/
abbrev.c
1344 lines (1303 loc) · 40.8 KB
/
abbrev.c
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#include <sys/stat.h>
#include <fcntl.h>
#include <stdio.h>
#include <string.h>
#include <stdint.h> /* dj: import intptr_t */
//#include "ode.h"
#include <rxode2parseSbuf.h>
#include <errno.h>
#include "dparser3.h"
#include <R.h>
#include <Rinternals.h>
#include <R_ext/Rdynload.h>
#include <Rmath.h>
#ifdef ENABLE_NLS
#include <libintl.h>
#define _(String) dgettext ("nonmem2rx", String)
/* replace pkg as appropriate */
#else
#define _(String) (String)
#endif
#include "abbrev.g.d_parser.h"
#include "strncmpi.h"
#define gBuf nonmem2rx_abbrev_gBuf
#define gBufFree nonmem2rx_abbrev_gBufFree
#define gBufLast nonmem2rx_abbrev_gBufLast
#define curP nonmem2rx_abbrev_curP
#define _pn nonmem2rx_abbrev__pn
#define freeP nonmem2rx_abbrev_freeP
#define parseFreeLast nonmem2rx_abbrev_parseFreeLast
#define parseFree nonmem2rx_abbrev_parseFree
#define max2( a , b ) ( (a) > (b) ? (a) : (b) )
#include "parseSyntaxErrors.h"
extern D_ParserTables parser_tables_nonmem2rxAbbrev;
extern char *eBuf;
extern int eBufLast;
extern sbuf sbTransErr;
char *gBuf;
int gBufFree=0;
int gBufLast = 0;
D_Parser *curP=NULL;
D_ParseNode *_pn = 0;
void freeP(void){
if (_pn){
free_D_ParseTreeBelow(curP,_pn);
free_D_ParseNode(curP,_pn);
}
_pn=0;
if (curP != NULL){
free_D_Parser(curP);
}
curP = NULL;
}
void parseFreeLast(void) {
if (gBufFree) R_Free(gBuf);
freeP();
}
void parseFree(int last) {
freeP();
if (last){
parseFreeLast();
}
}
extern sbuf curLine;
const char *abbrevPrefix;
const char *cmtInfoStr;
// from mkdparse_tree.h
typedef void (print_node_fn_t)(int depth, char *token_name, char *token_value, void *client_data);
void wprint_node_abbrev(int depth, char *name, char *value, void *client_data) {}
extern char * rc_dup_str(const char *s, const char *e);
SEXP nonmem2rxPushModelLine(const char *item1);
SEXP nonmem2rxPushScale(int scale);
SEXP nonmem2rxPushObservedDadt(int a);
SEXP nonmem2rxPushObservedThetaObs(int a);
SEXP nonmem2rxPushObservedEtaObs(int a);
SEXP nonmem2rxGetModelNum(const char *v);
SEXP nonmem2rxGetThetaNum(const char *v);
SEXP nonmem2rxGetEtaNum(const char *v);
SEXP nonmem2rxGetEpsNum(const char *v);
SEXP nonmem2rxAddLhsVar(const char* v);
SEXP nonmem2rxGetExtendedVar(const char *v);
SEXP nonmem2rxMixP(int p);
SEXP nonmem2rxNspop(int nspop);
SEXP nonmem2rxAdvan5handleK(const char* v);
int maxA = 0,
definingScale = 0;
void pushModel(void) {
if (curLine.s == NULL) return;
if (curLine.s[0] == 0) return;
nonmem2rxPushModelLine(curLine.s);
sClear(&curLine);
definingScale = 0;
}
void writeAinfo(const char *v);
int abbrevLin = 0;
int extendedCtrlInt = 0;
SEXP nonmem2rxGetScale(int scale);
int evidWarning = 0;
int idWarning = 0;
int icallWarning = 0;
int irepWarning = 0;
int simWarning=0;
int ipredSimWarning = 0;
int curMtime = 0;
int mtdiffWarning = 0;
int hasMnow = 0;
SEXP nonmem2rxPushTheta(const char *ini, const char *comment, const char *label, int nargs);
SEXP nonmem2rxNeedNmevid(void);
SEXP nonmem2rxNeedNmid(void);
SEXP nonmem2rxNeedNmid(void);
SEXP nonmem2rxNeedYtype(void);
SEXP nonmem2rxNeedDvid(void);
SEXP nonmem2rxPushScaleVolume(int scale, const char *v);
SEXP nonmem2rxHasVolume(const char *v);
SEXP nonmem2rxNeedExit(void);
int abbrev_identifier_or_constant(char *name, int i, D_ParseNode *pn) {
if (!strcmp("fbioi", name)) {
D_ParseNode *xpn = d_get_child(pn, 0);
