From b3409a821f69abb2ec1231e9fee3be0c0ae6688f Mon Sep 17 00:00:00 2001
From: Matthew Fidler <matthew.fidler@gmail.com>
Date: Sat, 30 Nov 2024 22:59:26 -0600
Subject: [PATCH] Get a bit farther on fixing issue

---
 src/genModelVars.h        | 40 ++++++++++++++++++++-------------------
 src/parseDdt.h            |  2 +-
 src/parseFunsDosing.h     |  7 +++++--
 tests/testthat/test-tad.R | 32 +++++++++++++++++++++++++++++++
 4 files changed, 59 insertions(+), 22 deletions(-)

diff --git a/src/genModelVars.h b/src/genModelVars.h
index 01a1ef5c5..3f7d29821 100644
--- a/src/genModelVars.h
+++ b/src/genModelVars.h
@@ -105,13 +105,13 @@ static inline void calcNparamsNlhsNslhs(void) {
 
 static inline void calcNextra(void) {
   int offCmt=0,nExtra = 0;
-  char *buf, buf2[200];
+  char *buf=NULL, buf2[200];
   for (int i = 0; i < tb.statei; i++){
     if (offCmt == 0 && tb.idu[i] == 0){
+      buf=tb.ss.line[tb.di[i]];
       offCmt = 1;
       nExtra++;
-      buf=tb.ss.line[tb.di[i]];
-    } else if (offCmt == 1 && tb.idu[i] == 1){
+    } else if (offCmt == 1 && tb.idu[i] == 1) {
       // There is an compartment that doesn't have a derivative
       if (tb.linCmt == 0){
         char *v = rc_dup_str(buf, 0);
@@ -203,55 +203,57 @@ static inline int sortStateVectorsErrHandle(int prop, int pass, int i) {
   if (prop == 0 || pass == 1) {
     return 1;
   }
+  char *buf = NULL;
+  buf = tb.ss.line[tb.di[i]];
   if ((prop & prop0) != 0) {
-    sAppend(&sbt, "'%s(0)', ", tb.ss.line[tb.di[i]]);
+    sAppend(&sbt, "'%s(0)', ", buf);
   }
   if ((prop & propF) != 0) {
-    sAppend(&sbt, "'f(%s)', ", tb.ss.line[tb.di[i]]);
+    sAppend(&sbt, "'f(%s)', ", buf);
   }
   if ((prop & propAlag) != 0) {
-    sAppend(&sbt, "'alag(%s)', ", tb.ss.line[tb.di[i]]);
+    sAppend(&sbt, "'alag(%s)', ", buf);
   }
   if ((prop & propRate) != 0) {
-    sAppend(&sbt, "'rate(%s)', ", tb.ss.line[tb.di[i]]);
+    sAppend(&sbt, "'rate(%s)', ", buf);
   }
   if ((prop & propDur) != 0) {
-    sAppend(&sbt, "'dur(%s)', ", tb.ss.line[tb.di[i]]);
+    sAppend(&sbt, "'dur(%s)', ", buf);
   }
   if ((prop & propTad) != 0) {
-    sAppend(&sbt, "'tad(%s)', ", tb.ss.line[tb.di[i]]);
+    sAppend(&sbt, "'tad(%s)', ", buf);
   }
   if ((prop & propTad0) != 0) {
-    sAppend(&sbt, "'tad0(%s)', ", tb.ss.line[tb.di[i]]);
+    sAppend(&sbt, "'tad0(%s)', ", buf);
   }
   if ((prop & propTafd) != 0) {
-    sAppend(&sbt, "'tafd(%s)', ", tb.ss.line[tb.di[i]]);
+    sAppend(&sbt, "'tafd(%s)', ", buf);
   }
   if ((prop & propTafd0) != 0) {
-    sAppend(&sbt, "'tafd0(%s)', ", tb.ss.line[tb.di[i]]);
+    sAppend(&sbt, "'tafd0(%s)', ", buf);
   }
   if ((prop & propTlast) != 0) {
-    sAppend(&sbt, "'tlast(%s)', ", tb.ss.line[tb.di[i]]);
+    sAppend(&sbt, "'tlast(%s)', ", buf);
   }
   if ((prop & propTlast0) != 0) {
-    sAppend(&sbt, "'tlast0(%s)', ", tb.ss.line[tb.di[i]]);
+    sAppend(&sbt, "'tlast0(%s)', ", buf);
   }
   if ((prop & propTfirst) != 0) {
-    sAppend(&sbt, "'tfirst(%s)', ", tb.ss.line[tb.di[i]]);
+    sAppend(&sbt, "'tfirst(%s)', ", buf);
   }
   if ((prop & propTfirst0) != 0) {
-    sAppend(&sbt, "'tfirst0(%s)', ", tb.ss.line[tb.di[i]]);
+    sAppend(&sbt, "'tfirst0(%s)', ", buf);
   }
   if ((prop & propPodo) != 0) {
-    sAppend(&sbt, "'podo(%s)', ", tb.ss.line[tb.di[i]]);
+    sAppend(&sbt, "'podo(%s)', ", buf);
   }
   if ((prop & propDose) != 0) {
-    sAppend(&sbt, "'dose(%s)', ", tb.ss.line[tb.di[i]]);
+    sAppend(&sbt, "'dose(%s)', ", buf);
   }
   // Take off trailing "',
   sbt.o -= 2;
   sbt.s[sbt.o] = 0;
-  sAppend(&sbt, " present, but d/dt(%s) not defined\n", tb.ss.line[tb.di[i]]);
+  sAppend(&sbt, " present, but d/dt(%s) not defined\n", buf);
   return 0;
 }
 
