Merge pull request #165 from nlmixr2/163-rhs-dadt

Add fix/test for dadt(#) on lhs
nlmixr2 · Sep 26, 2023 · 9f234ec · 9f234ec
2 parents c1b9a64 + c4a11a2
commit 9f234ec
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Showing 4 changed files with 3,226 additions and 3,102 deletions.
diff --git a/inst/abbrev.g b/inst/abbrev.g
@@ -1,50 +1,50 @@
 //loop
-statement_list : 
- (statement)+ ;
+statement_list :
+        (statement)+ ;
 
 // return and exit statements not supported
 
-statement 
-  : call_protocol_phrase singleLineComment?
-  | assignment singleLineComment?
-  | if1 singleLineComment?
-  | if1other singleLineComment?
-  | ifthen singleLineComment?
-  | ifcallrandom singleLineComment?
-  | ifcallsimeps singleLineComment?
-  | ifcallsimeta singleLineComment?
-  | elseif singleLineComment?
-  | else singleLineComment?
-  | endif singleLineComment?
-  | dowhile singleLineComment?
-  | enddo singleLineComment?
-  | ini singleLineComment?
-  | iniI singleLineComment?
-  | mtimeL singleLineComment?
-  | fbio singleLineComment?
-  | alag singleLineComment?     
-  | rate singleLineComment?
-  | dur singleLineComment?
-  | scale singleLineComment?
-  | derivative singleLineComment?
-  | derivativeI singleLineComment?
-  | prob singleLineComment?
-  | da singleLineComment?
-  | dp singleLineComment?
-  | callsimeta singleLineComment?
-  | callgeteta singleLineComment?
-  | callsimeps singleLineComment?
-  | callpassmode singleLineComment?
-  | callsupp singleLineComment?
-  | callrandom singleLineComment?
-  | exit_line singleLineComment?
-  | comresn1 singleLineComment?
-  | ifexit singleLineComment?
-  | callfl singleLineComment?
-  | nspop singleLineComment?
-  | verbatimCode singleLineComment?
-  | includeCode singleLineComment?
-  | singleLineComment;
+statement
+    : call_protocol_phrase singleLineComment?
+    | assignment singleLineComment?
+    | if1 singleLineComment?
+    | if1other singleLineComment?
+    | ifthen singleLineComment?
+    | ifcallrandom singleLineComment?
+    | ifcallsimeps singleLineComment?
+    | ifcallsimeta singleLineComment?
+    | elseif singleLineComment?
+    | else singleLineComment?
+    | endif singleLineComment?
+    | dowhile singleLineComment?
+    | enddo singleLineComment?
+    | ini singleLineComment?
+    | iniI singleLineComment?
+    | mtimeL singleLineComment?
+    | fbio singleLineComment?
+    | alag singleLineComment?
+    | rate singleLineComment?
+    | dur singleLineComment?
+    | scale singleLineComment?
+    | derivative singleLineComment?
+    | derivativeI singleLineComment?
+    | prob singleLineComment?
+    | da singleLineComment?
+    | dp singleLineComment?
+    | callsimeta singleLineComment?
+    | callgeteta singleLineComment?
+    | callsimeps singleLineComment?
+    | callpassmode singleLineComment?
+    | callsupp singleLineComment?
+    | callrandom singleLineComment?
+    | exit_line singleLineComment?
+    | comresn1 singleLineComment?
+    | ifexit singleLineComment?
+    | callfl singleLineComment?
+    | nspop singleLineComment?
+    | verbatimCode singleLineComment?
+    | includeCode singleLineComment?
+    | singleLineComment;
 
 
 ini         :  'A_0(' decimalintNo0 ')' '=' logical_or_expression;
@@ -70,8 +70,8 @@ callfl: 'CALLFL' '=' ('-' ('1' | '2') | '0' | '1');
 call_protocol_phrase: '(' ('OBSERVATION' 'EVENT'
         | 'OBS'
         | 'OBSERVATION' 'ONLY'
-        | 'ONLY' 'OBSERVATION' 
-        | 'ONLY' 'OBSERVATIONS' 
+        | 'ONLY' 'OBSERVATION'
+        | 'ONLY' 'OBSERVATIONS'
         | 'OBS' 'ONLY'
         | 'ONCE' 'PER' 'INDIVIDUAL' 'RECORD'
         | 'ONCE'
@@ -106,38 +106,38 @@ ifcallrandom: 'IF' '(' logical_or_expression ')' 'CALL' 'RANDOM' '(' "(10|[1-9])
 
 assignment : identifier  '='  logical_or_expression;
 
-logical_or_expression : logical_and_expression 
-    (or_expression_nm  logical_and_expression)* ;
+logical_or_expression : logical_and_expression
+        (or_expression_nm  logical_and_expression)* ;
 
 or_expression_nm: '.or.' | '.OR.';
 
-logical_and_expression : equality_expression0 
-    (and_expression_nm equality_expression0)* ;
+logical_and_expression : equality_expression0
+        (and_expression_nm equality_expression0)* ;
 
 and_expression_nm: '.and.' | '.AND.';
 
 equality_expression0 : equality_expression |
-    '(' equality_expression ')';
+        '(' equality_expression ')';
 