char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
sAppendN(&curLine, "rxf.", 4);
writeAinfo(v + 1);
sAppendN(&curLine, ".", 1);
return 1;
} else if (!strcmp("alagi", name)) {
D_ParseNode *xpn = d_get_child(pn, 0);
char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
sAppendN(&curLine, "rxalag.", 7);
writeAinfo(v + 4);
sAppendN(&curLine, ".", 1);
return 1;
} else if (!strcmp("ratei", name)) {
D_ParseNode *xpn = d_get_child(pn, 0);
char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
sAppendN(&curLine, "rxrate.", 7);
writeAinfo(v + 1);
sAppendN(&curLine, ".", 1);
return 1;
} else if (!strcmp("duri", name)) {
D_ParseNode *xpn = d_get_child(pn, 0);
char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
sAppendN(&curLine, "rxdur.", 6);
writeAinfo(v + 1);
sAppendN(&curLine, ".", 1);
return 1;
} else if (!strcmp("scalei", name)) {
D_ParseNode *xpn = d_get_child(pn, 0);
char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
sAppendN(&curLine, "scale", 5);
if (v[1] == 'O' || v[1] == '0') {
sAppendN(&curLine, "0", 1);
return 1;
}
if (i == 0 && v[1] == 'C') {
if (abbrevLin == 1) {
sAppendN(&curLine, "1", 1);
return 1;
} else if (abbrevLin == 2) {
sAppendN(&curLine, "2", 1);
return 1;
}
sAppendN(&curLine, "c", 1);
return 1;
}
sAppend(&curLine, "%s", v+1);
return 1;
} else if (!strcmp("avar", name)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "'A#' NONMEM reserved variable is not translated");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
return 1;
} else if (!strcmp("cvar", name)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "'C#' NONMEM reserved variable is not translated");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
} else if (!strcmp("constant", name)) {
D_ParseNode *xpn = d_get_child(pn, 0);
char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
sAppend(&curLine, "%s", v);
return 1;
} else if (!strcmp("identifier", name)) {
D_ParseNode *xpn = d_get_child(pn, 0);
char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
if (!nmrxstrcmpi("t", v)) {
sAppendN(&curLine, "t", 1);
return 1;
} else if (!nmrxstrcmpi("time", v)) {
sAppendN(&curLine, "t", 1);
return 1;
} else if (!nmrxstrcmpi("newind", v)) {
sAppendN(&curLine, "newind", 6);
return 1;
} else if (!nmrxstrcmpi("MIXNUM", v)) {
sAppendN(&curLine, "MIXNUM", 6);
return 1;
} else if (!nmrxstrcmpi("MIXEST", v)) {
sAppendN(&curLine, "MIXNUM", 6);
return 1;
} else if (!nmrxstrcmpi("MIXP", v)) {
sAppendN(&curLine, "cur.mixp", 8);
return 1;
} else if (!nmrxstrcmpi("ICALL", v)) {
if (icallWarning == 0) {
nonmem2rxPushTheta("icall <- fix(1)", "icall set to 1 for non-simulation",
NULL, 0);
Rf_warning("icall found and added as rxode2 parameter to model; set to 4 to activate simulation code");
icallWarning=1;
}
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);
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);
return 1;
} else if (!nmrxstrcmpi("MTDIFF", v)) {
//sClear(&sbTransErr);
if (mtdiffWarning == 0) {
Rf_warning("'MTDIFF' does not reset the system in rxode2; rxode2 calculates model times at first pass");
mtdiffWarning = 1;
}
sAppendN(&curLine, "MTDIFF", 6);
return 1;
} else if (!nmrxstrcmpi("COMACT", v)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "'COMACT' NONMEM reserved variable is not translated");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
} else if (!nmrxstrcmpi("COMSAV", v)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "'COMSAV' NONMEM reserved variable is not translated");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
