Merge branch 'main' into 68-use-new-steady-state-for-lincmt

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.0.17
-Date: 2023-12-09 14:16:33 UTC
-SHA: 322bf8f43bd079b336d33cd4e3af1f7a6a91648c
+Version: 2.0.18
+Date: 2024-01-29 00:09:27 UTC
+SHA: 94be647f14bed3ecf80d9cdc30525b61ecd881ff

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rxode2parse
 Title: Parsing and Code Generation Functions for 'rxode2'
-Version: 2.0.18
+Version: 2.0.19.9000
 Authors@R: c(
     person("Matthew L.", "Fidler", , "matthew.fidler@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8538-6691")),
@@ -16,7 +16,7 @@ Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
 Description: Provides the parsing needed for 'rxode2' (Wang, Hallow and
     James (2016) <doi:10.1002/psp4.12052>). It also provides the 'stan'
     based advan linear compartment model solutions with gradients
-    (Carpenter et al (2015), <arXiv:1509.07164>) needed in 'nlmixr2'
+    (Carpenter et al (2015), <doi:10.48550/arXiv.1509.07164>) needed in 'nlmixr2'
     (Fidler et al (2019) <doi:10.1002/psp4.12445>).
     This split will reduce computational burden of recompiling 'rxode2'.
 License: GPL (>= 3)

NEWS.md

@@ -1,3 +1,15 @@
+# rxode2parse (development version)
+
+* As requested by CRAN remove the C code `SET_TYPEOF` which is no
+  longer part of the C R API.
+
+# rxode2parse 2.0.19
+
+* Added a evid suffix of 60 for cases where evid=2 adds an on event
+  (fixes tad() calculation in certain edge cases)
+
+* Initialize all variables to `NA`
+
 # rxode2parse 2.0.18
 
 * Removed linear compartment solutions with gradients from rxode2parse

cran-comments.md

@@ -1,4 +1,8 @@
-# Cran comments
-- Fixes the m1mac issues flagged by CRAN, including the overlooked issue on 1323:19
-- Removes solved systems with gradients for intel c++ compilers (because they didn't compile)
-  - Have updated reverse dependencies to check if linear compartment solutions are present before running tests
+
+# Update for full nlmixr2 update
+- Once accepted, all the nlmixr2 stack will be updated
+
+- Until the new rxode2 and nlmixr2est is fixed all reverse
+  dependencies will be broken
+
+- Changed arXiv to doi

inst/include/rxode2parseHandleEvid.h

@@ -79,28 +79,29 @@ extern "C" {
 
 #define EVIDF_MODEL_RATE_ON  9
 #define EVIDF_MODEL_RATE_OFF 7
-  //      0 = no Infusion
-  //      1 = Infusion, AMT=rate (mg/hr for instance)
-  //      2 = Infusion, duration is fixed
-  //      4 = Replacement event
-  //      5 = Multiplication event
-  //      6 = Turn off modeled duration
-  //      7 = Turn off modeled rate compartment
-  //      8 = Duration is modeled, AMT=dose; Rate = AMT/(Modeled Duration) NONMEM RATE=-2
-  //      9 = Rate is modeled, AMT=dose; Duration = AMT/(Modeled Rate) NONMEM RATE=-1
-  // c1 = Compartment numbers below 99
-  // xx =  1, regular event (no lag time)
-  // xx =  2, An infusion/rate event that doesn't look for start/end of infusion AND does not apply lags
-  // xx =  8, possibly turn off steady state infusion with lag time (needed in case spans dur)
-  // xx =  9, steady state event SS=1 with lag time
-  // xx = 10, steady state event SS=1 (no lag)
-  // xx = 19, steady state event at dose time (SS=2) with lag
-  // xx = 20, steady state event + last observed info (not lagged)
-  // xx = 21, steady state event at dose time (with absorption lag) + last observed info
-  // xx = 30, Turn off compartment
-  // xx = 40, Steady state constant infusion
-  // xx = 50, Phantom event, used for transit compartments
-  // Steady state events need a II data item > 0
+//      0 = no Infusion
+//      1 = Infusion, AMT=rate (mg/hr for instance)
+//      2 = Infusion, duration is fixed
+//      4 = Replacement event
+//      5 = Multiplication event
+//      6 = Turn off modeled duration
+//      7 = Turn off modeled rate compartment
+//      8 = Duration is modeled, AMT=dose; Rate = AMT/(Modeled Duration) NONMEM RATE=-2
+//      9 = Rate is modeled, AMT=dose; Duration = AMT/(Modeled Rate) NONMEM RATE=-1
+// c1 = Compartment numbers below 99
+// xx =  1, regular event (no lag time)
+// xx =  2, An infusion/rate event that doesn't look for start/end of infusion AND does not apply lags
+// xx =  8, possibly turn off steady state infusion with lag time (needed in case spans dur)
+// xx =  9, steady state event SS=1 with lag time
+// xx = 10, steady state event SS=1 (no lag)
+// xx = 19, steady state event at dose time (SS=2) with lag
+// xx = 20, steady state event + last observed info (not lagged)
+// xx = 21, steady state event at dose time (with absorption lag) + last observed info
+// xx = 30, Turn off compartment
+// xx = 40, Steady state constant infusion
+// xx = 50, Phantom event, used for transit compartments
+// xx = 60, Dose that does not track as a dose turn on system
+// Steady state events need a II data item > 0
 #define EVID0_REGULAR  1
 #define EVID0_RATEADJ 2
 #define EVID0_INFRM 8
@@ -111,7 +112,7 @@ extern "C" {
 #define EVID0_OFF 30
 #define EVID0_SSINF 40
 #define EVID0_PHANTOM 50
-
+#define EVID0_ONDOSE 60
 
   static inline void getWh(int evid, int *wh, int *cmt, int *wh100, int *whI, int *wh0){
     *wh = evid;
@@ -356,10 +357,9 @@ extern "C" {
     }
   }
 