-equality_expression : relational_expression 
-    ((neq_expression_nm | eq_expression_nm ) relational_expression)* ;
+equality_expression : relational_expression
+        ((neq_expression_nm | eq_expression_nm ) relational_expression)* ;
 
 eq_expression_nm: '.eq.' | '.EQ.' | '==';
 neq_expression_nm: '.ne.' | '.NE.';
 
 relational_expression : additive_expression
-    ((lt_expression_nm | gt_expression_nm | le_expression_nm | ge_expression_nm) additive_expression)* ;
+        ((lt_expression_nm | gt_expression_nm | le_expression_nm | ge_expression_nm) additive_expression)* ;
 
 lt_expression_nm: '<' | '.lt.' | '.LT.';
 gt_expression_nm: '>' | '.gt.' | '.GT.';
 ge_expression_nm: '>='| '.ge.' | '.GE.';
 le_expression_nm: '<='| '.le.' | '.LE.';
 
 additive_expression : multiplicative_expression
-    (('+' | '-') multiplicative_expression)* ;
+        (('+' | '-') multiplicative_expression)* ;
 
-multiplicative_expression : unary_expression 
-    (mult_part)* ;
+multiplicative_expression : unary_expression
+        (mult_part)* ;
 
 mult_part : ('*' | '/') unary_expression ;
 
@@ -165,6 +165,9 @@ sigma  : ('SIGMA(' | 'sigma(') decimalintNo0 ',' decimalintNo0 ')';
 omega  : ('OMEGA(' | 'omega(') decimalintNo0 ',' decimalintNo0 ')';
 sigma1  : ('SIGMA(' | 'sigma(') decimalintNo0 ')';
 omega1  : ('OMEGA(' | 'omega(') decimalintNo0 ')';
+der  : ('DADT(' | 'dadt(' ) decimalintNo0 ')';
+derI : ('DADT(' | 'dadt(' ) identifier ')';
+
 
 avar:  "[Aa][0-9][0-9][0-9][0-9][0-9]";
 cvar:  "[Cc][0-9][0-9][0-9][0-9][0-9]";
@@ -185,43 +188,45 @@ duri         : "[Dd][1-9][0-9]*";
 scalei       : "[Ss]([0-9]+|C|O)";
 
 
-primary_expression 
-  : constant
-  | a0
-  | a0i
-  | fbioi
-  | alagi
-  | ratei
-  | duri
-  | scalei
-  | identifier
-  | theta
-  | thetaI
-  | eta
-  | etaI
-  | eps
-  | epsI
-  | err
-  | errI
-  | dt
-  | amt
-  | amtI
-  | mpast
-  | mnext
-  | mtime
-  | mixp
-  | mixpc
-  | avar
-  | cvar
-  | com
-  | pcmt
-  | sigma
-  | omega
-  | sigma1
-  | omega1
-  | function
-  | '(' logical_or_expression ')'
-  ;
+primary_expression
+    : constant
+    | derI
+    | der
+    | a0
+    | a0i
+    | fbioi
+    | alagi
+    | ratei
+    | duri
+    | scalei
+    | identifier
+    | theta
+    | thetaI
+    | eta
+    | etaI
+    | eps
+    | epsI
+    | err
+    | errI
+    | dt
+    | amt
+    | amtI
+    | mpast
+    | mnext
+    | mtime
+    | mixp
+    | mixpc
+    | avar
+    | cvar
+    | com
+    | pcmt
+    | sigma
+    | omega
+    | sigma1
+    | omega1
+    | function
+    | '(' logical_or_expression ')'
+    ;
 
 function : function_name (logical_or_expression)*  (',' logical_or_expression)* ')' ;
 
@@ -256,4 +261,3 @@ whitespace: ( "[ \t\r\n]+" | singleLineComment )*;
 singleLineComment: "[;:]" "[^\n]*";
 verbatimCode: '"' "[^\n]*";
 includeCode: 'include' "[^\n]*";
-
diff --git a/src/abbrev.c b/src/abbrev.c
@@ -227,13 +227,13 @@ int abbrev_identifier_or_constant(char *name, int i, D_ParseNode *pn) {
       sAppendN(&curLine, "icall", 5);
       return 1;
     } else if (!nmrxstrcmpi("IREP", v)) {
-       if (irepWarning == 0) {
-         nonmem2rxPushTheta("irep <- fix(0)", "irep set to 0 (not supported)",
-                            NULL, 0);
+      if (irepWarning == 0) {
+        nonmem2rxPushTheta("irep <- fix(0)", "irep set to 0 (not supported)",
+                           NULL, 0);
         Rf_warning("irep found and added as rxode2 parameter to model (=0); 'sim.id' is added to all multi-study simulations and currently cannot be accessed in the simulation code");
         irepWarning=1;
       }
-       sAppendN(&curLine, "irep", 4);
+      sAppendN(&curLine, "irep", 4);
       return 1;
     } else if (!nmrxstrcmpi("MTDIFF", v)) {
       //sClear(&sbTransErr);
@@ -426,6 +426,28 @@ int abbrevParamTheta(char *name, int i,  D_ParseNode *pn) {
   return 0;
 }
 
