#include <RcppArmadillo.h>
#include <vector>
#include <map>
#include "c_optim.h"
namespace rstpm2 {
// import namespaces
using namespace Rcpp;
using namespace arma;
// typedefs
typedef bool constraintfn(int, double *, void *);
// enums
enum IntervalCensoring {RightCensored, ExactTime, LeftCensored, IntervalCensored};
// structs
struct li_constraint { vec li; double constraint; };
struct gradli_constraint { mat gradli; mat constraint; };
li_constraint operator+(li_constraint const &left, li_constraint const &right) {
li_constraint out = {left.li+right.li,left.constraint+right.constraint};
return out;
}
gradli_constraint operator+(gradli_constraint const &left, gradli_constraint const &right) {
gradli_constraint out = {left.gradli+right.gradli,left.constraint+right.constraint};
return out;
}
// Hadamard element-wise multiplication for the _columns_ of a matrix with a vector
mat rmult(mat m, vec v) {
mat out(m);
out.each_col() %= v;
return out;
}
mat lmult(vec v, mat m) {
return rmult(m,v);
}
// print utilities
void Rprint(NumericMatrix const & m) {
for (int i=0; i<m.nrow(); ++i) {
for (int j=0; j<m.ncol(); ++j)
Rprintf("%f ", m(i,j));
Rprintf("\n");
}
}
void Rprint(NumericVector const & v) {
for (int i=0; i<v.size(); ++i)
Rprintf("%f ", v(i));
Rprintf("\n");
}
void Rprint(vec const & v) {
for (size_t i=0; i<v.size(); ++i)
Rprintf("%f ", v(i));
Rprintf("\n");
}
void Rprint(rowvec const & v) {
for (size_t i=0; i<v.size(); ++i)
Rprintf("%f ", v(i));
Rprintf("\n");
}
void Rprint(mat const & m) {
for (size_t i=0; i<m.n_rows; ++i) {
for (size_t j=0; j<m.n_cols; ++j)
Rprintf("%f ", m(i,j));
Rprintf("\n");
}
}
// vectorised functions
vec pnorm01(vec const & x) {
vec out(x.size());
for (size_t i=0; i<x.size(); ++i)
out(i) = R::pnorm(x(i),0.0,1.0,1,0);
return out;
}
vec qnorm01(vec const & x) {
vec out(x.size());
for (size_t i=0; i<x.size(); ++i)
out(i) = R::qnorm(x(i),0.0,1.0,1,0);
return out;
}
vec dnorm01(vec const & x) {
vec out(x.size());
for (size_t i=0; i<x.size(); ++i)
out(i) = R::dnorm(x(i),0.0,1.0,0);
return out;
}
// we could use templates for the following...
vec logit(vec const & p) {
return log(p/(1-p));
}
vec expit(vec const & x) {
return 1/(1+exp(-x));
}
double logit(double p) {
return log(p/(1-p));
}
double expit(double x) {
return 1/(1+exp(-x));
}
// utility for fast ragged sums
RcppExport SEXP tapplySum(SEXP s_y, SEXP s_group) {
NumericVector y(s_y);
NumericVector group(s_group);
NumericVector::iterator iy, igroup;
std::map<double,double> out;
for (iy = y.begin(), igroup = group.begin(); iy != y.end(); ++iy, ++igroup) {
out[*igroup] += *iy;
}
return wrap(out);
}
// Various link objects
class LogLogLink {
public:
vec link(vec S) { return log(-log(S)); }
vec ilink(vec x) { return exp(-exp(x)); }
vec h(vec eta, vec etaD) { return etaD % exp(eta); }
vec H(vec eta) { return exp(eta); }
mat gradH(vec eta, mat X) { return rmult(X,exp(eta)); }
mat gradh(vec eta, vec etaD, mat X, mat XD) {
return rmult(XD, exp(eta)) + rmult(X, etaD % exp(eta));
}
cube hessianH(vec beta, mat X) {
cube c(beta.size(), beta.size(), X.n_rows);
for (size_t i=0; i<X.n_rows; ++i)
c.slice(i) = X.row(i).t()*X.row(i)*exp(dot(X.row(i),beta));
return c;
}
cube hessianh(vec beta, mat X, mat XD) {
cube c(beta.size(), beta.size(), X.n_rows);
for (size_t i=0; i<X.n_rows; ++i) {
rowvec Xi = X.row(i);
rowvec XDi = XD.row(i);
c.slice(i) = (XDi.t()*Xi + Xi.t()*XDi + dot(XDi,beta)*Xi.t()*Xi)*exp(dot(Xi,beta));
}
return c;
}
};
// Useful relationship: d/dx expit(x)=expit(x)*expit(-x)
class LogitLink {
public:
vec link(vec S) { return -logit(S); }
vec ilink(vec x) { return expit(-x); }
// vec h(vec eta, vec etaD) { return etaD % exp(eta) % expit(-eta); }
vec h(vec eta, vec etaD) { return etaD % expit(eta); }
vec H(vec eta) { return -log(expit(-eta)); }
mat gradH(vec eta, mat X) {
return rmult(X,expit(eta));
}
mat gradh(vec eta, vec etaD, mat X, mat XD) {
// return rmult(X, etaD % exp(eta) % expit(-eta)) -
// rmult(X, exp(2*eta) % etaD % expit(-eta) % expit(-eta)) +
// rmult(XD, exp(eta) % expit(-eta));
return rmult(XD, expit(eta)) +
rmult(X, expit(eta) % expit(-eta) % etaD);
}
cube hessianH(vec beta, mat X) {
cube c(beta.size(), beta.size(), X.n_rows);
for (size_t i=0; i<X.n_rows; ++i) {
colvec Xi = X.row(i);
double Xibeta = dot(Xi,beta);
c.slice(i) = Xi.t()*Xi*expit(Xibeta)*expit(-Xibeta);
}
return c;
}
cube hessianh(vec beta, mat X, mat XD) {
cube c(beta.size(), beta.size(), X.n_rows);
for (size_t i=0; i<X.n_rows; ++i) {
colvec Xi = X.row(i);
colvec XDi = XD.row(i);
double Xibeta = dot(Xi,beta);
c.slice(i) = XDi.t()*Xi*expit(Xibeta) + Xi.t()*XDi*expit(-Xibeta)*expit(Xibeta);
}
return c;
}
};
class ProbitLink {
public:
vec link(vec S) { return -qnorm01(S); }
vec ilink(vec eta) { return pnorm01(-eta); }
vec H(vec eta) { return -log(pnorm01(-eta)); }
vec h(vec eta, vec etaD) { return etaD % dnorm01(-eta) / pnorm01(-eta); }
mat gradH(vec eta, mat X) {
return rmult(X, dnorm01(-eta) / pnorm01(-eta));
}
mat gradh(vec eta, vec etaD, mat X, mat XD) {
return rmult(X, -eta % dnorm01(eta) % etaD / pnorm01(-eta)) +
rmult(X, dnorm01(eta) % dnorm01(eta) / pnorm01(-eta) / pnorm01(-eta) % etaD) +
rmult(XD,dnorm01(eta) / pnorm01(-eta));
}
};
class LogLink {
public:
vec link(vec S) { return -log(S); }
vec ilink(vec x) { return exp(-x); }
vec h(vec eta, vec etaD) { return etaD; }
vec H(vec eta) { return eta; }
mat gradh(vec eta, vec etaD, mat X, mat XD) { return XD; }
mat gradH(vec eta, mat X) { return X; }
};
// wrappers to call class methods from C
template<class T>
double optimfunction(int n, double * beta, void * void_obj) {
T * obj = static_cast<T*>(void_obj);
vec coef(beta,n);
double value = obj->objective(coef % obj->parscale);
if (obj->bfgs.trace>1) {
Rprintf("beta="); Rprint(coef);
Rprintf("objective=%g\n",value);
};
return value;
}
template<class T>
void optimgradient(int n, double * beta, double * grad, void * void_obj) {
T * obj = static_cast<T*>(void_obj);
vec coef(beta,n);
if (obj->bfgs.trace>1) {
Rprintf("beta="); Rprint(coef);
}
if (obj->bfgs.trace>2) {
Rprintf("parscale="); Rprint(obj->parscale);
}
vec gr = obj->gradient(coef % obj->parscale);
if (obj->bfgs.trace>1) {
Rprintf("gradient="); Rprint(gr);
}
if (obj->bfgs.trace>2) {
Rprintf("fdgradient="); Rprint(obj->fdgradient(coef % obj->parscale));
}
for (int i=0; i<n; ++i) grad[i] = gr[i];
}
template<class T>
void optimfunction_nlm(int n, double * beta, double * f, void * void_obj) {
T * obj = static_cast<T*>(void_obj);
vec coef(beta,n);
*f = obj->objective(coef % obj->parscale);
}
class BFGS2 : public BFGS {
public:
NumericMatrix calc_hessian(optimgr gr, void * ex) {
if (parscale.size()==0) REprintf("parscale is not defined for BFGS2::calc_hessian.\n");
int n = coef.size();
NumericVector df1(n);
NumericVector df2(n);
NumericMatrix hess(n,n);
double tmp;
for(int i=0; i<n; ++i) {
tmp = coef[i];
coef[i] = tmp + epshess/parscale[i];
gr(n, &coef[0], &df1[0], ex);
coef[i] = tmp - epshess/parscale[i];
gr(n, &coef[0], &df2[0], ex);
for (int j=0; j<n; ++j)
hess(i,j) = (df1[j] - df2[j]) / (2*epshess);
coef[i] = tmp;
}
// now symmetrize
for(int i=0; i<n; ++i)
for(int j=i; j<n; ++j)
if (i != j)
hess(i,j) = hess(j,i) = (hess(i,j) + hess(j,i)) / 2.0;
return hess; // wrap()?
