R/as.nlmixr2.R

In nlmixr2/babelmixr: Use 'nlmixr2' to Interact with Open Source and Commercial Software

#' Convert an object to a nlmixr2 fit object
#'
#' @param x Object to convert
#' @param ... Other arguments
#' @param table is the `nlmixr2est::tableControl()` options
#' @param rxControl is the `rxode2::rxControl()` options, which is
#'   generally needed for how `addl` doses are handled in the
#'   translation
#' @param ci is the confidence interval of the residual differences
#'   calculated (by default 0.95)
#' @return nlmixr2 fit object
#' @export
#' @author Matthew L. Fidler
#' @examples
#'
#' \donttest{
#'
#' # First read in the model (but without residuals)
#' mod <- nonmem2rx(system.file("mods/cpt/runODE032.ctl", package="nonmem2rx"),
#'                  determineError=FALSE, lst=".res", save=FALSE)
#'
#' # define the model with residuals (and change the name of the
#' # parameters) In this step you need to be careful to not change the
#' # estimates and make sure the residual estimates are correct (could
#' # have to change var to sd).
#'
#'  mod2 <-function() {
#'    ini({
#'      lcl <- 1.37034036528946
#'      lvc <- 4.19814911033061
#'      lq <- 1.38003493562413
#'      lvp <- 3.87657341967489
#'      RSV <- c(0, 0.196446108190896, 1)
#'      eta.cl ~ 0.101251418415006
#'      eta.v ~ 0.0993872449483344
#'      eta.q ~ 0.101302674763154
#'      eta.v2 ~ 0.0730497519364148
#'    })
#'    model({
#'      cmt(CENTRAL)
#'      cmt(PERI)
#'      cl <- exp(lcl + eta.cl)
#'      v <- exp(lvc + eta.v)
#'      q <- exp(lq + eta.q)
#'      v2 <- exp(lvp + eta.v2)
#'      v1 <- v
#'      scale1 <- v
#'      k21 <- q/v2
#'      k12 <- q/v
#'      d/dt(CENTRAL) <- k21 * PERI - k12 * CENTRAL - cl * CENTRAL/v1
#'      d/dt(PERI) <- -k21 * PERI + k12 * CENTRAL
#'      f <- CENTRAL/scale1
#'      f ~ prop(RSV)
#'    })
#'  }
#'
#' # now we create another nonmem2rx object that validates the model above:
#'
#' new <- as.nonmem2rx(mod2, mod)
#'
#' # once that is done, you can translate to a full nlmixr2 fit (if you wish)
#'
#' fit <- as.nlmixr2(new)
#'
#' print(fit)
#'
#' }
as.nlmixr2 <- function(x, ..., table=nlmixr2est::tableControl(), rxControl=rxode2::rxControl(), ci=0.95) {
  UseMethod("as.nlmixr2")
}
#' @rdname as.nlmixr2
#' @export
as.nlmixr <- as.nlmixr2

#' @export
as.nlmixr2.default <- function(x, ..., table=nlmixr2est::tableControl(), rxControl=rxode2::rxControl(), ci=0.95) {
  stop("cannot figure out how to create an nlmixr2 object from the input",
       call.=FALSE)
}