inst/models/helper-prep_fit.R

In nlmixrdevelopment/nlmixr.examples: Nonlinear Mixed Effects Models in Population Pharmacokinetics and Pharmacodynamics

# This header variable assignment simplifies testing and comparison across
# platforms
if (!exists("fit")) {
  fit <- list()
}
if (!exists("expected_values")){
    expected_values <- list()
}
if (!exists("verbose_minimization")) verbose_minimization <- FALSE
default_control <-
  nlme::nlmeControl(
    returnObject=TRUE,
    msMaxiter = 100,
    maxIter = 100,
    pnlsMaxIter = 100,
    msVerbose = verbose_minimization
    )


defaultControl <- function(x){
    if (x == "nlme"){
        return(nlme::nlmeControl(
                   returnObject=TRUE,
                   msMaxiter = 100,
                   maxIter = 100,
                   pnlsMaxIter = 100,
                   msVerbose = verbose_minimization))
    } else if (x == "saem") {
        return(saemControl())
    } else {
        return(foceiControl())
    }
}

defaultTable <- tableControl(cwres=TRUE); ## CWRES needed for FOCEi likelihood

generate_expected_values <- function(x=FALSE) {
  .os <- .Platform$OS.type;
  .nlmixr <- packageVersion("nlmixr")
  if (Sys.info()["sysname"]=="Darwin") .os <- "mac"
  ret <-
    list(
      lik=round(c(logLik(fit[[runno]]), AIC(fit[[runno]]), BIC(fit[[runno]])), 2),
      param=unname(signif(fixef(fit[[runno]]), 5)),
      stdev_param=unname(signif(as.numeric(VarCorr(fit[[runno]])[1:length(fixef(fit[[runno]])), "StdDev"]), 5)),
      sigma=signif(fit[[runno]]$sigma, 5),
      parFixedDf=fit[[runno]]$parFixedDf,
      omega=fit[[runno]]$omega,
      time=fit[[runno]]$time,
      objDf=fit[[runno]]$objDf)
  if (x){
      sink(paste0("values-", .nlmixr, "-", runno, "-", .os, ".R"))
      on.exit(sink());
  }
  cat("expected_values[[runno]] <- ")
  cat(paste(deparse(ret), collapse="\n"), "\n");
  invisible(ret)
}


genIfNeeded <- function(gen=TRUE){
  .os <- .Platform$OS.type;
  .nlmixr <- packageVersion("nlmixr")
    if (Sys.info()["sysname"]=="Darwin") .os <- "mac"
    .ret <- paste0("values-", .nlmixr, "-", runno, "-", .os, ".R");
    if (gen && !file.exists(.ret)){
        generate_expected_values(TRUE);
    }
    return(.ret)
}