}
vec parscale;
};
class NelderMead2 : public NelderMead {
public:
NumericMatrix calc_hessian(optimfn fn, void * ex) {
if (parscale.size()==0) REprintf("parscale is not defined for NelderMead2::calc_hessian.");
int n = coef.size();
NumericMatrix hess(n,n);
double tmpi,tmpj,f1,f0,fm1,hi,hj,fij,fimj,fmij,fmimj;
f0 = fn(n,&coef[0],ex);
for(int i=0; i<n; ++i) {
tmpi = coef[i];
hi = epshess*(1.0+std::abs(tmpi))/parscale[i];
coef[i] = tmpi + hi;
f1=fn(n, &coef[0], ex);
coef[i] = tmpi - hi;
fm1=fn(n, &coef[0], ex);
// hess(i,i) = (-f2 +16.0*f1 - 30.0*f0 + 16.0*fm1 -fm2)/(12.0*hi*hi);
hess(i,i) = (f1 - 2.0*f0 + fm1)/(hi*hi*parscale[i]*parscale[i]);
coef[i] = tmpi;
for (int j=i; j<n; ++j) {
if (i != j) {
tmpj = coef[j];
hj = epshess*(1.0+std::abs(tmpj))/parscale[j];
coef[i] = tmpi + hi;
coef[j] = tmpj + hj;
fij=fn(n, &coef[0], ex);
coef[i] = tmpi + hi;
coef[j] = tmpj - hj;
fimj=fn(n, &coef[0], ex);
coef[i] = tmpi - hi;
coef[j] = tmpj + hj;
fmij=fn(n, &coef[0], ex);
coef[i] = tmpi - hi;
coef[j] = tmpj - hj;
fmimj=fn(n, &coef[0], ex);
hess(j,i) = hess(i,j) = (fij-fimj-fmij+fmimj)/(4.0*hi*hj*parscale[i]*parscale[j]);
coef[i] = tmpi;
coef[j] = tmpj;
}
}
}
return hess;
}
vec parscale;
};
class Nlm2 : public Nlm {
public:
NumericMatrix calc_hessian(fcn_p fn, void * ex) {
if (parscale.size()==0) REprintf("parscale is not defined for Nlm2::calc_hessian.");
int n = coef.size();
NumericMatrix hess(n,n);
double tmpi,tmpj,f1,f0,fm1,hi,hj,fij,fimj,fmij,fmimj;
fn(n,&coef[0],&f0,ex);
for(int i=0; i<n; ++i) {
tmpi = coef[i];
hi = epshess*(1.0+std::abs(tmpi))/parscale[i];
coef[i] = tmpi + hi;
fn(n, &coef[0], &f1, ex);
coef[i] = tmpi - hi;
fn(n, &coef[0], &fm1, ex);
// hess(i,i) = (-f2 +16.0*f1 - 30.0*f0 + 16.0*fm1 -fm2)/(12.0*hi*hi);
hess(i,i) = (f1 - 2.0*f0 + fm1)/(hi*hi*parscale[i]*parscale[i]);
coef[i] = tmpi;
for (int j=i; j<n; ++j) {
if (i != j) {
tmpj = coef[j];
hj = epshess*(1.0+std::abs(tmpj))/parscale[j];
coef[i] = tmpi + hi;
coef[j] = tmpj + hj;
fn(n, &coef[0], &fij, ex);
coef[i] = tmpi + hi;
coef[j] = tmpj - hj;
fn(n, &coef[0], &fimj, ex);
coef[i] = tmpi - hi;
coef[j] = tmpj + hj;
fn(n, &coef[0], &fmij, ex);
coef[i] = tmpi - hi;
coef[j] = tmpj - hj;
fn(n, &coef[0], &fmimj, ex);
hess(j,i) = hess(i,j) = (fij-fimj-fmij+fmimj)/(4.0*hi*hj*parscale[i]*parscale[j]);
coef[i] = tmpi;
coef[j] = tmpj;
}
}
}
return hess;
}
vec parscale;
};
// Main class for Stpm2 (fully parametric)
template<class Link = LogLogLink>
class Stpm2 : public Link {
public:
typedef Stpm2<Link> This;
using Link::h;
using Link::H;
using Link::gradh;
using Link::gradH;
Stpm2(SEXP sexp) : bfgs() {
List list = as<List>(sexp);
bfgs.coef = init = as<NumericVector>(list["init"]);
X = as<mat>(list["X"]);
XD = as<mat>(list["XD"]);
bhazard = as<vec>(list["bhazard"]);
wt = as<vec>(list["wt"]);
event = as<vec>(list["event"]);
time = as<vec>(list["time"]);
delayed = as<bool>(list["delayed"]);
interval = as<bool>(list["interval"]);
n = init.size(); // number of parameters
N = X.n_rows; // number of observations
X1 = as<mat>(list["X1"]);
X0 = as<mat>(list["X1"]);
wt0.set_size(N); wt0.fill(0.0);
if (delayed) {
X0 = as<mat>(list["X0"]);
wt0 = as<vec>(list["wt0"]);
}
if (interval) {
X1 = as<mat>(list["X1"]);
}
ind0 = as<uvec>(list["ind0"]); // length N boolean
map0 = as<uvec>(list["map0"]); // length N map from individuals to row of X0
which0 = as<uvec>(list["which0"]); // length N0 indicator for X0
kappa = as<double>(list["kappa"]);
optimiser = as<std::string>(list["optimiser"]);
bfgs.trace = as<int>(list["trace"]);
reltol = bfgs.reltol = as<double>(list["reltol"]);
bfgs.hessianp = false;
bfgs.parscale = parscale = as<vec>(list["parscale"]);
}
// log-likelihood components and constraints
// Note: the li and gradli components depend on other variables (bhazard, wt, wt0, wt, event);
// calculations should *not* be done on subsets
li_constraint li_right_censored(vec eta, vec etaD) {
vec h = Link::h(eta,etaD) + bhazard;
vec H = Link::H(eta);
vec eps = h*0.0 + 1.0e-16;
double constraint = kappa/2.0 * (sum(h % h % (h<0)) +
sum(H % H % (H<0)));
h = max(h,eps);
H = max(H,eps);
vec li = wt % event % log(h) - wt % H;
li_constraint out = {li, constraint};
return out;
}
li_constraint li_left_truncated(vec eta0) {
vec H0 = Link::H(eta0);
double constraint = kappa/2.0 * sum(H0 % H0 % (H0<0));
vec eps = H0*0.0 + 1e-16;
vec li = wt0 % max(H0,eps);
li_constraint out = {li, constraint};
return out;
}
li_constraint li_interval(vec eta, vec etaD, vec eta1) {
vec H = Link::H(eta);
vec H1 = Link::H(eta1);
vec h = Link::h(eta, etaD) + bhazard;
double constraint = kappa/2.0 * (sum(H % H % (H<0))+
sum(h % h % (h<0))+
sum(H1 % H1 % (H1<0)));
vec eps = H*0.0 + 1e-16;
H = max(H,eps);
H1 = max(H1,eps);
h = max(h,eps);
vec li(N,fill::zeros);
uvec index;
index = find(ttype == 0); // right censored
if (any(index)) li(index) -= wt(index) % H(index);
index = find(ttype == 1); // exact
if (any(index)) li(index) += wt(index) % (log(h(index)) - H(index));
index = find(ttype == 2); // left censored
if (any(index)) li(index) += wt(index) % log(1-exp(-H(index)));
index = find(ttype == 3); // interval censored
if (any(index)) li(index) += wt(index) % log(exp(-H(index)) - exp(-H1(index)));
li_constraint out = {li, constraint};
return out;
}
li_constraint li(vec eta, vec etaD, vec eta0, vec eta1) {
if (interval) {
return li_interval(eta, etaD, eta1);
}
else {
li_constraint s = li_right_censored(eta, etaD);
