PBPK Model made with MCSIM under R in Rshiny

[deepika060193]

Hi, I made a pbpk model using MCSIM under R. Now I want to publish it in Rshiny directly using MCSIM_under_R rather than converting all the code from MCSIM to Rstudio and solve ode using packages like rxode etc. I tried it and see that the file is running perfectly fine but i am not understanding how i can vary the dose without entering into simulation file directly. I am sending you the rshinycode for clarification.

library(shiny)

Define UI for application

ui <- fluidPage(

Application Panel

Application title

titlePanel("PBPK Model for TDCIPP"),

Sidebar with a slider input for number of bins

sidebarLayout( sidebarPanel( h4("Dosing details"), numericInput("dosing", label='Dose', value = 10,min=0, max=100) ),

#############################plotting here
mainPanel(
  plotOutput("v1")
)

) )

Define server logic required to draw a histogram

server <- function(input, output) { output$v1 <- renderPlot({

Server logic goes here

clear()

getwd() setwd("C:/MCSim_under_R-master") source(file = "MCSim/function.R") set_PATH(PATH = "c:/Useres/Rtools/mingw_32/bin")

this is where the problem is I want the dosing to be not in the simulation file, but rather I want the simulation file to take the dose directly from here (which means R).

##############dosing=input$dosing #this dosing I want to integrate in the simulation file which is "tdcipp_2_forward_1_f1_reverse_1.in.r"

v1<- mcsim(model="tdcipp_3_non-linear_elimination_f_6_reverse.model.r", input="tdcipp_2_forward_1_f1_reverse_1.in.r",dir="modeling/rshiny/FR",parallel = "F")

v1=read.delim("tdcipp_ftest.out",skip=1)

plot(v1$Time,v1$cplasma_2, type="l")

}) }

Run the application

shinyApp(ui = ui, server = server)

[nanhung]

This is a bit tricky. Maybe you can create a function to generate the simulation file (instead of creat by yourself) to change the dose in the R interface. Here is an example R function of creating a input file,

generate_infile <- function(infile.name = NULL,
                            rtol = 1e-6, atol = 1e-6,
                            outvars = c("A", "B"),
                            dose = 1, times = c(0.5, 1)){

  if(is.null(infile.name)) infile.name <- "sim.in"

  cat("#---------------------------------------- \n#",
      " ", infile.name , "\n#",
      " (Created by generate_infile)\n#",
      "----------------------------------------", "\n\n",
      file = infile.name, sep = "")

  cat("Integrate (Lsodes, ", rtol, ", ", atol, " , 1);", "\n\n",
      file=infile.name, append=TRUE, sep="")

  cat("Dose = ", dose, ";\n\n", 
        file=infile.name,append = TRUE, sep="") 
  cat("Print (", paste(outvars, collapse = ", "), ", ",
          paste(times, collapse=", "), ");\n", file = infile.name,
          append=TRUE, sep = "")
          cat("END.\n", file = infile.name, append = TRUE)
  message(paste('* Created input file "', infile.name, '".', sep =""))
}

After that, you can use it to your shiny app.

[deepika060193]

Thank you for a fast reply. I will try this and inform you.

Have a nice day!

[deepika060193]

The code is working fine now. Thank you!