// [[Rcpp::export]]
Rcpp::List SIMRE(int n1, Rcpp::NumericMatrix OMEGA, int n2, Rcpp::NumericMatrix SIGMA, int seed) {
arma::mat eta;
arma::mat eps;
if(OMEGA.nrow() > 0) eta = MVGAUSS(OMEGA,n1,-1);
if(SIGMA.nrow() > 0) eps = MVGAUSS(SIGMA,n2,-1);
Rcpp::List ans;
ans["eta"] = eta;
ans["eps"] = eps;
return(ans);
}
// [[Rcpp::export]]
Rcpp::List DEVTRAN(Rcpp::List parin,
Rcpp::NumericVector inpar,
Rcpp::CharacterVector parnames_,
Rcpp::NumericVector init,
Rcpp::CharacterVector cmtnames_,
Rcpp::List funs,
Rcpp::NumericMatrix data,
Rcpp::NumericMatrix idata,
Rcpp::NumericMatrix OMEGA,
Rcpp::NumericMatrix SIGMA) {
svec parnames = Rcpp::as<svec>(parnames_);
svec cmtnames = Rcpp::as<svec>(cmtnames_);
for(size_t i=0; i < cmtnames.size(); i++) cmtnames[i] += "_0";
bool lc = Rcpp::as<bool> (parin["lc"]);
unsigned int verbose = Rcpp::as<int> (parin["verbose"]);
bool debug = Rcpp::as<bool> (parin["debug"] );
int digits = Rcpp::as<int> (parin["digits"] );
double tscale = Rcpp::as<double> (parin["tscale"] );
bool obsonly = Rcpp::as<bool> (parin["obsonly"]);
bool obsaug = Rcpp::as<bool> (parin["obsaug"] );
int recsort = Rcpp::as<int> (parin["recsort"]);
bool filbak = Rcpp::as<bool> (parin["filbak"]);
int advan = Rcpp::as<int> (parin["advan"]);
double mindt = Rcpp::as<double> (parin["mindt"]);
if(mindt > 1E-4) Rcpp::Rcout << "Warning: mindt may be too large (" << mindt << ")" << std::endl;
// Create data objects from data and idata
dataobject *dat = new dataobject(data,parnames);
dat->map_uid();
dat->locate_tran(lc);
dataobject *idat = new dataobject(idata, parnames,cmtnames);
idat -> map_uid();
idat -> idata_row();
// Number of individuals in the data set
unsigned int NID = dat->nid();
int nidata = idat->nrow();
Rcpp::List ret; // list for returning stuff
int i=0,j=0,k=0;
double time0 = 0.0;
unsigned int crow =0, neq=0; //
Rodeproblem *prob;
size_t h=0;
obsaug = obsaug & (data.nrow() > 0);
bool ev_before_table = true;
bool put_ev_first = false;
bool addl_ev_first = true;
switch (recsort) {
case 1:
break;
case 2:
put_ev_first = false;
addl_ev_first = false;
break;
case 3:
put_ev_first = true;
addl_ev_first = true;
break;
case 4:
put_ev_first = true;
addl_ev_first = false;
break;
default:
CRUMP("recsort must be 1, 2, 3, or 4.");
}
// stime is a matrix, not a vector, with multiple columns to specify multiple designs
// Matrix of observations (stime), one column per design
Rcpp::NumericMatrix tgrid = Rcpp::as<Rcpp::NumericMatrix>(parin["tgridmatrix"]);
// Vector of length idata.nrow() that maps each ID to a design
// Already has C indexing
Rcpp::IntegerVector tgridi = Rcpp::as<Rcpp::IntegerVector>(parin["whichtg"]);
if(tgridi.size()==0) tgridi = Rcpp::rep(0,NID);
if(tgridi.size() < NID) CRUMP("Length of design indicator less than NID.");
if(max(tgridi) >= tgrid.ncol()) Rcpp::stop("Insufficient number of designs specified for this problem.");
// Number of designs
unsigned int ntgrid = tgrid.ncol();
// Number of non-na times in each design
std::vector<int> tgridn;
if(ntgrid>1) {
for(i = 0; i < tgrid.ncol(); i++) {
tgridn.push_back(Rcpp::sum(!Rcpp::is_na(tgrid(Rcpp::_,i))));
}
} else {
tgridn.push_back(tgrid.nrow());
}
// for(i=0; i < tgridn.size(); i++) nREP(tgridn[i]);
//obsonly = obsonly && (!(data.ncol() > 1));
int idataid = 0;
// find ID column in idata
if(idata.nrow() > 0) idataid = idat->idcol();
// These are the requested columns.