if (delayed) {
li_constraint s0 = li_left_truncated(eta0);
s.constraint += s0.constraint;
s.li(which0) += s0.li;
}
return s;
}
}
// negative log-likelihood
double objective(vec beta) {
li_constraint s = li(X * beta, XD * beta, X0 * beta, X1 * beta);
return -sum(s.li) + s.constraint;
}
// finite-differencing of the gradient for the objective
vec fdgradient(vec beta, double eps = 1.0e-8) {
int n = beta.size();
vec grad(n);
for (int i=0; i<n; ++i) {
vec lower(beta);
vec upper(beta);
upper(i) += eps;
lower(i) -= eps;
grad(i) = (objective(upper) - objective(lower)) / 2.0 / eps;
}
return grad;
}
// log-likelihood gradient components
// Note: gradH and gradh are currently calculated at eta and etaD and may not satisfy the constraints,
// while H and h may be transformed for the constraints
gradli_constraint gradli_right_censored(vec eta, vec etaD, mat X, mat XD) {
vec h = Link::h(eta,etaD) + bhazard;
vec H = Link::H(eta);
vec eps = h*0.0 + 1.0e-16; // hack
mat gradH = Link::gradH(eta,X);
mat gradh = Link::gradh(eta,etaD,X,XD);
mat Xconstraint = kappa * (rmult(gradh,h%(h<eps)) +
rmult(gradH,H % (H<eps)));
H = max(H,eps);
h = max(h,eps);
mat Xgrad = -rmult(gradH, wt) + rmult(gradh, event / h % wt);
gradli_constraint out = {Xgrad, Xconstraint};
return out;
}
gradli_constraint gradli_left_truncated(vec eta0, mat X0) {
mat gradH0 = Link::gradH(eta0, X0);
vec H0 = Link::H(eta0);
vec eps = H0*0.0 + 1.0e-16; // hack
mat Xconstraint = kappa * rmult(gradH0, H0 % (H0<eps));
H0 = max(H0,eps);
mat Xgrad = rmult(gradH0, wt0);
gradli_constraint out = {Xgrad, Xconstraint};
return out;
}
gradli_constraint gradli_interval_censored(vec eta, vec etaD, vec eta1,
mat X, mat XD, mat X1) {
vec H = Link::H(eta);
vec h = Link::h(eta,etaD);
vec H1 = Link::H(eta1);
mat gradH = Link::gradH(eta,X);
mat gradH1 = Link::gradH(eta1,X1);
mat gradh = Link::gradh(eta, etaD, X, XD);
vec eps = H*0.0 + 1e-16;
mat Xconstraint = kappa * (rmult(gradH, H % (H<eps))+
rmult(gradh, h % (h<eps))+
rmult(gradH1, H1 % (H1<eps)));
H = max(H,eps);
H1 = max(H1,eps);
h = max(h,eps);
mat li(N,n,fill::zeros);
uvec index;
index = find(ttype == 0); // right censored
if (any(index)) li(index) -= rmult(gradH.rows(index),wt(index));
index = find(ttype == 1); // exact
if (any(index)) li(index) += rmult(gradh.rows(index),wt(index) / h(index)) - rmult(gradH.rows(index),wt(index));
index = find(ttype == 2); // left censored
if (any(index)) li(index) += rmult(-gradH.rows(index),-exp(-H(index)) / (1-exp(-H(index))) % wt(index));
index = find(ttype == 3); // interval censored
if (any(index)) {
vec V = wt(index) / (exp(-H(index)) - exp(-H1(index)));
li(index) += rmult(gradH1.rows(index),V % exp(-H1(index))) -
rmult(gradH.rows(index),V % exp(-H(index)));
}
gradli_constraint out = {li, Xconstraint};
return out;
}
gradli_constraint gradli(vec eta, vec etaD, vec eta0, vec eta1,
mat X, mat XD, mat X0, mat X1) {
if (interval) return gradli_interval_censored(eta, etaD, eta1, X, XD, X1);
else {
gradli_constraint s = gradli_right_censored(eta, etaD, X, XD);
if (delayed) {
gradli_constraint s0 = gradli_left_truncated(eta0, X0);
s.constraint.rows(which0) += s0.constraint;
s.gradli.rows(which0) += s0.gradli;
}
return s;
}
}
// gradient of the negative log-likelihood
vec gradient(vec beta) {
gradli_constraint gc = gradli(X * beta, XD * beta, X0 * beta, X1 * beta,
X, XD, X0, X1);
rowvec dconstraint = sum(gc.constraint,0);
rowvec vgr = sum(gc.gradli,0);
vec gr(n);
for (size_t i = 0; i<beta.size(); ++i) {
gr[i] = vgr[i] - dconstraint[i];
}
return -gr;
}
bool feasible(vec beta) {
vec eta = X * beta;
vec etaD = XD * beta;
vec h = Link::h(eta, etaD) + bhazard;
vec H = Link::H(eta);
bool condition = all((h>0) % (H>0));
if (delayed) {
vec eta0 = X0 * beta;
// vec etaD0 = XD0 * beta;
vec H0 = Link::H(eta0);
condition = condition && all(H0>0);
}
return condition;
}
void pre_process() {
for (int i = 0; i<n; ++i) init[i] /= parscale[i];
}
void post_process() {
for (int i = 0; i<n; ++i) {
bfgs.coef[i] *= parscale[i];
init[i] *= parscale[i];
}
}
void optimWithConstraintBFGS(NumericVector init) {
bool satisfied;
do {
bfgs.optim(&optimfunction<This>, &optimgradient<This>, init, (void *) this);
vec vcoef(&bfgs.coef[0],n);
satisfied = feasible(vcoef % parscale);
if (!satisfied) kappa *= 2.0;
} while ((!satisfied) && kappa < 1.0e3);
}
void optimWithConstraintNM(NumericVector init) {
bool satisfied;
NelderMead2 nm;
nm.hessianp = false;
nm.parscale = parscale;
do {
nm.optim(&optimfunction<This>, init, (void *) this);
vec vcoef(&nm.coef[0],n);
satisfied = feasible(vcoef % parscale);
if (!satisfied) kappa *= 2.0;
} while ((!satisfied) && kappa < 1.0e3);
nm.hessian = nm.calc_hessian(&optimfunction<This>, (void *) this);
bfgs.coef = nm.coef;
bfgs.hessian = nm.hessian;
}
void optimWithConstraint(NumericVector init) {
if (this->optimiser == "NelderMead")
optimWithConstraintNM(init);
else
optimWithConstraintBFGS(init);
}
// find the left truncated values for a given index
uvec find0() { return map0(find(ind0)); }
uvec find0(vec index) { return (map0(index))(find(ind0(index))); }
NumericVector init;
mat X, XD, X0, X1;
vec bhazard,wt,wt0,event,time,parscale,ttype;
double kappa, reltol;
bool delayed, interval;
int n, N;
BFGS2 bfgs;
uvec ind0, map0, which0;
std::string optimiser;
};
// RcppExport SEXP optim_stpm2_nlm(SEXP args) {
// stpm2 data(args);
// data.init = ew_div(data.init,data.parscale);