} else if (!nmrxstrcmpi("tscale", v)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "'TSCALE' NONMEM reserved variable is not translated");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
} else if (!nmrxstrcmpi("xscale", v)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "'XSCALE' NONMEM reserved variable is not translated");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
} else if (!nmrxstrcmpi("id", v)) {
if (idWarning == 0) {
Rf_warning("'id' variable is supported differently rxode2, renamed to 'nmid', rename/copy in your data too");
idWarning = 1;
nonmem2rxNeedNmid();
}
sAppendN(&curLine, "nmid", 4);
return 1;
} else if (!nmrxstrcmpi("evid", v)) {
if (evidWarning == 0) {
Rf_warning("'evid' variable is not supported in rxode2, renamed to 'nmevid', rename/copy in your data too");
evidWarning = 1;
nonmem2rxNeedNmevid();
}
sAppendN(&curLine, "nmevid", 6);
return 1;
} else if (!nmrxstrcmpi("amt", v)) {
// make sure amt is lower case; works around a parser bug in rxode2parse
sAppendN(&curLine, "amt", 3);
return 1;
} else if (!nmrxstrcmpi("dvid", v)) {
nonmem2rxNeedDvid();
sAppendN(&curLine, "nmdvid", 6);
return 1;
} else if (!nmrxstrcmpi("ytype", v)) {
nonmem2rxNeedYtype();
sAppendN(&curLine, "nmytype", 7);
return 1;
} else if (!nmrxstrcmpi("sim", v)) {
if (simWarning == 0) {
Rf_warning("'sim' variable is used in rxode2 simulations, renamed to 'nmsim'");
simWarning = 1;
}
sAppendN(&curLine, "nmsim", 5);
return 1;
} else if (!nmrxstrcmpi("ipredSim", v)) {
if (ipredSimWarning == 0) {
Rf_warning("'ipredSim' variable is used in rxode2 simulations, renamed to 'nmipredsim'");
ipredSimWarning = 1;
}
sAppendN(&curLine, "nmipredsim", 10);
return 1;
}
if (v[0] == 'K') nonmem2rxAdvan5handleK(v);
// use only upper case in output since NONMEM is case insensitive and rxode2 is sensitive.
if (extendedCtrlInt && strstr(curLine.s, "<-") != NULL) {
char *v2 = (char*) rc_dup_str(CHAR(STRING_ELT(nonmem2rxGetExtendedVar(v), 0)),0);
if (strcmp(v, v2)) {
// different variable, swap and continue
sAppend(&curLine, v2);
return 1;
}
}
int i = 0;
while(v[i] != 0) {
v[i] = toupper(v[i]);
i++;
}
int hasV = v[0] == 'V';
if (hasV) {
nonmem2rxHasVolume(v);
}
if (definingScale && hasV) {
nonmem2rxPushScaleVolume(definingScale-1, v);
}
sAppend(&curLine, v);
return 1;
}
return 0;
}
void writeAinfo(const char *v) {
// abbrevLin = 0 is ode
// abbrevLin = 1 is linCmt() without ka
// abbrevLin = 2 is linCmt() with ka
//
// $error block abbrevLin
// abbrevLin = 3 is ode in block
// abbrevLin = 4 is linCmt() without ka
// abbrevLin = 5 is linCmt() with ka
if (abbrevLin == 0) {
int num = atoi(v);
maxA = max2(maxA, num);
sAppend(&curLine, "rxddta%s", v);
return;
}
int cur = atoi(v);
if (abbrevLin == 3) {
maxA = max2(maxA, cur);
sAppend(&curLine, "rxddta%s%s", v, CHAR(STRING_ELT(nonmem2rxGetScale(cur), 0)));
return;
}
if (abbrevLin == 2 && cur == 1) {
sAppendN(&curLine, "depot", 5);
return;
}
if (abbrevLin == 5 && cur == 1) {
sAppend(&curLine, "dose(depot)*exp(-KA*tad(depot))%s", CHAR(STRING_ELT(nonmem2rxGetScale(cur), 0)));
return;
}
if ((abbrevLin == 1 && cur == 1) || (abbrevLin == 2 && cur == 2)) {
sAppendN(&curLine, "central", 7);
return;
}
if ((abbrevLin == 4 && cur == 1) || (abbrevLin == 5 && cur == 2)) {
sAppend(&curLine, "rxLinCmt1%s", CHAR(STRING_ELT(nonmem2rxGetScale(cur), 0)));
return;
}
sClear(&sbTransErr);
