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Creates a basic simulation app for a given R model

Source: R/mod2shiny.r
mod2shiny.Rd

This function fills in a default template for simulations within shiny

Usage

mod2shiny(
  parvector,
  modfile,
  evnt,
  init = NULL,
  naming = NULL,
  apptitle = "Shiny app title",
  outloc = ".",
  omega = NULL,
  sigma = NULL,
  delloc = FALSE,
  framework = "deSolve",
  logo = paste0(system.file(package = "amp.sim"), "/logo.png"),
  times = NULL
)

Arguments

parvector

named vector with the model parameters, should contain all parameters used by the model

modfile

A script with the model defined in it, it is assumed that this file is created using convert_nonmem

evnt

dataframe with the events used by the model (this is saved as rds together with the app)

init

vector with the compartment initialization (only applicable for deSolve framework)

naming

named vector with the names in parvector and the new values to use within the shiny app

apptitle

string with the title to be used for the app

outloc

character with location where the resulting shiny app should be saved

omega

vector with the omega matrix for the model (only applicable for rxode2 framework)

sigma

vector with the sigma matrix for the model (only applicable for rxode2 framework)

delloc

logical indicating if the location should be deleted first

framework

character indicating the simulation framework that was used, currently "deSolve", "rxode2", "nonmem2rx" and "mrgsolve" are supported

character with a png of the company logo added in the header of the shiny app

times

character vector with the times to simulate or set to NULL to use a default time vector

Value

creates necessary app files for a shiny simulation app

Details

This function creates a default shiny app that can be used as a starting point for further development. There are already some basic features available but it is intended to be adapted when used for production. For the automatic creation of an app it is assumed that the model is created using the convert_nonmem function. Although it is not strictly necessary, the information provided to this function will be in the correct format when this function is used. Some of the arguments in this function are only necessary in case a certain conversion framework is used. In general a single subject is simulated, but be aware that for the deSolve and rxode2 framework OMEGA/ETA is implemented.

Author

Richard Hooijmaijers

Examples


nmmod <- system.file("example_models","PK.1CMT.ORAL.mod", package = "amp.sim")
outf  <- tempfile()
convert_nonmem(nmmod, out=outf, verbose = FALSE)
prm   <- c(THETA1 = 0.3, THETA2 = 2, THETA3 = 5)
evnt  <- mrgsolve::ev(amt = 100, ii = 24, addl = 1)
nams  <- c(THETA1 = "KA (1/h)", THETA2 = "CL (l/h)", THETA3 = "V (l)") 
mod2shiny(prm, modfile= paste0(outf,".cpp"), evnt = evnt,
          naming = nams, framework = "mrgsolve", outloc=tempdir())
#> Shiny app created in location '/tmp/Rtmp1kLZwy'. It can be submitted using:
#> shiny::runApp('/tmp/Rtmp1kLZwy',launch.browser=TRUE)