// int n = data.init.size();
// Nlm nlm;
// nlm.gradtl = nlm.steptl = data.reltol;
// //nlm.method=2; nlm.stepmx=0.0;
// bool satisfied;
// do {
// nlm.optim(& fminfn_nlm<stpm2>, & grfn<stpm2>, data.init, (void *) &data);
// satisfied = fminfn_constraint<stpm2>(n,&nlm.coef[0],(void *) &data);
// if (!satisfied) data.kappa *= 2.0;
// } while (!satisfied && data.kappa<1.0e5);
// nlm.coef = ew_mult(nlm.coef, data.parscale);
// return List::create(_("itrmcd")=wrap(nlm.itrmcd),
// _("niter")=wrap(nlm.itncnt),
// _("coef")=wrap(nlm.coef),
// _("hessian")=wrap(nlm.hessian));
// }
// penalised smoothers
// _Not_ sub-classes of Pstpm2, hence the longer function signatures
class SmoothLogH {
public:
struct Smoother {
int first_para, last_para;
mat S;
};
SmoothLogH(SEXP sexp) {
List list = as<List>(sexp);
List lsmooth = as<List>(list["smooth"]);
for(int i=0; i<lsmooth.size(); ++i) {
List lsmoothi = as<List>(lsmooth[i]);
List lsmoothiS = as<List>(lsmoothi["S"]);
Smoother smoothi = {
as<int>(lsmoothi["first.para"]) - 1,
as<int>(lsmoothi["last.para"]) - 1,
as<mat>(lsmoothiS[0])
};
smooth.push_back(smoothi);
}
}
double penalty(vec vbeta, vec sp) {
double value = 0.0;
for (size_t i=0; i < smooth.size(); ++i) {
Smoother smoothi = smooth[i];
value += sp[i]/2 *
dot(vbeta.subvec(smoothi.first_para,smoothi.last_para),
smoothi.S * vbeta.subvec(smoothi.first_para,smoothi.last_para));
}
return value;
}
vec penalty_gradient(vec vbeta, vec sp) {
int n = vbeta.size();
rowvec vgr(n, fill::zeros);
for (size_t i=0; i < smooth.size(); ++i) {
Smoother smoothi = smooth[i];
vgr.subvec(smoothi.first_para,smoothi.last_para) +=
sp[i] * (smoothi.S * vbeta.subvec(smoothi.first_para,smoothi.last_para)).t();
}
vec gr(n);
for (int i=0; i<n; ++i) gr[i] = vgr[i];
return gr;
}
vec traces(mat X) {
vec values(smooth.size(), fill::zeros);
for (size_t i=0; i < smooth.size(); ++i) {
Smoother smoothi = smooth[i];
for (size_t j=smoothi.first_para; j <= static_cast<size_t>(smoothi.last_para); ++j)
values[i] += X(j,j);
}
return values;
}
std::vector<Smoother> smooth;
};
// // TODO: include first_para and last_para class data for the traces() method
// class SmoothHaz {
// public:
// struct Smoother {
// mat X0, X1, X2, X3;
// vec w;
// double lambda;
// };
// SmoothHaz(SEXP sexp) {
// List list = as<List>(sexp);
// List lsmooth = as<List>(list["smooth"]);
// for(int i=0; i<lsmooth.size(); ++i) {
// List lsmoothi = as<List>(lsmooth[i]);
// Smoother smoothi = {
// as<mat>(lsmoothi["X0"]),
// as<mat>(lsmoothi["X1"]),
// as<mat>(lsmoothi["X2"]),
// as<mat>(lsmoothi["X3"]),
// as<vec>(lsmoothi["w"]),
// as<double>(lsmoothi["lambda"])
// };
// smooth.push_back(smoothi);
// }
// }
// double penalty(vec vbeta, vec sp) {
// double value = 0.0;
// for (size_t i=0; i < smooth.size(); ++i) {
// Smoother obj = smooth[i];
// vec s0 = obj.X0 * vbeta;
// vec s1 = obj.X1 * vbeta;
// vec s2 = obj.X2 * vbeta;
// vec s3 = obj.X3 * vbeta;
// vec h2 = exp(s0) % (s3 + 3*s1%s2 + s1%s1%s1);
// value += sp[i]/2 * obj.lambda * sum(obj.w % h2 % h2);
// }
// return value;
// }
// vec penalty_gradient(vec vbeta, vec sp) {
// int n = vbeta.size();
// rowvec vgr(n, fill::zeros);
// for (size_t i=0; i < smooth.size(); ++i) {
// Smoother obj = smooth[i];
// vec s0 = obj.X0 * vbeta;
// vec s1 = obj.X1 * vbeta;
// vec s2 = obj.X2 * vbeta;
// vec s3 = obj.X3 * vbeta;
// vec h2 = exp(s0) % (s3 + 3*s1%s2 + s1%s1%s1);
// mat dh2sq_dbeta =
// 2*lmult(h2 % exp(s0),
// obj.X3+3*(rmult(obj.X1,s2)+rmult(obj.X2,s1))+3*lmult(s1%s1,obj.X1))+
// 2*lmult(h2 % h2,obj.X0);
// vgr += sp[i]*obj.lambda*sum(lmult(obj.w, dh2sq_dbeta),0);
// }
// vec gr(n);
// for (int i = 0; i<n; ++i) gr[i] = vgr[i];
// return gr;
// }
// std::vector<Smoother> smooth;
// };
template<class T>
double pstpm2_multivariate_step(int n, double * logsp_ptr, void * model_ptr) {
T * model = static_cast<T *>(model_ptr);
vec logsp(logsp_ptr,n);
R_CheckUserInterrupt(); /* be polite -- did the user hit ctrl-C? */
return model->multivariate_step(logsp);
}
template<class T>
double pstpm2_first_step(double logsp, void * model_ptr) {
T * model = static_cast<T *>(model_ptr);
R_CheckUserInterrupt(); /* be polite -- did the user hit ctrl-C? */
return model->first_step(logsp);
}
template<class T>
void pstpm2_multivariate_stepNlm(int n, double * logsp_ptr, double * objective, void * model_ptr) {
T * model = static_cast<T *>(model_ptr);
vec logsp(logsp_ptr,n);
R_CheckUserInterrupt(); /* be polite -- did the user hit ctrl-C? */
*objective = model->multivariate_step(logsp);
}
// Penalised link-based models
template<class Stpm2Type = Stpm2<LogLogLink>, class Smooth = SmoothLogH>
class Pstpm2 : public Stpm2Type, public Smooth {
public:
typedef Pstpm2<Stpm2Type,Smooth> This;
Pstpm2(SEXP sexp) : Stpm2Type(sexp), Smooth(sexp) {
List list = as<List>(sexp);
sp = as<vec>(list["sp"]);
reltol_search = as<double>(list["reltol_search"]);
reltol_outer = as<double>(list["reltol_outer"]);
alpha = as<double>(list["alpha"]);
criterion = as<int>(list["criterion"]);
outer_optim = as<int>(list["outer_optim"]);
}
double objective(vec beta) {
return Stpm2Type::objective(beta) + Smooth::penalty(beta,sp);
}
double objective0(vec beta) {
return Stpm2Type::objective(beta);
}
vec gradient(vec beta) {
return Stpm2Type::gradient(beta) + Smooth::penalty_gradient(beta,sp);
}
vec gradient0(vec beta) {
return Stpm2Type::gradient(beta);
}
// is the following strictly needed - or even correct?