Rcpp::IntegerVector request;
ivec data_carry, idata_carry;
svec tran_carry;
// Number of requested compartments
// Number of items from data carried into answer
// Number of items in idata matrix carried into answer
// Number of tran data items carried into answer
int nreq=0, n_data_carry=0, n_idata_carry=0, n_tran_carry=0;
request = parin["request"];
nreq = request.size();
// Columns from the data set to carry:
data_carry = Rcpp::as<ivec >(parin["carry_data"]);
n_data_carry = data_carry.size();
// Tran Items to carry:
tran_carry = Rcpp::as<svec >(parin["carry_tran"]);
n_tran_carry = tran_carry.size();
if(idata.nrow()>0) {
idata_carry = Rcpp::as<ivec>(parin["carry_idata"]);
n_idata_carry = idata_carry.size();
}
// Vector of simulation times
// only active if no evid=0 records in data (cleared out in that case).
dvec stimes = Rcpp::as<dvec>(parin["stimes"]);
dvec ptimes = Rcpp::as<dvec>(parin["ptimes"]);
dvec mtimes = Rcpp::as<dvec>(parin["mtime"]);
svec tablenames = Rcpp::as<svec> (parin["table_names"]);
int ntable = tablenames.size();
if(debug) say("Creating Rodeproblem object");
prob = new Rodeproblem(inpar, init);
prob->copy_parin(parin);
prob->copy_funs(funs);
neq = prob->neq();
prob->advan(advan);
prob->init_call_record(time0);
switch(advan) {
case 13:
break;
case 2:
break;
case 4:
break;
case 1:
break;
case 3:
break;
default:
CRUMP("advan must be either 13, 2, or 4");
}
// Every ID in the data set needs to be found in idata if supplied:
// dataobject.cpp
if(nidata > 0) dat->check_idcol(idat);
// Allocate the record list and resize for each ID:
// stimes will get push_backed for now;
if(debug) say("Allocating the record stack.");
recstack a(NID);
if(data.ncol()>1) {
// if data is full, this will be all observations and events;
// if data is condensed, this will be just events and observations from stimes
if(debug) say("Resizing ...");
for(recstack::iterator it = a.begin(); it !=a.end(); ++it) {
i = it - a.begin();
(*it).resize((dat->end(i) - dat->start(i))+1);
}
if(debug) say("done.");
}
double tto, tfrom;
//double ttmp;
int obscount = 0;
int evcount = 0;
// dataobject.cpp
// Extract data records from the data set
dat->get_records(a, NID, neq, obscount, evcount,obsonly,debug);
// Offset for getting parameters from the data set (not idata)
//int posoff = t2cov && obscount > 0 ? 1 : 0;
// Deal with stimes:
// Observations from stime will always come after events;
unsigned int nextpos = 0;
if((obscount > 0) && (!obsaug)) {
if(debug) say("Clearing stimes ...");
stimes.clear();
ptimes.clear();
}
bool extra_times = (stimes.size()>0) || (ptimes.size()>0);
if(extra_times) {
nextpos = put_ev_first ? (data.nrow() + 10) : -100;
double id;
size_t n = stimes.size();
size_t m = ptimes.size();
unsigned int thisind=0;
if(debug) Rcpp::Rcout << "Adding observations from stime and sorting " << std::endl;
//if(debug && (!ipass)) say(" No ipass; will sort now");
for(recstack::iterator it = a.begin(); it != a.end(); ++it) {
thisind = it-a.begin();
id = dat->get_uid(thisind);
j = idat->get_idata_row(id);
n = tgridn[tgridi[j]];
for(h=0; h < n; h++) {
rec_ptr obs(new datarecord(0,tgrid(h,tgridi[j]),0,nextpos,id));
(*it).push_back(obs);
++obscount;
} // done adding stimes;
for(h=0; h < m; h++) {
rec_ptr obs(new datarecord(0,ptimes[h], 0, nextpos, id));
obs->output(false);
(*it).push_back(obs);
}
// sort the records by time and original position only if we're not doing checkout
std::sort((*it).begin(), (*it).end(), CompByTimePosRec);
}
}
unsigned int NN = obscount;
if(!obsonly) NN = NN + evcount;
// Create results matrix:
// rows: ntime*nset
// cols: rep, time, eq[0], eq[1], ..., yout[0], yout[1],...