sAppend(&sbTransErr, "can only request depot and central compartments for solved systems in rxode2 translations");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
}
int abbrevParamA0(char *name, int i, D_ParseNode *pn) {
int needName=0;
if (!strcmp("a0", name) ||
(needName = !strcmp("a0I", 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(nonmem2rxGetThetaNum(v));
v = (char*)rc_dup_str(CHAR(STRING_ELT(namePar, 0)), 0);
UNPROTECT(1);
}
sAppendN(&curLine, "rxini.", 6);
cmtInfoStr=v;
writeAinfo(v);
sAppendN(&curLine, ".", 1);
}
return 1;
}
return 0;
}
int abbrevParamTheta(char *name, int i, D_ParseNode *pn) {
int needName=0;
if (!strcmp("theta", name) ||
(needName = !strcmp("thetaI", 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(nonmem2rxGetThetaNum(v));
v = (char*)rc_dup_str(CHAR(STRING_ELT(namePar, 0)), 0);
UNPROTECT(1);
}
int num = atoi(v);
nonmem2rxPushObservedThetaObs(num);
sAppend(&curLine, "theta%d", num);
}
return 1;
}
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) ||
(needName = !strcmp("etaI", 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(nonmem2rxGetEtaNum(v));
v = (char*)rc_dup_str(CHAR(STRING_ELT(namePar, 0)), 0);
UNPROTECT(1);
}
int num = atoi(v);
nonmem2rxPushObservedEtaObs(num);
sAppend(&curLine, "eta%d", num);
}
return 1;
}
return 0;
}
int abbrevParamEps(char *name, int i, D_ParseNode *pn) {
int needName = 0;
if (!strcmp("eps", 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);
if (needName) {
SEXP namePar = PROTECT(nonmem2rxGetEpsNum(v));
v = (char*)rc_dup_str(CHAR(STRING_ELT(namePar, 0)), 0);
UNPROTECT(1);
}
sAppend(&curLine, "eps%s", v);
}
return 1;
}
return 0;
}
int abbrevParamErr(char *name, int i, D_ParseNode *pn) {
int needName = 0;
if (!strcmp("err", name) ||
(needName = !strcmp("errI", 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(nonmem2rxGetEpsNum(v));
v = (char*)rc_dup_str(CHAR(STRING_ELT(namePar, 0)), 0);
UNPROTECT(1);
}
// since parser translates $sigma
sAppend(&curLine, "eps%s", v);
}
return 1;
}
return 0;
}
int abbrevParamAmt (char *name, int i, D_ParseNode *pn) {
int needName = 0;
if (!strcmp("amt", 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);
if (needName) {
SEXP namePar = PROTECT(nonmem2rxGetModelNum(v));
v = (char*)rc_dup_str(CHAR(STRING_ELT(namePar, 0)), 0);
UNPROTECT(1);
}
// since parser translates $sigma
writeAinfo(v);
}
return 1;
}
return 0;
}
int abbrevParamMixp(char *name, int i, D_ParseNode *pn) {
if (!strcmp("mixp", name)) {
if (i == 0) {
D_ParseNode *xpn = d_get_child(pn, 1);
char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
sAppend(&curLine, "rxp.%s.", v);
return 1;
}
return 1;
} else if (!strcmp("mixpc", name)) {
if (i == 0) {
sAppendN(&curLine, "cur.mixp", 8);
}
return 1;
}
return 0;
}
int abbrev_params(char *name, int i, D_ParseNode *pn) {
return abbrevParamTheta(name, i, pn) ||
abbrevParamEta(name, i, pn) ||
abbrevParamEps(name, i, pn) ||
abbrevParamErr(name, i, pn) ||
abbrevParamAmt(name, i, pn) ||
abbrevParamA0(name, i, pn) ||
abbrevParamDaDt(name, i, pn) ||
abbrevParamMixp(name, i, pn);
}
int abbrev_function(char *name, int i, D_ParseNode *pn) {
if (!strcmp("function", name)) {
if (i == 0) {
D_ParseNode *xpn = d_get_child(pn, 0);
char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
if (v[0] == 'D' || v[0] == 'd') v++;
if (!nmrxstrcmpi("LOG(", v)) {
sAppendN(&curLine, "log(", 4);
return 1;
} else if (!nmrxstrcmpi("LOG10(", v)) {
sAppendN(&curLine, "log10(", 6);
return 1;