void optimWithConstraint(NumericVector init) {
bool satisfied;
if (this->bfgs.trace > 0)
Rprintf("Starting optimization\n");
do {
this->bfgs.optim(&optimfunction<This>, &optimgradient<This>, init, (void *) this);
vec vcoef(&this->bfgs.coef[0],this->n);
satisfied = Stpm2Type::feasible(vcoef % this->parscale);
if (!satisfied) this->kappa *= 2.0;
} while ((!satisfied) && this->kappa < 1.0e3);
}
double first_step(double logsp) {
sp[0] = exp(logsp);
this->pre_process();
this->optimWithConstraint(this->init);
this->bfgs.hessian = this->bfgs.calc_hessian(&optimgradient<This>, (void *) this);
NumericMatrix hessian0 = this->bfgs.calc_hessian(&optimgradient<Stpm2Type>, (void *) this);
if (this->bfgs.trace > 1) {
Rprintf("Debug on trace calculation. Coef:\n");
Rprint(this->bfgs.coef);
if (this->bfgs.trace > 1) {
Rprintf("Hessian0:\n");
Rprint(hessian0);
Rprintf("Hessian:\n");
Rprint(this->bfgs.hessian);
}
}
double edf = arma::trace(solve(as<mat>(this->bfgs.hessian),as<mat>(hessian0)));
double negll = this->bfgs.calc_objective(&optimfunction<Stpm2Type>, (void *) this);
double gcv = negll + alpha*edf;
double bic = negll + alpha*edf*log(sum(this->event));
this->init = this->bfgs.coef;
if (this->bfgs.trace > 0)
Rprintf("sp=%f\tedf=%f\tnegll=%f\tgcv=%f\tbic=%f\talpha=%f\n",sp[0],edf,negll,gcv,bic,alpha);
this->post_process();
return criterion==1 ? gcv : bic;
}
double multivariate_step(vec logsp) {
this->pre_process();
double lsp = -9.0, usp = 9.0;
for (size_t i=0; i < sp.size(); ++i)
sp[i] = exp(bound(logsp[i],lsp,usp));
if (this->bfgs.trace > 0) {
for (size_t i = 0; i < sp.size(); ++i)
Rprintf("sp[%i]=%f\t",i,sp[i]);
}
this->optimWithConstraint(this->init);
this->bfgs.hessian = this->bfgs.calc_hessian(&optimgradient<This>, (void *) this);
NumericMatrix hessian0 = this->bfgs.calc_hessian(&optimgradient<Stpm2Type>, (void *) this);
double edf = arma::trace(solve(as<mat>(this->bfgs.hessian),as<mat>(hessian0)));
double negll = this->bfgs.calc_objective(&optimfunction<Stpm2Type>, (void *) this);
double gcv = negll + alpha*edf;
double bic = 2.0*negll + alpha*edf*log(sum(this->event));
this->init = this->bfgs.coef;
// simple boundary constraints
double constraint = 0.0;
// double kappa = 1.0;
for (size_t i=0; i < sp.size(); ++i) {
if (logsp[i] < lsp)
constraint += pow(logsp[i]-lsp,2.0);
if (logsp[i] > usp)
constraint += pow(logsp[i]-usp,2.0);
}
double objective = criterion==1 ?
gcv + this->kappa/2.0*constraint :
bic + this->kappa/2.0*constraint;
if (this->bfgs.trace > 0) {
Rprintf("edf=%f\tnegll=%f\tgcv=%f\tbic=%f\tobjective=%f\n",edf,negll,gcv,bic,objective);
}
this->post_process();
return objective;
}
SEXP optim_fixed() {
this->pre_process();
this->optimWithConstraint(this->init);
this->bfgs.hessian = this->bfgs.calc_hessian(&optimgradient<This>, (void *) this);
NumericMatrix hessian0 = this->bfgs.calc_hessian(&optimgradient<Stpm2Type>, (void *) this);
mat Proj = solve(as<mat>(wrap(this->bfgs.hessian)),as<mat>(wrap(hessian0)));
double edf = trace(Proj);
NumericVector edf_var = as<NumericVector>(wrap(Smooth::traces(Proj)));
this->post_process();
return List::create(_("sp")=wrap(sp),
_("coef")=wrap(this->bfgs.coef),
_("hessian")=wrap(this->bfgs.hessian),
_("edf")=wrap(edf),
_("edf_var")=wrap(edf_var)
);
}
SEXP optim_first() {
this->bfgs.reltol = reltol_search;
double opt_sp = exp(Brent_fmin(log(0.001),log(1000.0),&(pstpm2_first_step<This>),(void *) this,reltol_outer));
sp[0] = opt_sp;
this->bfgs.reltol = this->reltol;
return optim_fixed();
}
SEXP optim_multivariate() {
if (outer_optim==1) return optim_multivariate_NelderMead();
else return optim_multivariate_Nlm();
}
SEXP optim_multivariate_NelderMead() {
this->kappa = 10.0;
NelderMead2 nm;
nm.reltol = reltol_outer;
nm.maxit = 500;
nm.hessianp = false;
nm.parscale = this->parscale;
this->bfgs.reltol = reltol_search;
NumericVector logsp(sp.size());
for (size_t i=0; i < sp.size(); ++i)
logsp[i] = log(sp[i]);
bool satisfied;
do {
nm.optim(&pstpm2_multivariate_step<This>, logsp, (void *) this);
satisfied = true;
for (size_t i=0; i < sp.size(); ++i)
if (logsp[i]< -7.0 || logsp[i] > 7.0) satisfied = false;
if (!satisfied) this->kappa *= 2.0;
} while (!satisfied && this->kappa<1.0e5);
for (int i=0; i < nm.coef.size(); ++i)
sp[i] = exp(nm.coef[i]);
this->bfgs.coef = this->init;
this->bfgs.reltol = this->reltol;
return optim_fixed();
}
SEXP optim_multivariate_Nlm() {
this->kappa = 10.0;
Nlm2 nm;
nm.gradtl = nm.steptl = reltol_outer;
nm.itnlim = 100;
// nm.hessianp = false;
nm.parscale = this->parscale;
this->bfgs.reltol = reltol_search;
NumericVector logsp(sp.size());
for (size_t i=0; i < sp.size(); ++i)
logsp[i] = log(sp[i]);
bool satisfied;
do {
nm.optim(&pstpm2_multivariate_stepNlm<This>, logsp, (void *) this);
satisfied = true;
for (size_t i=0; i < sp.size(); ++i)
if (logsp[i]< -7.0 || logsp[i] > 7.0) satisfied = false;
if (!satisfied) this->kappa *= 2.0;
} while (!satisfied && this->kappa<1.0e5);
for (int i=0; i < nm.coef.size(); ++i)
sp[i] = exp(nm.coef[i]);
this->bfgs.coef = this->init;
this->bfgs.reltol = this->reltol;
return optim_fixed();
}
vec sp;
double alpha, reltol_search, reltol_outer;
int criterion, outer_optim;
};
// template<class Smooth, class Stpm2>
// void pstpm2_step_multivariate_nlm(int n, double * logsp, double * f, void *ex) {
// *f = pstpm2_step_multivariate<Smooth,Stpm2>(n, logsp, ex);
// };
/**
