Revert "add popedPostSolveMat() for use in script"

This reverts commit 8553764.

NAMESPACE

@@ -175,7 +175,6 @@ export(popedGetMultipleEndpointModelingTimes)
 export(popedMultipleEndpointIndexDataFrame)
 export(popedMultipleEndpointParam)
 export(popedMultipleEndpointResetTimeIndex)
-export(popedPostSolveMat)
 export(rxModelVars)
 export(rxToMonolix)
 export(rxToNonmem)

R/RcppExports.R

@@ -149,53 +149,6 @@ popedSetup <- function(e, full) {
     .Call(`_babelmixr2_popedSetup`, e, full)
 }
 
-#' @title Get Solved f based on matched solving times
-#' @description
-#'
-#' This function takes the solved matrix and matches it to the order
-#'   of the input times and model_switch from `PopED`.  It assumes
-#'   the global time indexer has been setup with something like
-#'   `babelmixr2::popedMultipleEndpointParam()`
-#'
-#'
-#'
-#' @param matMT This is the solved matrix that with the following columns (in order):
-#'
-#' - `time`
-#'
-#' - For each endpoint it needs the following (repeated for each endpoint):
-#'
-#'   - endpoint prediction (f)
-#'   - endpoint prediction variance (w)
-#'
-#' @param env This is an R environment where the boolean indexes of
-#'   which item is a which modeling switch is saved (as well as the
-#'   last data frame solved created by this method)
-#'
-#' @return A data.frame with the following output items:
-#'
-#' - `t` The time points
-#'
-#' - `ms` The model switch
-#'
-#' - `rx_pred_` The predicted value
-#'
-#' - `w` The variance of the predicted value
-#'
-#' This also has a side effect of saving the data.frame in the
-#' environment as `s` and the boolean indexes of which item is a
-#' which modeling switch is saved in the environment as `we`
-#'
-#' (i.e. env$we[[1]] is a boolean vector of which items are model switch 1,
-#' env$we[[2]] is a boolean vector of which items are model switch 2, etc.)
-#'
-#' @keywords internal
-#'
-#' @export
-popedPostSolveMat <- function(matMT, env) {
-    .Call(`_babelmixr2_popedPostSolveMat`, matMT, env)
-}
-
 popedSolveIdME <- function(theta, id) {
     .Call(`_babelmixr2_popedSolveIdME`, theta, id)
 }

src/RcppExports.cpp

@@ -105,18 +105,6 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-// popedPostSolveMat
-Rcpp::DataFrame popedPostSolveMat(Rcpp::NumericMatrix& matMT, Rcpp::Environment& env);
-RcppExport SEXP _babelmixr2_popedPostSolveMat(SEXP matMTSEXP, SEXP envSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::NumericMatrix& >::type matMT(matMTSEXP);
-    Rcpp::traits::input_parameter< Rcpp::Environment& >::type env(envSEXP);
-    rcpp_result_gen = Rcpp::wrap(popedPostSolveMat(matMT, env));
-    return rcpp_result_gen;
-END_RCPP
-}
 // popedSolveIdME
 Rcpp::DataFrame popedSolveIdME(NumericVector& theta, int id);
 RcppExport SEXP _babelmixr2_popedSolveIdME(SEXP thetaSEXP, SEXP idSEXP) {

src/init.c

@@ -20,10 +20,8 @@ SEXP _babelmixr2_popedGetMultipleEndpointModelingTimes(SEXP, SEXP, SEXP);
 SEXP _babelmixr2_popedMultipleEndpointResetTimeIndex(void);
 SEXP _babelmixr2_popedMultipleEndpointIndexDataFrame(SEXP);
 SEXP _babelmixr2_popedMultipleEndpointParam(SEXP, SEXP, SEXP, SEXP, SEXP);
-SEXP _babelmixr2_popedPostSolveMat(SEXP, SEXP);
 
 static const R_CallMethodDef CallEntries[] = {
-  {"_babelmixr2_popedPostSolveMat", (DL_FUNC) &_babelmixr2_popedPostSolveMat, 2},
   {"_babelmixr2_popedMultipleEndpointParam",
    (DL_FUNC) &_babelmixr2_popedMultipleEndpointParam, 5},
   {"_babelmixr2_popedMultipleEndpointIndexDataFrame", (DL_FUNC) &_babelmixr2_popedMultipleEndpointIndexDataFrame, 1},

src/poped.cpp

@@ -490,15 +490,16 @@ void popedSolveFidMat(arma::mat &matMT, NumericVector &theta, int id, int nrow,
   }
 }
 