} else if (!nmrxstrcmpi("EXP(", v)) {
sAppendN(&curLine, "exp(", 4);
return 1;
} else if (!nmrxstrcmpi("SQRT(", v)) {
sAppendN(&curLine, "sqrt(", 5);
return 1;
} else if (!nmrxstrcmpi("SIN(", v)) {
sAppendN(&curLine, "sin(", 4);
return 1;
} else if (!nmrxstrcmpi("COS(", v)) {
sAppendN(&curLine, "cos(", 4);
return 1;
} else if (!nmrxstrcmpi("ABS(", v)) {
sAppendN(&curLine, "abs(", 4);
return 1;
} else if (!nmrxstrcmpi("TAN(", v)) {
sAppendN(&curLine, "tan(", 4);
return 1;
} else if (!nmrxstrcmpi("ASIN(", v)) {
sAppendN(&curLine, "asin(", 5);
return 1;
} else if (!nmrxstrcmpi("ACOS(", v)) {
sAppendN(&curLine, "acos(", 5);
return 1;
} else if (!nmrxstrcmpi("ATAN(", v)) {
sAppendN(&curLine, "atan(", 5);
return 1;
} else if (!nmrxstrcmpi("MIN(", v)) {
sAppendN(&curLine, "min(", 4);
return 1;
} else if (!nmrxstrcmpi("MAX(", v)) {
sAppendN(&curLine, "max(", 4);
return 1;
} else if (!nmrxstrcmpi("PHI(", v)) {
sAppendN(&curLine, "phi(", 4);
return 1;
} else if (!nmrxstrcmpi("GAMLN(", v)) {
sAppendN(&curLine, "lgamma(", 7);
return 1;
} else if (!nmrxstrcmpi("mod(", v)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "'MOD' function not supported in translation");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
} else if (!nmrxstrcmpi("int(", v)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "'INT' function not supported in translation");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
}
}
return 0;
}
return 0;
}
int abbrev_if1_clauses(char *name, int i, D_ParseNode *pn) {
if (!strcmp("if1", name)) {
if (i == 0) {
sAppendN(&curLine, "if (", 4);
return 1;
} else if (i == 1) {
return 1;
} else if (i == 3) {
sAppendN(&curLine, ") ", 2);
return 1;
}
return 0;
} else if (!strcmp("if1other", name)) {
if (i == 0) {
sAppendN(&curLine, "if (", 4);
return 1;
} else if (i == 1) {
return 1;
} else if (i == 3) {
sAppendN(&curLine, ") {", 3);
pushModel();
return 1;
}
return 0;
}
return 0;
}
int abbrev_if_while_clause(char *name, int i, D_ParseNode *pn) {
if (!strcmp("ifthen", name)) {
if (i == 0) {
sAppendN(&curLine, "if (", 4);
return 1;
} else if (i == 1 || i == 3) {
return 1;
} else if (i == 4) {
sAppendN(&curLine, ") {", 3);
pushModel();
return 1;
}
return 0;
} else if (!strcmp("elseif", name)) {
if (i == 0) {
sAppendN(&curLine, "} else if (", 11);
return 1;
} else if (i == 1 || i == 3) {
return 1;
} else if (i == 4) {
sAppendN(&curLine, ") {", 3);
pushModel();
return 1;
}
return 0;
} else if (!strcmp("ifcallsimeta", name)) {
if (i == 0) {
sAppendN(&curLine, "if (", 4);
return 1;
} else if (i == 3) {
sAppendN(&curLine, ") simeta()", 10);
return 1;
} else if (i != 2) {
return 1;
}
return 0;
} else if (!strcmp("ifcallsimeps", name)) {
if (i == 0) {
sAppendN(&curLine, "if (", 4);
return 1;
} else if (i == 3) {
sAppendN(&curLine, ") simeps()", 10);
return 1;
} else if (i != 2) {
return 1;
}
return 0;
} else if (!strcmp("ifcallrandom", name)) {
if (i == 0) {
sAppendN(&curLine, "if (", 4);
return 1;
} else if (i == 3) {
sAppendN(&curLine, ") R <- rxunif()", 15);
return 1;
} else if (i != 2) {
return 1;
}
return 0;
} else if (!strcmp("ifexit", name)) {
if (i == 0) {
sAppendN(&curLine, "if (", 4);
return 1;
} else if (i == 1 || i == 4 || i == 5 || i == 6) {
return 1;
} else if (i == 3) {
D_ParseNode *xpn = d_get_child(pn, 5);
char *v1 = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
xpn = d_get_child(pn, 6);
char *v2 = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
