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Safe api
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@mattfidler
mattfidler committed Sep 9, 2024
1 parent 2edc22b commit af8a9d1
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Showing 3 changed files with 46 additions and 16 deletions.
1 change: 1 addition & 0 deletions inst/include/rxode2parseStruct.h
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Original file line number Diff line number Diff line change
Expand Up @@ -272,6 +272,7 @@ typedef struct {
int hasEvid2;
int useStdPow;
bool ss2cancelAllPending;
int npars;
} rx_solve;


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29 changes: 29 additions & 0 deletions src/rx2api.c
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Original file line number Diff line number Diff line change
@@ -1,11 +1,17 @@
#include "../inst/include/rxode2.h"
#include "rx2api.h"

rx_solve *getRxSolve_(void);

rx_solving_options* getSolvingOptions(rx_solve* rx) {
return rx->op;
}

rx_solving_options_ind *getSolvingOptionsInd(rx_solve *rx, int id) {
int nall = rx->nsub*rx->nsim;
if (id < 0 || id >= nall) {
Rf_error("[getSolvingOptionsInd]: id (%d) should be between [0, %d)", id, nall);
}
return &(rx->subjects[id]);
}

Expand All @@ -31,10 +37,18 @@ double getIndLogitHi(rx_solving_options_ind* ind) {


void setIndParPtr(rx_solving_options_ind* ind, int i, double val) {
rx_solve* rx = getRxSolve_();
if (i < 0 || i >= rx->npars) {
Rf_error("[setIndParPtr]: i (%d) should be between [0, %d) when assigning %f", i, rx->npars, val);
}
ind->par_ptr[i] = val;
}

double getIndParPtr(rx_solving_options_ind* ind, int i) {
rx_solve* rx = getRxSolve_();
if (i < 0 || i >= rx->npars) {
Rf_error("[getIndParPtr]: i (%d) should be between [0, %d)", i, rx->npars);
}
return ind->par_ptr[i];
}

Expand All @@ -47,10 +61,16 @@ void setIndIdx(rx_solving_options_ind* ind, int j) {
}

int getIndIx(rx_solving_options_ind* ind, int j) {
if (j < 0 || j >= ind->n_all_times) {
Rf_error("[getIndIx]: j (%d) should be between [0, %d)", j, ind->n_all_times);
}
return ind->ix[j];
}

int getIndEvid(rx_solving_options_ind* ind, int kk) {
if (kk < 0 || kk >= ind->n_all_times) {
Rf_error("[getIndEvid]: kk (%d) should be between [0, %d)", kk, ind->n_all_times);
}
return ind->evid[kk];
}

Expand All @@ -75,6 +95,9 @@ double *getIndSolve(rx_solving_options_ind* ind) {
}

double getIndDv(rx_solving_options_ind* ind, int j) {
if (j < 0 || j >= ind->n_all_times) {
Rf_error("[getIndDv]: j (%d) should be between [0, %d)", j, ind->n_all_times);
}
return ind->dv[j];
}

Expand All @@ -83,10 +106,16 @@ int getIndYj(rx_solving_options_ind* ind) {
}

double getIndLimit(rx_solving_options_ind* ind, int kk) {
if (kk < 0 || kk >= ind->n_all_times) {
Rf_error("[getIndLimit]: kk (%d) should be between [0, %d)", kk, ind->n_all_times);
}
return ind->limit[kk];
}

int getIndCens(rx_solving_options_ind* ind, int kk) {
if (kk < 0 || kk >= ind->n_all_times) {
Rf_error("[getIndCens]: kk (%d) should be between [0, %d)", kk, ind->n_all_times);
}
return ind->cens[kk];
}

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32 changes: 16 additions & 16 deletions src/rxData.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2877,7 +2877,6 @@ struct rxSolve_t {
int parType = 1;
int nPopPar = 1;
CharacterVector nmP;
int npars;
NumericVector mvIni;
int nsvar;
bool idFactor;
Expand Down Expand Up @@ -3706,7 +3705,7 @@ static inline void rxSolve_datSetupHmax(const RObject &obj, const List &rxContro
//
bool isLinearOrMidpointInterp = op->is_locf == 0 || op->is_locf == 3;
for (i = dfN; i--;){
for (j = rxSolveDat->npars; j--;){
for (j = rx->npars; j--;){
if (pars[j] == dfNames[i]){
_globals.gpar_cov[ncov] = j+1;
// We minus 2 here because that way that the covariates
Expand Down Expand Up @@ -3905,14 +3904,14 @@ static inline void rxSolve_parOrder(const RObject &obj, const List &rxControl,
rx_solve* rx = getRxSolve_();
rx_solving_options* op = rx->op;
if (_globals.gParPos != NULL) free(_globals.gParPos);
_globals.gParPos = (int*)calloc(rxSolveDat->npars*2 +
_globals.gParPos = (int*)calloc(rx->npars*2 +
rxSolveDat->sigmaN.size() + rxSolveDat->omegaN.size(), sizeof(int));// [npars]
if (_globals.gParPos == NULL){
rxSolveFree();
stop(_("cannot allocate enough memory to sort input parameters"));
}
_globals.gParPos2 = _globals.gParPos + rxSolveDat->npars; // [npars]
_globals.gsvar = _globals.gParPos2 + rxSolveDat->npars;//[sigmaN.size()]
_globals.gParPos2 = _globals.gParPos + rx->npars; // [npars]
_globals.gsvar = _globals.gParPos2 + rx->npars;//[sigmaN.size()]
_globals.govar = _globals.gsvar + rxSolveDat->sigmaN.size(); // [omegaN.size()]
std::string errStr = "";
bool allPars = true;
Expand All @@ -3927,7 +3926,7 @@ static inline void rxSolve_parOrder(const RObject &obj, const List &rxControl,
}
int i, j;