int neta = 0;
arma::mat eta;
if(OMEGA.nrow() > 0) {
eta = MVGAUSS(OMEGA,NID,-1);
neta = eta.n_cols;
}
prob->neta(OMEGA.ncol());
int neps = 0;
arma::mat eps;
if(SIGMA.nrow() > 0) {
eps = MVGAUSS(SIGMA, NN, -1);
neps = eps.n_cols;
}
prob->neps(SIGMA.ncol());
// Figure out the output data set:
const unsigned int n_out_col = 2 + n_tran_carry + n_data_carry + n_idata_carry + nreq + ntable;
Rcpp::NumericMatrix ans(NN,n_out_col);
const unsigned int tran_carry_start = 2;
const unsigned int data_carry_start = tran_carry_start + n_tran_carry;
const unsigned int idata_carry_start = data_carry_start + n_data_carry;
const unsigned int req_start = idata_carry_start+n_idata_carry;
const unsigned int table_start = req_start+nreq;
// Fill in id and time:
/// This happens no matter what
if(debug) Rcpp::Rcout << "Filling in time and ID ... " << std::endl;
crow = 0; // current row counter:
for(recstack::const_iterator it = a.begin(); it !=a.end(); ++it) {
for(reclist::const_iterator itt = (*it).begin(); itt != (*it).end(); ++itt) {
// Only if this is an output record:
// may not be output record if obsonly was TRUEs
if((*itt)->output()) {
ans(crow, 0) = (*itt)->id();
ans(crow,1) = (*itt)->time();
crow++;
}
}
}
// Carry along TRAN data items (evid, amt, ii, ss, rate)
Rcpp::CharacterVector tran_names;
if(n_tran_carry > 0) {
if(debug) say("Filling in carried items ...");
svec::const_iterator tcbeg = tran_carry.begin();
svec::const_iterator tcend = tran_carry.end();
// items in tran_carry are always lc
bool carry_evid = std::find(tcbeg,tcend, "evid") != tcend;
bool carry_cmt = std::find(tcbeg,tcend, "cmt") != tcend;
bool carry_amt = std::find(tcbeg,tcend, "amt") != tcend;
bool carry_ii = std::find(tcbeg,tcend, "ii") != tcend;
bool carry_addl = std::find(tcbeg,tcend, "addl") != tcend;
bool carry_ss = std::find(tcbeg,tcend, "ss") != tcend;
bool carry_rate = std::find(tcbeg,tcend, "rate") != tcend;
bool carry_aug = std::find(tcbeg,tcend, "a.u.g") != tcend;
if(carry_evid) tran_names.push_back("evid");
if(carry_amt) tran_names.push_back("amt");
if(carry_cmt) tran_names.push_back("cmt");
if(carry_ss) tran_names.push_back("ss");
if(carry_ii) tran_names.push_back("ii");
if(carry_addl) tran_names.push_back("addl");
if(carry_rate) tran_names.push_back("rate");
if(carry_aug) tran_names.push_back("a.u.g");
crow = 0; // current output row
for(recstack::const_iterator it = a.begin(); it !=a.end(); ++it) {
for(reclist::const_iterator itt = (*it).begin(); itt != (*it).end(); ++itt) {
if(!(*itt)->output()) continue;
int n = 0;
if(carry_evid) {ans(crow,n+2) = (*itt)->evid(); n++;}
if(carry_amt) {ans(crow,n+2) = (*itt)->amt(); n++;}
if(carry_cmt) {ans(crow,n+2) = (*itt)->cmt(); n++;}
if(carry_ss) {ans(crow,n+2) = (*itt)->ss(); n++;}
if(carry_ii) {ans(crow,n+2) = (*itt)->ii(); n++;}
if(carry_addl) {ans(crow,n+2) = (*itt)->addl(); n++;}
if(carry_rate) {ans(crow,n+2) = (*itt)->rate(); n++;}
if(carry_aug) {ans(crow,n+2) = ((*itt)->pos()==nextpos) && obsaug; n++;}
crow++;
}
}
}
// Carry items from data or idata
if(((n_idata_carry > 0) || (n_data_carry > 0)) ) {
if(debug) {
Rcpp::Rcout << "Copying items from data and idata into answer..." << std::endl;