+
   static inline int syncIdx(rx_solving_options_ind *ind) {
     if (ind->idx < 0) return 1; // additional dose; technically the idx doesn't relate to idose/ix
-    if (ind->ixds >= ind->ndoses) ind->ixds=ind->ndoses-1;
-    else if (ind->ixds < 0) ind->ixds=0;
     if (ind->ix[ind->idx] != ind->idose[ind->ixds]) {
       // bisection https://en.wikipedia.org/wiki/Binary_search_algorithm
       int m = getDoseNumberFromIndex(ind, ind->ix[ind->idx]);

src/codegen.h

@@ -152,7 +152,7 @@ static inline void printParamLags(char *buf, int *j) {
   sAppendN(&sbOut, "#define last_", 13);
   doDot(&sbOut, buf);
   sAppend(&sbOut, "1(x) _getParCov(_cSub, _solveData, %d, (&_solveData->subjects[_cSub])->n_all_times - 1)\n", *j);
-  
+
   sAppendN(&sbOut, "#undef lead_", 12);
   doDot(&sbOut, buf);
   sAppendN(&sbOut, "1\n", 2);
@@ -169,14 +169,14 @@ static inline void printParamLags(char *buf, int *j) {
 
   sAppendN(&sbOut, "#undef lag_", 11);
   doDot(&sbOut, buf);
-  sAppendN(&sbOut, "1\n", 2);  
+  sAppendN(&sbOut, "1\n", 2);
   sAppendN(&sbOut, "#define lag_", 12);
   doDot(&sbOut, buf);
   sAppend(&sbOut, "1(x) _getParCov(_cSub, _solveData, %d, (&_solveData->subjects[_cSub])->idx - 1)\n", *j);
 
   sAppendN(&sbOut, "#undef lag_", 11);
   doDot(&sbOut, buf);
-  sAppendN(&sbOut, "\n", 1);  
+  sAppendN(&sbOut, "\n", 1);
   sAppendN(&sbOut, "#define lag_", 12);
   doDot(&sbOut, buf);
   sAppend(&sbOut, "(x,y) _getParCov(_cSub, _solveData, %d, (&_solveData->subjects[_cSub])->idx - (y))\n", *j);
@@ -219,7 +219,7 @@ static inline void printDoubleDeclaration(char *buf) {
       !strcmp("rx_hi_", buf) || !strcmp("rx_low_", buf)){
     sAppendN(&sbOut, "__", 2);
   }
-  sAppendN(&sbOut, ";\n", 2);
+  sAppendN(&sbOut, " = NA_REAL;\n", 12);
 }
 
 static inline void printVoidDeclaration(char *buf) {

src/etTran.cpp

@@ -1224,7 +1224,7 @@ List etTransParse(List inData, List mv, bool addCmt=false,
     else caddl = inAddl[i];
     if (IntegerVector::is_na(caddl)) caddl = 0;
     // EVID flag
-    if (evidCol == -1){
+    if (evidCol == -1) {
       // Missing EVID
       if (rateI == 0 && (ISNA(camt) || camt == 0.0)){
         cevid = 0;
@@ -1256,7 +1256,7 @@ List etTransParse(List inData, List mv, bool addCmt=false,
         cevid=0;
       }
     }
-    switch(cevid){
+    switch(cevid) {
     case 0:
       // Observation
       nobs++;
@@ -1421,10 +1421,10 @@ List etTransParse(List inData, List mv, bool addCmt=false,
         ndose++;
         // + cmt needs to turn on cmts.
         // This gives a zero dose to cmt
-        if (cmtCol != -1 && cmt > 0 && cmt <= baseSize){
+        if (cmtCol != -1 && cmt > 0 && cmt <= baseSize) {
           // Turn on state with dose
           id.push_back(cid);
-          evid.push_back(cevid);
+          evid.push_back(cevid-flg+60);
           cmtF.push_back(cmt);
           time.push_back(ctime);
           amt.push_back(0.0);

src/getOption.c

@@ -8,8 +8,7 @@
 int R_get_option(const char *option, int def) {
   SEXP s, t;
   int ret, pro=0;
-  PROTECT(t = s = allocList(3));pro++;
-  SET_TYPEOF(s, LANGSXP);
+  PROTECT(t = s = LCONS(R_NilValue, allocList(2)));pro++;
   SETCAR(t, install("getOption")); t = CDR(t);
   SETCAR(t, mkString(option)); t = CDR(t);
   if (def){

tests/testthat/test-etTrans.R

@@ -534,7 +534,7 @@ d/dt(blood)     = a*intestine - b*blood
   })
 
   test_that("dat3 has evid w/amt 0", {
-    expect_equal(dat3$EVID, c(101L, 2L, 0L, 0L, 0L, 101L, 2L, 0L, 0L, 0L))
+    expect_equal(dat3$EVID, c(160L, 2L, 0L, 0L, 0L, 160L, 2L, 0L, 0L, 0L))
     expect_equal(dat3$AMT, c(0, NA, NA, NA, NA, 0, NA, NA, NA, NA))
   })