Extension of stpm2 and pstpm2 to include gamma shared frailties with a cluster variable
**/
template<class Base>
class GammaSharedFrailty : public Base {
public:
typedef std::vector<int> Index;
typedef std::map<int,Index> IndexMap;
typedef GammaSharedFrailty<Base> This;
GammaSharedFrailty(SEXP sexp) : Base(sexp) {
List list = as<List>(sexp);
ivec cluster = as<ivec>(list["cluster"]);
// wragged array indexed by a map of vectors
for (size_t id=0; id<cluster.size(); ++id) {
clusters[cluster[id]].push_back(id);
if (this->event[id]==1)
cluster_events[cluster[id]].push_back(id);
}
}
/**
Objective function for a Gamma shared frailty
Assumes that weights == 1.
**/
double objective(vec beta) {
int n = beta.size();
if (this->bfgs.trace>0) {
Rprint(beta);
}
vec vbeta(beta); // logtheta is the last parameter in beta
vbeta.resize(n-1);
double theta = exp(beta[n-1]);
vec eta = this->X * vbeta;
vec etaD = this->XD * vbeta;
vec h = Base::h(eta,etaD) + this->bhazard;
vec H = Base::H(eta);
double constraint = this->kappa/2.0 * (sum(h % h % (h<0)) + sum(H % H % (H<0)));
vec eps = h*0.0 + 1.0e-16;
h = max(h,eps);
H = max(H,eps);
vec H0;
if (this->delayed) {
vec eta0 = this->X0 * vbeta;
H0 = Base::H(eta0);
constraint += this->kappa/2.0 * sum(H0 % H0 % (H0<0));
}
double ll = 0.0;
for (IndexMap::iterator it=clusters.begin(); it!=clusters.end(); ++it) {
uvec index = as<uvec>(wrap(it->second));
int mi = sum(this->event(index));
double sumH = sum(H(index));
double sumHenter = 0.0;
ll += sum(log(h(index)) % this->event(index));
if (this->delayed && cluster_events.count(it->first) > 0) {
uvec ind00 = as<uvec>(wrap(cluster_events[it->first]));
sumHenter = sum(H0(ind00));
}
ll += -(1.0/theta+mi)*log(1.0+theta*(sumH)) + 1.0/theta*log(1.0+theta*sumHenter); // Rondeau et al
// ll -= (1.0/theta+mi)*log(1.0+theta*(sumH - sumHenter)); // conditional (Gutierrez 2002)
if (mi>0) {
for (int k=1; k<=mi; ++k)
ll += log(1.0+theta*(mi-k));
}
}
ll -= constraint;
return -ll;
}
vec gradient(vec beta) {
int n = beta.size();
vec gr = zeros<vec>(n);
vec grconstraint = zeros<vec>(n);
vec vbeta(beta); // theta is the last parameter in beta
vbeta.resize(n-1);
double theta = exp(beta[n-1]);
vec eta = this->X * vbeta;
vec etaD = this->XD * vbeta;
vec h = Base::h(eta,etaD);
vec H = Base::H(eta);
mat gradh = Base::gradh(eta,etaD,this->X,this->XD);
mat gradH = Base::gradH(eta,this->X);
vec eps = h*0.0 + 1.0e-16;
h = max(h,eps);
H = max(H,eps);
vec H0;
mat gradH0;
if (this->delayed) {
vec eta0 = this->X0 * vbeta;
// vec etaD0 = this->XD0 * vbeta;
H0 = Base::H(eta0);
gradH0 = Base::gradH(eta0,this->X0);
}
for (IndexMap::iterator it=clusters.begin(); it!=clusters.end(); ++it) {
int mi=0;
double sumH = 0.0, sumHenter = 0.0;
vec gradi = zeros<vec>(n-1);
vec gradHi = zeros<vec>(n-1);
vec gradH0i = zeros<vec>(n-1);
vec grconstraint = zeros<vec>(n-1);
for (Index::iterator j=it->second.begin(); j!=it->second.end(); ++j) {
sumH += H(*j);
gradHi += gradH.row(*j).t();
gradi += gradh.row(*j).t() / h(*j) * this->event(*j);
if (this->event(*j)==1)
mi++;
if (this->delayed && this->ind0[*j]) {
int jj = this->map0[*j];
sumHenter += H0(jj);
gradH0i += gradH0.row(jj).t();
grconstraint += this->kappa * (gradH0.row(jj).t() * H0(jj) * (H0(jj)<0));
}
grconstraint += this->kappa * ((gradh.row(*j).t() * h(*j) * (h(*j)<0)) + (gradH.row(*j).t() * H(*j) * (H(*j)<0)));
}
for (int k=0; k<n-1; ++k) {
// gr(k) += gradi(k) - (1+mi*theta)*(gradHi(k)-gradH0i(k))/(1+theta*(sumH-sumHenter)) - grconstraint(k); // Gu tierrez
gr(k) += gradi(k) - (1+mi*theta)*gradHi(k)/(1+theta*(sumH)) + 1.0/(1+theta*sumHenter)*gradH0i(k) - grconstraint(k); // Rondeau et al
}
double lastterm = 0.0;
if (mi>0) {
for (int k=1; k<=mi; ++k)
lastterm += theta*(mi-k)/(1.0+theta*(mi-k));
}
// gr(n-1) += log(1.0+theta*(sumH-sumHenter))/theta -
// (1.0/theta+mi)*theta*(sumH-sumHenter)/(1.0+theta*(sumH-sumHenter)) +
// lastterm; // Gutierrez
gr(n-1) += log(1.0+theta*sumH)/theta -
(1.0+mi*theta)*sumH/(1.0+theta*sumH) +
sumHenter/(1.0+theta*sumHenter) -
log(1.0+theta*sumHenter)/theta +
lastterm; // Rondeau et al
}
if (this->bfgs.trace>1) {
Rprintf("Calculating fdgradient:\n"); Rprint(this->fdgradient(beta)); Rprintf("(=fdgradient)\n");
}
return -gr;
}
bool feasible(vec beta) {
vec coef(beta);
coef.resize(this->n-1);
return Base::feasible(coef);
}
void optimWithConstraint(NumericVector init) {
bool satisfied;
if (this->bfgs.trace > 0)
Rprintf("Starting optimization\n");
do {
this->bfgs.optim(&optimfunction<This>, &optimgradient<This>, this->init, (void *) this);
vec vcoef(&this->bfgs.coef[0],this->n);
satisfied = feasible(vcoef % this->parscale);
if (!satisfied) this->kappa *= 2.0;
} while ((!satisfied) && this->kappa < 1.0e3);
}
void optimWithConstraintNM(NumericVector init) {
bool satisfied;
NelderMead2 nm;
nm.hessianp = false;
nm.parscale = this->parscale;
do {
nm.optim(&optimfunction<This>, this->init, (void *) this);
vec vcoef(&this->bfgs.coef[0],this->n);
satisfied = feasible(vcoef % this->parscale);
if (!satisfied) this->kappa *= 2.0;
} while ((!satisfied) && this->kappa < 1.0e3);
nm.hessian = nm.calc_hessian(&optimfunction<This>, (void *) this);
this->bfgs.coef = nm.coef;
this->bfgs.hessian = nm.hessian;
}
IndexMap clusters, cluster_events;
};
/**
Extension of stpm2 and pstpm2 to include log-normal shared frailties with a cluster variable
**/
template<class Base>