Rcpp::Rcout << "Carrying " << n_idata_carry << " items from idata." << std::endl;
Rcpp::Rcout << "Carrying " << n_data_carry << " items from data set." << std::endl;
}
crow = 0;
int lastpos = -1;
unsigned int idatarow=0;
bool carry_from_data = n_data_carry > 0;
for(recstack::iterator it=a.begin(); it!=a.end(); ++it) {
j = it-a.begin();
if((n_idata_carry > 0) && (nidata > 0)) {
idatarow = idat->get_idata_row(dat->get_uid(j));
}
std::vector<rec_ptr> thisi = *it;
for(size_t i=0; i < thisi.size(); i++) {
if(carry_from_data) {
// Need to reset this for each ID; indicates that
// We haven't hit a dataset record yet
if(i==0) lastpos = -1;
// Need to log lastpos here regardless
if(thisi.at(i)->from_data()) lastpos = thisi.at(i)->pos();
}
if(!thisi.at(i)->output()) continue;
// Copy from idata:
for(k=0; k < n_idata_carry; k++) {
ans(crow, idata_carry_start+k) = idata(idatarow,idata_carry[k]);
}
if(carry_from_data) {
if(lastpos >=0) {
for(k=0; k < n_data_carry; k++) ans(crow, data_carry_start+k) = data(lastpos,data_carry[k]);
} else {
for(k=0; k < n_data_carry; k++) ans(crow, data_carry_start+k) = data(dat->start(j),data_carry[k]);
}
}
// Increment current row:
++crow;
}
}
}
if((verbose||debug)) {
//Rcpp::Rcout << std::endl << "========================" << std::endl;
Rcpp::Rcout << std::endl;
Rcpp::Rcout << "THIS IS MRGSOLVE (DEVTRAN) " << std::endl;
Rcpp::Rcout << "TOT. NO. OF INDIVIDUALS: " << NID << std::endl;
Rcpp::Rcout << "TOT. NO. OF OBS RECS: " << obscount << std::endl;
Rcpp::Rcout << "TOT. NO. OF EV RECS: " << evcount << std::endl;
Rcpp::Rcout << "TOT. NO. OF ETA: " << neta << std::endl;
Rcpp::Rcout << "TOT. NO. OF EPS: " << neps << std::endl;
Rcpp::Rcout << "Parameters: " << prob->npar() << std::endl;
Rcpp::Rcout << "Equations: " << neq << std::endl;
Rcpp::Rcout << "Requested compartments: ";
for(i=0; i < nreq; i++) Rcpp::Rcout << (1+request[i]) << " ";
Rcpp::Rcout << std::endl;
Rcpp::Rcout << "OUTPUT MATRIX: " << NN << " rows, " << n_out_col << " columns" << std::endl;
}
if(debug) {
Rcpp::Rcout << "========================" << std::endl;
Rcpp::Rcout << "id in data column " << (dat->idcol()+1) << std::endl;
Rcpp::Rcout << "time in data column " << (dat->col_n("time") + 1) << std::endl;
Rcpp::Rcout << "evid in data column " << (dat->col_n("evid") + 1) << std::endl ;
Rcpp::Rcout << "amt in data column " << (dat->col_n("amt")+1) << std::endl;
Rcpp::Rcout << "cmt in data column " << (dat->col_n("cmt")+1) << std::endl;
Rcpp::Rcout << "rate in data column " << (dat->col_n("rate")+1) << std::endl ;
Rcpp::Rcout << "========================" << std::endl;
}
crow = 0;
if(verbose||debug) Rcpp::Rcout << "Solving ... ";
int this_cmt = 0;
//prob->reset_newid(this_id);
// Do one last reset on parameters:
dat->reload_parameters(inpar,prob);
// First, get idata parameters from the first ID in data
idat->copy_parameters(idat->get_idata_row(dat->get_uid(0)),prob);
// Then, copy parameters from the first record in data
dat->copy_parameters(0,prob);
// The current difference between tto and tfrom
double dt = 0;
double denom = 1;
// LOOP ACROSS IDS:
for(size_t i=0; i < a.size(); i++) {