sAppend(&curLine, ") ierprdu <- 100000 * %s + %s", v1, v2);
nonmem2rxNeedExit();
return 1;
}
return 0;
} else if (!strcmp("dowhile", name)) {
if (i == 0) {
sClear(&curLine);
sAppendN(&curLine, "while (", 7);
return 1;
} else if (i == 1 || i == 2) {
return 1;
} else if (i ==4) {
sAppendN(&curLine, ") {", 3);
pushModel();
return 1;
}
return 0;
}
return 0;
}
SEXP nonmem2rxPushSigmaEst(int x, int y);
SEXP nonmem2rxPushOmegaEst(int x, int y);
int verbWarning = 0,
includeWarning = 0;
int abbrev_unsupported_lines(char *name, int i, D_ParseNode *pn) {
if (!strcmp("verbatimCode", name)) {
if (verbWarning == 0) {
Rf_warning("verbatim code is not supported in translation\nignored verbatim in %s", abbrevPrefix);
verbWarning = 1;
}
return 1;
} else if (!strcmp("includeCode", name)) {
if (verbWarning == 0) {
Rf_warning("include is not supported in translation\nignored include in %s", abbrevPrefix);
verbWarning = 1;
}
return 1;
} else if (!strcmp("comresn1", name)) {
if (i ==0) Rf_warning("'COMRES = -1' ignored");
} else if (!strcmp("callfl", name)) {
if (i == 1) Rf_warning("'CALLFL = ' ignored");
return 1;
} else if (!strcmp("call_protocol_phrase", name)) {
if (i == 1) {
char *v = (char*)rc_dup_str(pn->start_loc.s, pn->end);
Rf_warning("NONMEM call protocol phrase ignored\n %s", v);
}
return 1;
} else if (!strcmp("callpassmode", name)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "'CALL PASS(MODE)' statements not supported in translation");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
} else if (!strcmp("callsupp", name)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "'CALL SUPP(# , #)' statements not supported in translation");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
} else if (!strcmp("dt", name)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "DT(#) not supported in translation");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
} else if (!strcmp("mtime", name)) {
if (i != 0) return 1;
D_ParseNode *xpn = d_get_child(pn, 1);
char *v1 = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
int p = atoi(v1);
sAppend(&curLine, "rx.mtime.%d.", p);
return 0;
} else if (!strcmp("mnext", name)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "MNEXT(#) not supported in translation");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
} else if (!strcmp("mpast", name)) {
if (i != 0) return 1;
D_ParseNode *xpn = d_get_child(pn, 1);
char *v1 = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
int p = atoi(v1);
sAppend(&curLine, "rx.mpast.%d.", p);
return 0;
} else if (!strcmp("com", name)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "COM(#) not supported in translation");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
} else if (!strcmp("pcmt", name)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "PCMT(#) not supported in translation");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
} else if (!strcmp("sigma", name)) {
if (i != 0) return 1;
D_ParseNode *xpn = d_get_child(pn, 1);
char *v1 = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
xpn = d_get_child(pn, 3);
char *v2 = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
//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);
sAppend(&curLine, "sigma.%d.%d", x, y);
nonmem2rxPushSigmaEst(x, y);
return 0;
} else if (!strcmp("sigma1", name)) {
if (i != 0) return 1;
D_ParseNode *xpn = d_get_child(pn, 1);
char *v1 = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
xpn = d_get_child(pn, 3);
