + W_lu)

    #Regional blood flows (in mL per hour)
    fQl = 0.183 # fraction of cardiac output to liver, unitless
    fQrob = 1-fQl # fraction of cardiac output to rest of the body,  unitless
    Q_tot <- 4980 # cardiac output, mL/h
    Q_li <- fQl*Q_tot    # blood flow to liver, mL/h
    Q_rob <- fQrob*Q_tot # blood flow to rest of the body, mL/h

    P <-1.435445 # partition coefficient tissue:blood, unitless
    CLE_f <- 9.958839e-05 # clearance rate to feces from liver,  mL/h

    return(list("W_lu" = W_lu, "W_li" = W_li, "W_rob" = W_rob, "W_blood" = W_blood, "Q_tot" =  Q_tot,
                "Q_li" = Q_li, "Q_rob" = Q_rob, "P" = P,"CLE_f" = CLE_f, "dose" = dose,
                "administration.time" = administration.time, "weight" = weight))
  })
}

#################################################
# Function for creating initial values for ODEs #
#################################################

create.inits <- function(parameters){
  with( as.list(parameters),{
    Lu <- 0; Rob <- 0;Li <- 0; Mart <- 0; Mven <- 0;

    return(c("Mlu" = Lu, "Mrob" = Rob, "Mli" = Li, "Mart" = Mart,
             "Mven" = Mven))
  })
}

#################################################
# Function for creating events #
#################################################
create.events<- function(parameters){
  with( as.list(parameters),{

    ldose <- length(dose)
    ltimes <- length(administration.time)

    addition <- dose
    if (ltimes == ldose){
      events <- list(data = rbind(data.frame(var = "Mven",  time = administration.time,
                                             value = addition, method = c("add")) ))
    }else{
      stop("The times when the drug is injected should be equal in number to the doses")
    }


    return(events)
  })
}


###################
# Custom function #
###################
custom.func <- function(W_li){
  if (W_li<15){
    a = 10
  }else{
    a = 15
  }
  return(a)
}

#################
# ODEs system #
#################

ode.func <- function(time, Initial.values, Parameters, custom.func){
  with( as.list(c(Initial.values, Parameters)),{

    #'cleararance coefficient
    CL = custom.func(weight)
    #' concentrations in tissues
    C_lu <- Mlu/W_lu
    C_rob  <-  Mrob/W_rob
    C_li  <-  Mli/W_li
    C_art <- Mart/(0.2*W_blood)
    C_ven <- Mven/(0.8*W_blood)

    #' Lungs
    dMlu <- Q_tot * (C_ven - C_lu/P)
    #' Rest of the body
    dMrob <-  Q_rob * (C_art - C_rob/P)
    #' Liver
    dMli <- Q_li * (C_art - C_li/P)- CLE_f*CL*C_li
    #' Arterial blood
    dMart <- Q_tot* C_lu/P - C_art * (Q_li + Q_rob)
    #' Venous blood
    dMven <- Q_li*C_li/P + Q_rob*C_rob/P - Q_tot * C_ven
    list(c(dMlu = dMlu, dMrob = dMrob,  dMli = dMli, dMart = dMart, dMven = dMven))
  })
}

user.input <-list("weight" = 250,"dose" = c(10,12), "administration.time" = c(0,1.5) )
out.vars <- c("Li")
params <- create.params(user.input)
inits <- create.inits(params)
events <- create.events(params)
sample_time <- seq(1,10,1)
solution <- data.frame(deSolve::ode(times = sample_time,  func = ode.func,
                                    y = inits,custom.func = custom.func, parms = params,
                                    events = events,
                                    method="lsodes",rtol = 1e-07, atol = 1e-07))
deploy.pbpk(user.input, out.vars, create.params, create.inits, create.events,
            custom.func, ode.fun, method = "bdf", list(rtol=1e-07, atol=1e-09))

## End(Not run)

KinkyDesign/jaqpotr documentation built on Nov. 27, 2024, 1:20 a.m.