std::vector<rec_ptr> thisi = a.at(i);
tfrom = thisi.at(0)->time();
double id = thisi.at(0)->id();
double maxtime = thisi.back()->time();
prob->reset_newid(id);
if(i==0) prob->newind(0);
// Copy eta values for this ID
for(j=0; j < neta; j++) prob->eta(j,eta(i,j));
// Copy eps values:
for(j=0; j < neps; j++) prob->eps(j,eps(crow,j));
// Refresh parameters in data:
dat->reload_parameters(inpar,prob);
//Copy parameters from idata
idat->copy_parameters(idat->get_idata_row(id),prob);
// Copy parameters from data
rec_ptr this_rec = thisi.at(0);
if(this_rec->from_data()) {
// If this record is from the data set, copy parameters from data
dat->copy_parameters(this_rec->pos(), prob);
} else {
if(filbak) dat->copy_parameters(dat->start(i),prob);
}
// Calculate initial conditions:
for(k=0; k < neq; k++) prob->y_init(k,init[k]);
// Copy initials from idata
idat -> copy_inits(idat->get_idata_row(id),prob);
// Call $MAIN
prob->init_call(tfrom);
add_mtime(thisi, mtimes, prob->mtime(),(debug||verbose));
prob->table_call();
// LOOP ACROSS EACH RECORD for THIS ID:
for(size_t j=0; j < thisi.size(); j++) {
if(j==0) {
prob->solving(true);
} else {
prob->newind(2);
}
rec_ptr this_rec = thisi.at(j);
// Fill in the remaining records once system is turned off
if(prob->systemoff()) {
if(this_rec->output()) {
if(prob->CFONSTOP()) {
for(int i=0; i < ntable; i++) ans(crow,(i+table_start)) = prob->table(tablenames.at(i));
for(int k=0; k < nreq; k++) ans(crow,(k+req_start )) = prob->y(request[k]);
} else {
ans(crow,0) = NA_REAL;
}
crow++;
}
continue;
}
// For this ID, we already have parameters from the first row; only update when
// we come across a record from the data set
if(this_rec->from_data()) {
dat->copy_parameters(this_rec->pos(), prob);
}
tto = this_rec->time();
denom = tfrom == 0 ? 1 : tfrom;
dt = (tto-tfrom)/denom;
// If tto is too close to tfrom, set tto to tfrom
// dt is never negative; dt will never be < mindt when mindt==0
if((dt > 0.0) && (dt < mindt)) { // don't bother if dt==0
if(debug) {
Rcpp::Rcout << "" << std::endl;
Rcpp::Rcout << "Two records are too close to each other:" << std::endl;
Rcpp::Rcout << " evid: " << this_rec->evid() << std::endl;
Rcpp::Rcout << " tfrom: " << tfrom << std::endl;
Rcpp::Rcout << " tto: " << tto << std::endl;
Rcpp::Rcout << " dt: " << tto - tfrom << std::endl;
Rcpp::Rcout << " pos: " << this_rec->pos() << std::endl;
Rcpp::Rcout << " id: " << this_rec->id() << std::endl;
}
tto = tfrom;
}
// Only copy in a new eps value if we are actually advancing in time:
if((tto > tfrom) && (crow < NN)) {
for(int k = 0; k < neps; k++) {
prob->eps(k,eps(crow,k));
}
}
prob->evid(this_rec->evid());
prob->init_call_record(tto);
prob->INITSOLV();
// Schedule ADDL and infusion end times
if((this_rec->is_event()) && (this_rec->from_data())) {
ev_ptr ev = boost::dynamic_pointer_cast<pkevent>(this_rec);
//if(ev->evid()==11) {
// ev->amt(prob->xdose());
// ev->rate();
//}
// Grab Bioavailability
double biofrac = prob->fbio(abs(ev->cmt())-1);
if(biofrac < 0) {
CRUMP("mrgsolve: Bioavailability fraction is less than zero.");
}
ev->fn(biofrac);
// We already found an negative rate or duration in the data set.
