R/RcppExports.R

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

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

convertDataBack <- function(id, time, amt, ii, evid, cmt, cmtDvid, dvidDvid, linNcmt = 0L, linKa = 0L, neq = 0L, replaceEvid = 5L, zeroDose2 = TRUE) {
    .Call(`_babelmixr2_convertDataBack`, id, time, amt, ii, evid, cmt, cmtDvid, dvidDvid, linNcmt, linKa, neq, replaceEvid, zeroDose2)
}

#' @title Get Multiple Endpoint Modeling Times
#'
#' @description
#'
#' This function takes a vector of times and a corresponding vector
#'   of IDs, groups the times by their IDs, initializes an internal
#'   C++ global TimeIndexer, that is used to efficiently lookup the
#'   final output from the rxode2 solve and then returns the sorted
#'   unique times.
#'
#' The `popedMultipleEndpointIndexDataFrame()` function can be used
#'   to visualize the internal data structure inside R, but it does
#'   not show all the indexes in the case of time ties for a given
#'   ID.  Rather it shows one of the indexs and the total number of
#'   indexes in the data.frame
#'
#' @param times A numeric vector of times.
#'
#' @param modelSwitch An integer vector of model switch indicator
#'   corresponding to the times
#'
#' @param sorted A boolean indicating if the returned times should be sorted
#'
#' @param print boolean for `popedMultipleEndpointIndexDataFrame()`
#'   when `TRUE` show each id/index per time even though it may not
#'   reflect in the returned data.frame
#'
#' @return A numeric vector of unique times.
#'
#' @export
#'
#' @examples
#'
#'
#' \donttest{
#'
#' times <- c(1.1, 1.2, 1.3, 2.1, 2.2, 3.1)
#' modelSwitch <- c(1, 1, 1, 2, 2, 3)
#' sortedTimes <- popedGetMultipleEndpointModelingTimes(times, modelSwitch, TRUE)
#' print(sortedTimes)
#'
#' # now show the output of the data frame representing the model
#' # switch to endpoint index
#'
#' popedMultipleEndpointIndexDataFrame()
#'
#' # now show a more complex example with overlaps etc.
#'
#' times <- c(1.1, 1.2, 1.3, 0.5, 2.2, 1.1, 0.75,0.75)
#' modelSwitch <- c(1, 1, 1, 2, 2, 2, 3, 3)
#' sortedTimes <- popedGetMultipleEndpointModelingTimes(times, modelSwitch, TRUE)
#' print(sortedTimes)
#'
#' popedMultipleEndpointIndexDataFrame(TRUE) # Print to show individual matching
#'
#' }
popedGetMultipleEndpointModelingTimes <- function(times, modelSwitch, sorted = FALSE) {
    .Call(`_babelmixr2_popedGetMultipleEndpointModelingTimes`, times, modelSwitch, sorted)
}

#' @title Reset the Global Time Indexer for Multiple Endpoint Modeling
#'
#' @description
#'
#' This clears the memory and resets the global time indexer used for
#'   multiple endpoint modeling.
#'
#' @return NULL, called for side effects
#'
#' @export
#'
#' @examples
#'
#' \donttest{
#'
#' popedMultipleEndpointResetTimeIndex()
#'
#' }
popedMultipleEndpointResetTimeIndex <- function() {
    .Call(`_babelmixr2_popedMultipleEndpointResetTimeIndex`)
}

#' @rdname popedGetMultipleEndpointModelingTimes
#' @export
popedMultipleEndpointIndexDataFrame <- function(print = FALSE) {
    .Call(`_babelmixr2_popedMultipleEndpointIndexDataFrame`, print)
}

#' Populates Multiple Endpoint Parameters for internal solving
#'
#' This function populates a numeric vector with parameters and
#' unique times and also populates the internal C++ global index
#'
#' @param p A numeric vector of parameters
#'
#' @param times A numeric vector of times
#'
#' @param modelSwitch An integer vector indicating model switches from PopED
#'
#' @param maxMT An integer specifying the maximum number of time
#'   points in the mtimes model
#'
#' @return A numeric vector containing the parameters followed by
#'   unique times, if the maximum number of times is greater than the
#'   input this will append the maximum observed times in the
#'   input. This assumes the first parameter is the id and is dropped
#'   fro the output.
#'
#' @details
#'
#'  - This function first uses the input times and model switches to
#'   a global time indexer.
#'
#'  - It then creates a new numeric vector
#'    that combines the input parameters and unique times.  If the
#'    number of times is less than `maxMT`, the remaining elements are
#'    filled with the maximum time.
#'
#' @examples
#'
#' \donttest{
#'
#' p <- c(1.0, 2.0, 3.0)
#' times <- c(0.5, 1.5, 2.5)
#' modelSwitch <- c(1, 2, 3)
#' maxMT <- 5
#' popedMultipleEndpointParam(p, times, modelSwitch, maxMT)
#'
#' }
#' @export
#' @keywords internal
#' @author Matthew L. Fidler
popedMultipleEndpointParam <- function(p, times, modelSwitch, maxMT, optTime = TRUE) {
    .Call(`_babelmixr2_popedMultipleEndpointParam`, p, times, modelSwitch, maxMT, optTime)
}

popedFree <- function() {
    .Call(`_babelmixr2_popedFree`)
}

popedGetLoadedInfo <- function() {
    .Call(`_babelmixr2_popedGetLoadedInfo`)
}

popedSetup <- function(e, eglobal, full) {
    .Call(`_babelmixr2_popedSetup`, e, eglobal, full)
}

popedSolveIdME <- function(theta, umt, mt, ms, nend, id, totn) {
    .Call(`_babelmixr2_popedSolveIdME`, theta, umt, mt, ms, nend, id, totn)
}

popedSolveIdME2 <- function(theta, umt, mt, ms, nend, id, totn) {
    .Call(`_babelmixr2_popedSolveIdME2`, theta, umt, mt, ms, nend, id, totn)
}

transDv <- function(inDv, inCmt, cmtTrans, lambda, yj, low, high) {
    .Call(`_babelmixr2_transDv`, inDv, inCmt, cmtTrans, lambda, yj, low, high)
}