Revert "Reduce arguments in preparation for DRY script indexer use"

This reverts commit 7f29919.

R/RcppExports.R

@@ -149,8 +149,8 @@ popedSetup <- function(e, full) {
     .Call(`_babelmixr2_popedSetup`, e, full)
 }
 
-popedSolveIdME <- function(theta, id) {
-    .Call(`_babelmixr2_popedSolveIdME`, theta, id)
+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) {

R/poped.R

@@ -42,8 +42,8 @@
 #' @export
 #' @author Matthew L. Fidler
 #' @keywords internal
-.popedSolveIdME <- function(theta, id) {
-  .Call(`_babelmixr2_popedSolveIdME`, theta, id)
+.popedSolveIdME <- function(theta, umt, mt, ms, nend, id, totn) {
+  .Call(`_babelmixr2_popedSolveIdME`, theta, umt, mt, ms, nend, id, totn)
 }
 
 #' @rdname dot-popedSolveIdME
@@ -340,7 +340,8 @@ rxUiGet.popedFfFun <- function(x, ...) {
                                                    .(.poped$maxn),
                                                    poped.db$babelmixr2$optTime)
       .popedRxRunSetup(poped.db)
-      .ret <- .popedSolveIdME(.p, .id-1)
+      .ret <- .popedSolveIdME(.p, .u, .xt, model_switch, .(length(.predDf$cond)),
+                              .id-1, .totn)
     } else if (.lu > .(.poped$maxn)) {
       .p <- p[-1]
       .popedRxRunFullSetupMe(poped.db, .xt, model_switch)

inst/poped/ex.1.a.PK.1.comp.oral.md.intro.babelmixr2.R

@@ -46,16 +46,6 @@ e <- et(list(c(0, 10),
 #xt
 e$time <-  c(1,2,8,240,245)
 
-f <- f()
-
-babel.db <- nlmixr2(f, e, "poped",
-                        popedControl(groupsize=20,
-                                     bUseGrouped_xt=TRUE,
-                                     a=list(c(DOSE=20,TAU=24),
-                                            c(DOSE=40, TAU=24)),
-                                     maxa=c(DOSE=200,TAU=24),
-                                     mina=c(DOSE=0,TAU=24),
-                                     script=TRUE))
 
 babel.db <- nlmixr2(f, e, "poped",
                         popedControl(groupsize=20,

src/RcppExports.cpp

@@ -106,14 +106,19 @@ BEGIN_RCPP
 END_RCPP
 }
 // popedSolveIdME
-Rcpp::DataFrame popedSolveIdME(NumericVector& theta, int id);
-RcppExport SEXP _babelmixr2_popedSolveIdME(SEXP thetaSEXP, SEXP idSEXP) {
+Rcpp::DataFrame popedSolveIdME(NumericVector& theta, NumericVector& umt, NumericVector& mt, IntegerVector& ms, int nend, int id, int totn);
+RcppExport SEXP _babelmixr2_popedSolveIdME(SEXP thetaSEXP, SEXP umtSEXP, SEXP mtSEXP, SEXP msSEXP, SEXP nendSEXP, SEXP idSEXP, SEXP totnSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< NumericVector& >::type theta(thetaSEXP);
+    Rcpp::traits::input_parameter< NumericVector& >::type umt(umtSEXP);
+    Rcpp::traits::input_parameter< NumericVector& >::type mt(mtSEXP);
+    Rcpp::traits::input_parameter< IntegerVector& >::type ms(msSEXP);
+    Rcpp::traits::input_parameter< int >::type nend(nendSEXP);
     Rcpp::traits::input_parameter< int >::type id(idSEXP);
-    rcpp_result_gen = Rcpp::wrap(popedSolveIdME(theta, id));
+    Rcpp::traits::input_parameter< int >::type totn(totnSEXP);
+    rcpp_result_gen = Rcpp::wrap(popedSolveIdME(theta, umt, mt, ms, nend, id, totn));
     return rcpp_result_gen;
 END_RCPP
 }

src/init.c

@@ -14,7 +14,7 @@ SEXP _babelmixr2_iniRxodePtrs(SEXP in);
 