for (i = rxSolveDat->npars; i--;) {
for (i = rx->npars; i--;) {
curPar = false;
const char *p0 = CHAR(pars[i]);
// Check for the omega-style simulated parameters.
Expand Down Expand Up @@ -4053,7 +4052,7 @@ static inline void rxSolve_resample(const RObject &obj,
rx->sample = true;
if (rx->par_sample != NULL) free(rx->par_sample);
rx->par_sample = (int*)calloc(pars.size(), sizeof(int));
for (int ip = rxSolveDat->npars; ip--;){
for (int ip = rx->npars; ip--;){
for (int is = Rf_length(sampleVars); is--;){
if (!strcmp(pars[ip],CHAR(STRING_ELT(sampleVars, is)))){
rx->par_sample[ip] = 1;
Expand All @@ -4072,7 +4071,7 @@ static inline void rxSolve_resample(const RObject &obj,
parListF = clone(parList);
updatePar = true;
}
int nrow = rxSolveDat->npars;
int nrow = rx->npars;
int ncol = rx->nsub;
int size = rx->nsub*rx->nsim;
NumericMatrix iniPars(nrow, ncol,&_globals.gpars[0]);
Expand Down Expand Up @@ -4182,7 +4181,7 @@ static inline void rxSolve_normalizeParms(const RObject &obj, const List &rxCont
}
case 3: // NumericMatrix
{
gparsCovSetup(rxSolveDat->npars, rxSolveDat->nPopPar, rx->nsub*rx->nsim, ev1, rx);
gparsCovSetup(rx->npars, rxSolveDat->nPopPar, rx->nsub*rx->nsim, ev1, rx);
rxSolve_assignGpars(rxSolveDat);
rxSolve_resample(obj, rxControl, specParams, extraArgs, pars, ev1,
inits, rxSolveDat);
Expand Down Expand Up @@ -4216,7 +4215,7 @@ static inline void rxSolve_normalizeParms(const RObject &obj, const List &rxCont
ind = &(rx->subjects[cid]);
ind->linCmt = linCmt;
setupRxInd(ind, 1);
ind->par_ptr = &_globals.gpars[cid*rxSolveDat->npars];
ind->par_ptr = &_globals.gpars[cid*rx->npars];
ind->mtime = &_globals.gmtime[rx->nMtime*cid];
if (rx->nMtime > 0) ind->mtime[0]=-1;
ind->BadDose = &_globals.gBadDose[op->neq*cid];
Expand Down Expand Up @@ -4579,9 +4578,10 @@ static inline void rxSolveSaveRxSolve(rxSolve_t* rxSolveDat){
RObject _curPar;
static inline void rxSolve_assignGpars(rxSolve_t* rxSolveDat){
unsigned int i;
rx_solve* rx = getRxSolve_();
for (unsigned int j = 0; j < (unsigned int)rxSolveDat->nPopPar; j++){
for (unsigned int k = 0; k < (unsigned int)rxSolveDat->npars; k++){
i = k+rxSolveDat->npars*j;
for (unsigned int k = 0; k < (unsigned int)rx->npars; k++){
i = k+rx->npars*j;
if (ISNA(_globals.gpars[i])){
if (_globals.gParPos[k] == 0){
_globals.gpars[i] = 0;
Expand Down Expand Up @@ -4645,8 +4645,8 @@ static inline void rxSolve_assignGpars(rxSolve_t* rxSolveDat){
// rxSolveDat->parMat.attr("dimnames") = List::create(R_NilValue, rxSolveDat->parNumeric.attr("names"));
// }
// RObject ev1=_rxModels[".lastEv1"];
// std::fill_n(&_globals.gpars[0], rxSolveDat->npars*rxSolveDat->nPopPar, NA_REAL);
// gparsCovSetupConstant(ev1, rxSolveDat->npars);
// std::fill_n(&_globals.gpars[0], rx->npars*rxSolveDat->nPopPar, NA_REAL);
// gparsCovSetupConstant(ev1, rx->npars);
// // Setup a possibly new scale.
// RObject scale = rxControl[Rxc_scale];
// NumericVector scaleC = rxSetupScale(obj, scale, extraArgs);
Expand Down Expand Up @@ -5068,7 +5068,7 @@ SEXP rxSolve_(const RObject &obj, const List &rxControl,
_lastT0 = clock();
#endif// rxSolveT
CharacterVector pars = rxSolveDat->mv[RxMv_params];
rxSolveDat->npars = pars.size();
rx->npars = pars.size();
rxSolveDat->hasCmt = INTEGER(rxSolveDat->mv[RxMv_flags])[RxMvFlag_hasCmt] == 1;
// Assign Pointers
rxAssignPtr(rxSolveDat->mv);
Expand Down Expand Up @@ -5384,7 +5384,7 @@ SEXP rxSolve_(const RObject &obj, const List &rxControl,
// The event table can contain covariate information, if it is acutally a data frame or matrix.
Nullable<CharacterVector> covnames0, simnames0;
CharacterVector covnames, simnames;
rxSolveDat->eGparPos = IntegerVector(rxSolveDat->npars);
rxSolveDat->eGparPos = IntegerVector(rx->npars);
CharacterVector state = rxSolveDat->mv[RxMv_state];
CharacterVector lhs = rxSolveDat->mv[RxMv_lhs];
op->neq = state.size();
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