-Rcpp::DataFrame popedPostSolveMat(arma::mat& matMT, Rcpp::Environment& env) {
-  if (!globalTimeIndexer.isInitialized()) {
-     Rcpp::stop("time indexer has not been initialized");
-  }
-  size_t nrow = globalTimeIndexer.getUniqueTimes().size();//umt.size();
-  size_t nend = globalTimeIndexer.getNid();
+//[[Rcpp::export]]
+Rcpp::DataFrame popedSolveIdME(NumericVector &theta, int id) {
+  if (solveCached(theta, id)) return(as<Rcpp::DataFrame>(_popedE["s"]));
   size_t totn = globalTimeIndexer.getTimes().size();
+  size_t nend = globalTimeIndexer.getNid();
+  NumericVector t(totn);
   arma::vec f(totn);
   arma::vec w(totn);
+  size_t nrow = globalTimeIndexer.getUniqueTimes().size();//umt.size();
+  arma::mat matMT(nrow, nend*2+1);
   List we(nend);
   for (int i = 0; i < nend; i++) {
     LogicalVector curLV = LogicalVector(totn);
@@ -507,7 +508,7 @@ Rcpp::DataFrame popedPostSolveMat(arma::mat& matMT, Rcpp::Environment& env) {
     we[i] = curLV;
   }
 
-
+  popedSolveFidMat(matMT, theta, id, nrow, nend);
   // this gets the information from:
   // - the model time
   // - the model_switch
@@ -544,72 +545,12 @@ Rcpp::DataFrame popedPostSolveMat(arma::mat& matMT, Rcpp::Environment& env) {
                                     Rcpp::wrap(globalTimeIndexer.getModelSwitch()),
                                     _["rx_pred_"]=f, // match rxode2/nlmixr2 to simplify code of mtime models
                                     _["w"]=w); // w = sqrt(rx_r_)
-  env["s"] = ret;
-  env["we"] = we;
+  _popedE["s"] = ret;
+  _popedE["we"] = we;
   return ret;
 }
 
 
-//' @title Get Solved f based on matched solving times
-//' @description
-//'
-//' This function takes the solved matrix and matches it to the order
-//'   of the input times and model_switch from `PopED`.  It assumes
-//'   the global time indexer has been setup with something like
-//'   `babelmixr2::popedMultipleEndpointParam()`
-//'
-//'
-//'
-//' @param matMT This is the solved matrix that with the following columns (in order):
-//'
-//' - `time`
-//'
-//' - For each endpoint it needs the following (repeated for each endpoint):
-//'
-//'   - endpoint prediction (f)
-//'   - endpoint prediction variance (w)
-//'
-//' @param env This is an R environment where the boolean indexes of
-//'   which item is a which modeling switch is saved (as well as the
-//'   last data frame solved created by this method)
-//'
-//' @return A data.frame with the following output items:
-//'
-//' - `t` The time points
-//'
-//' - `ms` The model switch
-//'
-//' - `rx_pred_` The predicted value
-//'
-//' - `w` The variance of the predicted value
-//'
-//' This also has a side effect of saving the data.frame in the
-//' environment as `s` and the boolean indexes of which item is a
-//' which modeling switch is saved in the environment as `we`
-//'
-//' (i.e. env$we[[1]] is a boolean vector of which items are model switch 1,
-//' env$we[[2]] is a boolean vector of which items are model switch 2, etc.)
-//'
-//' @keywords internal
-//'
-//' @export
-//[[Rcpp::export]]
-Rcpp::DataFrame popedPostSolveMat(Rcpp::NumericMatrix& matMT, Rcpp::Environment& env) {
-  arma::mat matMT2 = as<arma::mat>(matMT);
-  return popedPostSolveMat(matMT2, env);
-}
-
-//[[Rcpp::export]]
-Rcpp::DataFrame popedSolveIdME(NumericVector &theta, int id) {
-  if (solveCached(theta, id)) return(as<Rcpp::DataFrame>(_popedE["s"]));
-  size_t nrow = globalTimeIndexer.getUniqueTimes().size();//umt.size();
-  size_t nend = globalTimeIndexer.getNid();
-  arma::mat matMT(nrow, nend*2+1);
-  popedSolveFidMat(matMT, theta, id, nrow, nend);
-  return popedPostSolveMat(matMT, _popedE);
-}
-
-
 void popedSolveFidMat2(arma::mat &matMT, NumericVector &theta, int id, int nrow, int nend) {
   // arma::vec ret(retD, nobs, false, true);
   rx_solving_options_ind *ind =  updateParamRetInd(theta, id);