+int abbrevParamDaDt(char *name, int i, D_ParseNode *pn) {
+  int needName=0;
+  if (!strcmp("der", name) ||
+      (needName = !strcmp("derI", name))) {
+    if (i == 0) {
+      D_ParseNode *xpn = d_get_child(pn, 1);
+      char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
+      if (needName) {
+        SEXP namePar = PROTECT(nonmem2rxGetModelNum(v));
+        v  = (char*)rc_dup_str(CHAR(STRING_ELT(namePar, 0)), 0);
+        UNPROTECT(1);
+      }
+      int cur = atoi(v);
+      maxA = max2(maxA, cur);
+      nonmem2rxPushObservedDadt(cur);
+      sAppend(&curLine, "d/dt(rxddta%s)", v);
+    }
+    return 1;
+  }
+  return 0;
+}
+
 int abbrevParamEta(char *name, int i,  D_ParseNode *pn) {
   int needName=0;
   if (!strcmp("eta", name) ||
@@ -449,7 +471,7 @@ int abbrevParamEta(char *name, int i,  D_ParseNode *pn) {
 int abbrevParamEps(char *name, int i,  D_ParseNode *pn) {
   int needName = 0;
   if (!strcmp("eps", name) ||
-             (needName = !strcmp("epsI", name))) {
+      (needName = !strcmp("epsI", name))) {
     if (i == 0) {
       D_ParseNode *xpn = d_get_child(pn, 1);
       char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
@@ -488,7 +510,7 @@ int abbrevParamErr(char *name, int i,  D_ParseNode *pn) {
 int abbrevParamAmt (char *name, int i,  D_ParseNode *pn) {
   int needName = 0;
   if (!strcmp("amt", name) ||
-             (needName = !strcmp("amtI", name))) {
+      (needName = !strcmp("amtI", name))) {
     if (i == 0) {
       D_ParseNode *xpn = d_get_child(pn, 1);
       char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
@@ -530,6 +552,7 @@ int abbrev_params(char *name, int i,  D_ParseNode *pn) {
     abbrevParamErr(name, i,  pn) ||
     abbrevParamAmt(name, i,  pn) ||
     abbrevParamA0(name, i,  pn) ||
+    abbrevParamDaDt(name, i, pn) ||
     abbrevParamMixp(name, i, pn);
 }
 
@@ -810,7 +833,7 @@ int abbrev_unsupported_lines(char *name, int i, D_ParseNode *pn) {
     //parseFree(0);
     int x = atoi(v1), y = atoi(v2);
     Rf_warning("SIGMA(%d, %d) does not have an equivalent rxode2/nlmixr2 code\nreplacing with a constant from the model translation\nthis will not be updated with simulations",
-                 x, y);
+               x, y);
     sAppend(&curLine, "sigma.%d.%d", x, y);
     nonmem2rxPushSigmaEst(x, y);
     return 0;
@@ -834,7 +857,7 @@ int abbrev_unsupported_lines(char *name, int i, D_ParseNode *pn) {
     char *v2 = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
     int x = atoi(v1), y = atoi(v2);
     Rf_warning("OMEGA(%d, %d) does not have an equivalent rxode2/nlmixr2 code\nreplacing with a constant from the model translation\nthis will not be updated with simulations",
-                 x, y);
+               x, y);
     sAppend(&curLine, "omega.%d.%d", x, y);
     nonmem2rxPushOmegaEst(x, y);
   } else if (!strcmp("omega1", name)) {
@@ -843,7 +866,7 @@ int abbrev_unsupported_lines(char *name, int i, D_ParseNode *pn) {
     char *v1 = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
     int x = atoi(v1);
     Rf_warning("OMEGA(%d) does not have an equivalent rxode2/nlmixr2 code\nreplacing with a constant from the model translation\nthis will not be updated with simulations",
-                 x);
+               x);
     sAppend(&curLine, "omega.%d.", x);
     nonmem2rxPushOmegaEst(x, -1);
   }
@@ -1164,12 +1187,12 @@ void wprint_parsetree_abbrev(D_ParserTables pt, D_ParseNode *pn, int depth, prin
     pushModel();
     return;
   } else if (extendedCtrlInt &&
-              (!strcmp("assignment", name) ||
-               !strcmp("fbio", name) ||
-               !strcmp("alag", name) ||
-               !strcmp("rate", name) ||
-               !strcmp("dur", name)  ||
-               !strcmp("scale", name))) {
+             (!strcmp("assignment", name) ||
+              !strcmp("fbio", name) ||
+              !strcmp("alag", name) ||
+              !strcmp("rate", name) ||
+              !strcmp("dur", name)  ||
+              !strcmp("scale", name))) {
     D_ParseNode *xpn = d_get_child(pn, 0);
     char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
     nonmem2rxAddLhsVar(v);