class NormalSharedFrailty : public Base {
public:
typedef std::vector<int> Index;
typedef std::map<int,Index> IndexMap;
typedef NormalSharedFrailty<Base> This;
NormalSharedFrailty(SEXP sexp) : Base(sexp) {
List list = as<List>(sexp);
IntegerVector cluster = as<IntegerVector>(list["cluster"]);
gauss_x = as<vec>(list["gauss_x"]); // node values
gauss_w = as<vec>(list["gauss_w"]); // probability weights
// wragged array indexed by a map of vectors
for (int id=0; id<cluster.size(); ++id) {
clusters[cluster[id]].push_back(id);
if (this->event[id]==1) {
cluster_events[cluster[id]].push_back(id);
cluster_event_indices[cluster[id]].push_back(id);
}
}
}
/**
Objective function for a log-normal shared frailty
Assumes that weights == 1.
**/
double objective(vec beta) {
int n = beta.size();
vec vbeta(beta); // nu=log(variance) is the last parameter in beta; exp(nu)=sigma^2
vbeta.resize(n-1);
double sigma = exp(0.5*beta[n-1]); // standard deviation
int K = gauss_x.size(); // number of nodes
mat lijk(this->N,K);
double constraint = 0.0;
vec wstar = gauss_w/sqrt(datum::pi);
vec eta = this->X * vbeta;
vec etaD = this->XD * vbeta;
vec eta0 = this->X0 * vbeta;
vec eta1 = this->X1 * vbeta;
for (int k=0; k<K; ++k) {
double bi = sqrt(2.0)*sigma*this->gauss_x[k];
li_constraint lik = Base::li(eta+bi,etaD,eta0+bi,eta1+bi);
lijk.col(k) = lik.li;
constraint += lik.constraint;
}
double ll = 0.0;
for (IndexMap::iterator it=clusters.begin(); it!=clusters.end(); ++it) {
uvec index = as<uvec>(wrap(it->second));
double Li = dot(exp(sum(lijk.rows(index),0)),wstar);
ll += log(Li);
}
// ll -= constraint;
return -ll;
}
/// Another way for gradients
/// gradient of objective
vec gradient_new(vec beta) {
int n = beta.size();
double sigma = exp(0.5*beta[n-1]);
mat Z(this->N,1,fill::ones);
mat ZD(this->N,1,fill::zeros);
mat Z0(this->X0.n_rows,1,fill::ones);
mat Z1(this->X1.n_rows,1,fill::ones);
mat Xstar = join_horiz(this->X, Z);
mat XDstar = join_horiz(this->XD, ZD); // assumes time-invariant random effects
mat X0star = join_horiz(this->X0, Z0);
mat X1star = join_horiz(this->X1, Z1);
int K = gauss_x.size(); // number of nodes
vec wstar = gauss_w/sqrt(datum::pi);
int G = clusters.size();
vec Li(G,fill::zeros);
mat gradLi(G,n,fill::zeros);
vec betastar = beta;
rowvec dconstraint(n,fill::zeros);
mat likeli_jk(this->N,K,fill::zeros);
vec likeli_k(K,fill::zeros);
cube grad_jk(this->N,n,K,fill::zeros);
mat grad_kn(K,n,fill::zeros);
// for K nodes calculation
for (int k=0; k<K; ++k) {
double bi = sqrt(2.0)*sigma*gauss_x[k];
betastar[betastar.size()-1] = bi;
vec etastar = Xstar * betastar;
vec etaDstar = XDstar * betastar;
vec eta0star = X0star * betastar;
vec eta1star = X1star * betastar;
li_constraint lik = Base::li(etastar, etaDstar, eta0star, eta1star);
gradli_constraint gradlik = Base::gradli(etastar, etaDstar, eta0star, eta1star,Xstar, XDstar, X0star, X1star);
// adjust the last column of the gradient to account for the variance components:
// chain rule: d lik/d bi * d bi/d nu where bi = sqrt(2)*exp(nu/2)*x_k
gradlik.gradli.col(gradlik.gradli.n_cols-1) *= bi*0.5;
dconstraint += sum(gradlik.constraint,0); // ignores clustering??
likeli_jk.col(k) = lik.li;
grad_jk.slice(k) = gradlik.gradli;
}
// Iteration in each cluster and get vec Li(g) and mat gradLi(g,n)
int g = 0;
for (IndexMap::iterator it=clusters.begin(); it!=clusters.end(); ++it, ++g) {
uvec index = as<uvec>(wrap(it->second));
vec likeli_k = exp(sum(likeli_jk.rows(index),0)).t(); // sum index components at all nodes for cluster i
for(int k=0; k<K; ++k){
grad_kn.row(k) = sum(grad_jk.slice(k).rows(index),0);
}
Li(g) = dot(likeli_k,wstar);
gradLi.row(g) = sum(rmult(grad_kn,wstar%likeli_k),0);
// gradLi.row(g) = grad_kn.t() * (wstar%likeli_k);
}
// Last step to summarize all clusters
rowvec grad = sum(rmult(gradLi,1/Li),0); // Rows of matrix is multiplied with elements of vector
if (this->bfgs.trace>0) {
Rprintf("fdgradient="); Rprint(this->fdgradient(beta));
}
vec gr(n,fill::zeros);
for (int i=0; i<n; i++) gr(i) = grad(i); // - dconstraint(i);
return -gr;
}
vec gradient(vec beta) {
int n = beta.size();
double sigma = exp(0.5*beta[n-1]);
mat Z(this->N,1,fill::ones);
mat ZD(this->N,1,fill::zeros);
mat Z0(this->X0.n_rows,1,fill::ones);
mat Z1(this->X1.n_rows,1,fill::ones);
mat Xstar = join_horiz(this->X, Z);
mat XDstar = join_horiz(this->XD, ZD); // assumes time-invariant random effects
mat X0star = join_horiz(this->X0, Z0);
mat X1star = join_horiz(this->X1, Z1);
int K = gauss_x.size(); // number of nodes
vec wstar = gauss_w/sqrt(datum::pi);
int G = clusters.size();
vec Li(G,fill::zeros);
mat gradLi(G,n,fill::zeros);
vec betastar = beta;
rowvec dconstraint(n,fill::zeros);
for (int k=0; k<K; ++k) {
double bi = sqrt(2.0)*sigma*gauss_x[k];
betastar[betastar.size()-1] = bi;
vec etastar = Xstar * betastar;
vec etaDstar = XDstar * betastar;
vec eta0star = X0star * betastar;
vec eta1star = X1star * betastar;
li_constraint lik = Base::li(etastar, etaDstar, eta0star, eta1star);
gradli_constraint gradlik = Base::gradli(etastar, etaDstar, eta0star, eta1star,
Xstar, XDstar, X0star, X1star);
// adjust the last column of the gradient to account for the variance components:
// chain rule: d lik/d bi * d bi/d nu where bi = sqrt(2)*exp(nu/2)*x_k
gradlik.gradli.col(gradlik.gradli.n_cols-1) *= bi*0.5;
dconstraint += sum(gradlik.constraint,0); // ignores clustering??