diff --git a/src/parseDdt.h b/src/parseDdt.h
index 5fd6d1adb..295296f95 100644
--- a/src/parseDdt.h
+++ b/src/parseDdt.h
@@ -40,7 +40,7 @@ static inline int new_de(const char *s, int fromWhere) {
 
 static inline int isCmtLhsStatement(nodeInfo ni, char *name, char *v) {
   int hasLhs = 0;
-  if (nodeHas(cmt_statement)){
+  if (nodeHas(cmt_statement)) {
     new_or_ith(v);
     if (tb.lh[tb.ix] || tb.ini[tb.ix]){
       hasLhs=1;
diff --git a/src/parseFunsDosing.h b/src/parseFunsDosing.h
index 72e2f51d4..ae37c2be1 100644
--- a/src/parseFunsDosing.h
+++ b/src/parseFunsDosing.h
@@ -59,11 +59,14 @@ static inline int handleFunctionTadSingleStateCcode(transFunctions *tf,char *v2)
 	if (new_de(v2, 0)){
 		// cannot be lhs statements in tad style assignments
 		// also cannot be from anywhere
+		// temporarily turn off that this is a function
+		int fn = tb.fn;
+		tb.fn = 0;
 		add_de(tf->ni, tf->name, v2, 0, 0);
-		aProp(tb.de.n);
+		// turn back on that this is a function
+		tb.fn = fn;
 	} else {
 		new_or_ith(v2);
-    aProp(tb.ix);
 	}
   sAppend(&sb, "__DDT%d__)", tb.id);
   sAppend(&sbDt, "__DDT%d__)", tb.id);
diff --git a/tests/testthat/test-tad.R b/tests/testthat/test-tad.R
index bbb7ebfb9..36352568f 100644
--- a/tests/testthat/test-tad.R
+++ b/tests/testthat/test-tad.R
@@ -519,4 +519,36 @@ rxTest({
     expect_false(isTRUE(all.equal(x$tad, x$tade)))
 
   })
+
+  test_that("tad parsing", {
+
+    mod2 <- function() {
+      ini({
+        ## Table 3 from Savic 2007
+        cl  <- 17.2 # (L/hr)
+        vc  <- 45.1 # L
+        ka  <- 0.38 # 1/hr
+        mtt <- 1.37 # hr
+        f2 <-0.5    # Fraction of 1st Order portion
+        n   <- 20.1
+      })
+      model({
+        k           <- cl/vc
+        bio <- 1-f2
+        ktr = (n+1)/mtt
+        ## note that lgammafn is the same as lgamma in R.
+        d/dt(depot1) = exp(log(bio*podo(depot))+
+                             log(ktr)+n*log(ktr*tad(depot))-
+                             ktr*tad(depot)-lgammafn(n+1))-ka*depot1
+        d/dt(depot2) <- -ka*depot2
+        f(depot2) <-f2
+        d/dt(cen)   <- ka*depot1 + ka*depot2-k*cen
+      })
+    }
+
+    mod2 <- mod2()
+
+    mod2$simulationModel
+
+  })
 })