if(ev->rate() < 0) {
if(ev->rate() == -1) {
this_cmt = ev->cmt()-1;
if(prob->rate(this_cmt) <=0) {
Rcpp::Rcout << "R(" << this_cmt + 1 << ") must be set to a positive value in $MAIN." << std::endl;
Rcpp::stop("Invalid infusion settings.");
}
ev->rate(prob->rate(this_cmt));
}
if(ev->rate() == -2) {
this_cmt = ev->cmt()-1;
if(prob->dur(this_cmt) <= 0) {
Rcpp::Rcout << "D(" << this_cmt + 1 << ") must be set to a positive value in $MAIN." << std::endl;
Rcpp::stop("Invalid infusion settings.");
}
ev->rate(ev->amt() * biofrac / prob->dur(this_cmt));
}
}
// If alag set for this compartment
// spawn a new event with no output and time modified by alag
// disarm this event
if(prob->alag(ev->cmt()) > 0) {
ev->unarm();
//int nextpos = put_ev_first ? -100 : (thisi.size() + 10);
ev_ptr newev(new pkevent(ev->cmt(),
ev->evid(),
ev->amt(),
(ev->time() + prob->alag(ev->cmt())),
ev->rate()));
newev->addl(ev->addl());
newev->ii(ev->ii());
newev->ss(ev->ss());
newev->id(ev->id());
newev->pos(-100);
newev->fn(biofrac);
newev->output(false);
reclist::iterator it = thisi.begin()+j;
advance(it,1);
thisi.insert(it,newev);
newev->schedule(thisi, maxtime,addl_ev_first);
std::sort(thisi.begin()+j,thisi.end(), CompByTimePosRec);
} else {
ev->schedule(thisi, maxtime,addl_ev_first); //pkevent.cpp
if(ev->needs_sorting()) {
std::sort(thisi.begin()+j, thisi.end(), CompByTimePosRec);
}
}
}
// Implement dosing events:
//ttmp = this_rec->time();
//prob->advance(tfrom,ttmp);
//tfrom = ttmp;
prob -> advance(tfrom,tto);
if(ev_before_table) {
if(this_rec->evid()!=2) {
this_rec->implement(prob);
if(this_rec->evid() !=0) prob->lsoda_init();
}
}
//prob->advance(tfrom,tto);
// Write save values to output matrix:
prob->table_call();
if(this_rec->output()) {
if(ntable>0) {
k=0;
for(int i=0; i < ntable; i++) {
ans(crow,k+table_start) = prob->table(tablenames.at(i));
++k;
}
}
for(int k=0; k < nreq; k++) ans(crow,(k+req_start)) = prob->y(request[k]);
crow++;
}// end if ouput()
// if(!ev_before_table) {
// if(this_rec->evid()!=2) {
// this_rec->implement(prob);
// if(this_rec->evid() !=0) prob->lsoda_init();
// }
// }
// Reset or other events:
if(this_rec->evid()==2) {
this_rec->implement(prob);
prob->lsoda_init();
}
tfrom = tto;
}
}
if((verbose||debug)) Rcpp::Rcout << "done. " << std::endl;
// Significant digits in simulated variables and outputs too
if(digits>0) for(size_t i=req_start; i < ans.ncol(); i++) ans(Rcpp::_, i) = signif(ans(Rcpp::_,i), digits);
if((tscale !=1) && (tscale >= 0)) ans(Rcpp::_,1) = ans(Rcpp::_,1) * tscale;
// // Assemble return List
ret["data"] = ans;
ret["outnames"] = tablenames;
ret["trannames"] = tran_names;
ret["issues"] = Rcpp::CharacterVector(0);
// // Clean up
delete prob;
delete dat;
delete idat;
return ret;
}