//parseFree(0);
int x = atoi(v1);
Rf_warning("SIGMA(%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);
sAppend(&curLine, "sigma.%d.", x);
nonmem2rxPushSigmaEst(x, -1);
return 0;
} else if (!strcmp("omega", name)) {
if (i != 0) return 1;
D_ParseNode *xpn = d_get_child(pn, 1);
char *v1 = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
xpn = d_get_child(pn, 3);
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);
sAppend(&curLine, "omega.%d.%d", x, y);
nonmem2rxPushOmegaEst(x, y);
} else if (!strcmp("omega1", name)) {
if (i != 0) return 1;
D_ParseNode *xpn = d_get_child(pn, 1);
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);
sAppend(&curLine, "omega.%d.", x);
nonmem2rxPushOmegaEst(x, -1);
}
return 0;
}
int abbrev_mtime_related(char *name, int i, D_ParseNode *pn) {
if (!strcmp("mtimeL", name)) {
if (i == 0) {
D_ParseNode *xpn = d_get_child(pn, 1);
char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
int p = atoi(v);
curMtime = p;
sAppend(&curLine, "mtime(rx.mtime.%d.) <- ", p);
return 1;
} else if (i == 1 || i == 2 || i == 3) {
return 1;
}
}
return 0;
}
int abbrev_mix_related(char *name, int i, D_ParseNode *pn) {
if (!strcmp("prob", name)) {
if (i ==0) {
sAppendN(&curLine, "rxp.", 4);
D_ParseNode *xpn = d_get_child(pn, 1);
char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
int p = atoi(v);
nonmem2rxMixP(p);
sAppend(&curLine, "%s", v);
sAppendN(&curLine, ". <- ", 5);
return 1;
} else if (i == 1 || i == 2 || i == 3) {
return 1;
}
} else if (!strcmp("nspop", name)) {
if (i == 0) {
D_ParseNode *xpn = d_get_child(pn, 2);
char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
int p = atoi(v);
nonmem2rxNspop(p);
return 1;
} else {
return 1;
}
}
return 0;
}
int abbrev_cmt_ddt_related(char *name, int i, D_ParseNode *pn) {
int needName = 0;
if (!strcmp("derivative", name) ||
(needName = !strcmp("derivativeI", 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;
} else if (i == 1 || i == 2 || i == 3) {
return 1;
}
return 0;
} else if (!strcmp("da", name)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "DA(#, #) not supported in translation");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
} else if (!strcmp("dp", name)) {
sClear(&sbTransErr);
sAppend(&sbTransErr, "DP(#, #) not supported in translation");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
}
return 0;
}
int abbrev_cmt_properties(char *name, int i, D_ParseNode *pn) {
int needName = 0;
if (!strcmp("ini", name) ||
(needName = !strcmp("iniI", 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);
}
// a1(0) <- ....
sAppendN(&curLine, "rxini.", 6);
cmtInfoStr=v;
writeAinfo(v);
sAppendN(&curLine, ". <- ", 5);
return 1;
} else if (i == 1 || i == 2 || i == 3) {
return 1;
}
return 0;
} else if (!strcmp("fbio", name)) {
// would have to parse what the output compartment is....
// f0 and FO default to absorption lag parameters if they are not in abbreviated code
// for the translation you are out of luck.
if (i == 0) {
D_ParseNode *xpn = d_get_child(pn, 0);
char *v = (char*)rc_dup_str(xpn->start_loc.s, xpn->end);
if (v[1] == 'O' || v[1] == '0') {
sClear(&sbTransErr);
sAppend(&sbTransErr, "F0/FO is not supported in translation");
updateSyntaxCol();
trans_syntax_error_report_fn0(sbTransErr.s);
finalizeSyntaxError();
}
// f(a1) <- ....
sAppendN(&curLine, "rxf.", 4);
cmtInfoStr = v + 1;
writeAinfo(v + 1);
sAppendN(&curLine, ". <- ", 5);
return 1;
} else if (i == 1) {
return 1;