 SEXP _babelmixr2_popedFree(void);
 SEXP _babelmixr2_popedSetup(SEXP eSEXP, SEXP fullSEXP);
-SEXP _babelmixr2_popedSolveIdME(SEXP thetaSEXP, SEXP idSEXP);
+SEXP _babelmixr2_popedSolveIdME(SEXP thetaSEXP, SEXP umtSEXP, SEXP mtSEXP, SEXP msSEXP, SEXP nendSEXP, SEXP idSEXP, SEXP totnSEXP);
 SEXP _babelmixr2_popedSolveIdME2(SEXP thetaSEXP, SEXP umtSEXP, SEXP mtSEXP, SEXP msSEXP, SEXP nendSEXP, SEXP idSEXP, SEXP totnSEXP);
 SEXP _babelmixr2_popedGetMultipleEndpointModelingTimes(SEXP, SEXP, SEXP);
 SEXP _babelmixr2_popedMultipleEndpointResetTimeIndex(void);
@@ -30,7 +30,7 @@ static const R_CallMethodDef CallEntries[] = {
    (DL_FUNC) &_babelmixr2_popedGetMultipleEndpointModelingTimes, 3},
   {"_babelmixr2_popedFree", (DL_FUNC) &_babelmixr2_popedFree, 0},
   {"_babelmixr2_popedSetup", (DL_FUNC) &_babelmixr2_popedSetup, 2},
-  {"_babelmixr2_popedSolveIdME", (DL_FUNC) &_babelmixr2_popedSolveIdME, 2},
+  {"_babelmixr2_popedSolveIdME", (DL_FUNC) &_babelmixr2_popedSolveIdME, 7},
   {"_babelmixr2_popedSolveIdME2", (DL_FUNC) &_babelmixr2_popedSolveIdME2, 7},
   {"_babelmixr2_iniRxodePtrs", (DL_FUNC) &_babelmixr2_iniRxodePtrs, 1},
   {"_babelmixr2_convertDataBack", (DL_FUNC) &_babelmixr2_convertDataBack, 13},

src/poped.cpp

@@ -491,14 +491,15 @@ void popedSolveFidMat(arma::mat &matMT, NumericVector &theta, int id, int nrow,
 }
 
 //[[Rcpp::export]]
-Rcpp::DataFrame popedSolveIdME(NumericVector &theta, int id) {
+Rcpp::DataFrame popedSolveIdME(NumericVector &theta,
+                               NumericVector &umt,
+                               NumericVector &mt, IntegerVector &ms,
+                               int nend, int id, int totn) {
   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();
+  int nrow = umt.size();
   arma::mat matMT(nrow, nend*2+1);
   List we(nend);
   for (int i = 0; i < nend; i++) {
@@ -524,12 +525,13 @@ Rcpp::DataFrame popedSolveIdME(NumericVector &theta, int id) {
   // This is not how rxode2/nlmixr2 handles the information, but this
   // routine should put it in whatever order is supplied to
   // model_switch and time
+  size_t nId = globalTimeIndexer.getNid();
   std::vector<double> ut = globalTimeIndexer.getUniqueTimes();
   for (int i = 0; i < (int)ut.size(); ++i) {
     double curT = matMT(i, 0);
     const auto& infos= globalTimeIndexer.getTimeInfo(curT);
     for (const auto& info : infos) {
-      if (info.id > (int)nend ||
+      if (info.id > (int)nId ||
           info.id <= 0) {
         Rcpp::stop("modelSwitch need to be sequential 1, 2, 3, ..., n");
       }
@@ -540,9 +542,8 @@ Rcpp::DataFrame popedSolveIdME(NumericVector &theta, int id) {
       }
     }
   }
-  DataFrame ret = DataFrame::create(_["t"]=Rcpp::wrap(globalTimeIndexer.getTimes()),
-                                    _["ms"]=
-                                    Rcpp::wrap(globalTimeIndexer.getModelSwitch()),
+  DataFrame ret = DataFrame::create(_["t"]=mt,
+                                    _["ms"]=ms,
                                     _["rx_pred_"]=f, // match rxode2/nlmixr2 to simplify code of mtime models
                                     _["w"]=w); // w = sqrt(rx_r_)
   _popedE["s"] = ret;