int g = 0;
for (IndexMap::iterator it=clusters.begin(); it!=clusters.end(); ++it, ++g) {
uvec index = as<uvec>(wrap(it->second));
double Lgk = exp(sum(lik.li(index)));
Li(g) += Lgk*wstar[k];
gradLi.row(g) += wstar[k]*Lgk*sum(gradlik.gradli.rows(index),0);
}
}
rowvec grad = sum(rmult(gradLi,1/Li),0);
if (this->bfgs.trace>0) {
Rprintf("fdgradient="); Rprint(this->fdgradient(beta));
}
vec gr(n,fill::zeros);
for (int i=0; i<n; i++) gr(i) = grad(i); // - dconstraint(i);
return -gr;
}
bool feasible(vec beta) {
vec coef(beta);
coef.resize(beta.size()-1);
return Base::feasible(coef);
}
void optimWithConstraint(NumericVector init) {
bool satisfied;
int n = init.size();
if (this->bfgs.trace > 0)
Rprintf("Starting optimization\n");
do {
this->bfgs.optim(&optimfunction<This>, &optimgradient<This>, init, (void *) this);
vec vcoef(&this->bfgs.coef[0],n);
satisfied = feasible(vcoef % this->parscale);
if (!satisfied) this->kappa *= 2.0;
} while ((!satisfied) && this->kappa < 1.0e3);
}
void optimWithConstraintNM(NumericVector init) {
bool satisfied;
NelderMead2 nm;
nm.hessianp = false;
nm.parscale = this->parscale;
do {
nm.optim(&optimfunction<This>, this->init, (void *) this);
vec vcoef(&this->bfgs.coef[0],this->n);
satisfied = feasible(vcoef % this->parscale);
if (!satisfied) this->kappa *= 2.0;
} while ((!satisfied) && this->kappa < 1.0e3);
nm.hessian = nm.calc_hessian(&optimfunction<This>, (void *) this);
this->bfgs.coef = nm.coef;
this->bfgs.hessian = nm.hessian;
}
IndexMap clusters, cluster_events, cluster_event_indices;
vec gauss_x, gauss_w;
};
template<class T>
SEXP stpm2_model_output_(SEXP args) {
T model(args);
List list = as<List>(args);
std::string return_type = as<std::string>(list["return_type"]);
vec beta(&model.init[0],model.n);
if (return_type == "optim") {
model.pre_process();
model.optimWithConstraint(model.init);
model.bfgs.hessian = model.bfgs.calc_hessian(&optimgradient<T>, (void *) &model);
model.post_process();
return List::create(_("fail")=model.bfgs.fail,
_("coef")=wrap(model.bfgs.coef),
_("hessian")=wrap(model.bfgs.hessian));
}
else if (return_type == "objective")
return wrap(model.objective(beta));
else if (return_type == "gradient")
return wrap(model.gradient(beta));
else if (return_type == "feasible")
return wrap(model.feasible(beta));
else {
REprintf("Unknown return_type.\n");
return wrap(-1);
}
}
template<class T>
SEXP pstpm2_model_output_(SEXP args) {
T model(args);
List list = as<List>(args);
std::string return_type = as<std::string>(list["return_type"]);
vec beta(&model.init[0],model.n);
if (return_type == "optim_fixed")
return(model.optim_fixed());
else if (return_type == "optim_first")
return(model.optim_first());
else if (return_type == "optim_multivariate")
return(model.optim_multivariate());
else if (return_type == "objective")
return wrap(model.objective(beta));
else if (return_type == "objective0")
return wrap(model.objective0(beta));
else if (return_type == "gradient")
return wrap(model.gradient(beta));
else if (return_type == "gradient0")
return wrap(model.gradient0(beta));
else if (return_type == "constraint")
return wrap(model.feasible(beta));
else if (return_type == "feasible")
return wrap(model.feasible(beta));
else {
REprintf("Unknown return_type.\n");
return wrap(-1);
}
}
RcppExport SEXP model_output(SEXP args) {
List list = as<List>(args);
std::string link = as<std::string>(list["link"]);
std::string type = as<std::string>(list["type"]);
if (type=="stpm2") {
if (link == "PH")
return stpm2_model_output_<Stpm2<LogLogLink> >(args);
else if (link == "PO")
return stpm2_model_output_<Stpm2<LogitLink> >(args);
else if (link == "AH")
return stpm2_model_output_<Stpm2<LogLink> >(args);
else if (link == "probit")
return stpm2_model_output_<Stpm2<ProbitLink> >(args);
else {
REprintf("Unknown link function.\n");
return wrap(-1);
}
}
else if (type=="pstpm2") {
if (link == "PH")
return pstpm2_model_output_<Pstpm2<Stpm2<LogLogLink>,SmoothLogH> >(args);
else if (link == "PO")
return pstpm2_model_output_<Pstpm2<Stpm2<LogitLink>,SmoothLogH> >(args);
else if (link == "AH")
return pstpm2_model_output_<Pstpm2<Stpm2<LogLink>,SmoothLogH> >(args);
else if (link == "probit")
return pstpm2_model_output_<Pstpm2<Stpm2<ProbitLink>,SmoothLogH> >(args);
else {
REprintf("Unknown link function.\n");
return wrap(-1);
}
}
else if (type=="stpm2_gamma_frailty") {
if (link == "PH")
return stpm2_model_output_<GammaSharedFrailty<Stpm2<LogLogLink> > >(args);
else if (link == "PO")
return stpm2_model_output_<GammaSharedFrailty<Stpm2<LogitLink> > >(args);
else if (link == "AH")
return stpm2_model_output_<GammaSharedFrailty<Stpm2<LogLink> > >(args);
else if (link == "probit")
return stpm2_model_output_<GammaSharedFrailty<Stpm2<ProbitLink> > >(args);
else {
REprintf("Unknown link function.\n");
return wrap(-1);
}
}
else if (type=="pstpm2_gamma_frailty") {
if (link == "PH")
return pstpm2_model_output_<Pstpm2<GammaSharedFrailty<Stpm2<LogLogLink> >,SmoothLogH> >(args);
else if (link == "PO")
return pstpm2_model_output_<Pstpm2<GammaSharedFrailty<Stpm2<LogitLink> >,SmoothLogH> >(args);
else if (link == "AH")
return pstpm2_model_output_<Pstpm2<GammaSharedFrailty<Stpm2<LogLink> >,SmoothLogH> >(args);
else if (link == "probit")
return pstpm2_model_output_<Pstpm2<GammaSharedFrailty<Stpm2<ProbitLink> >,SmoothLogH> >(args);
else {
REprintf("Unknown link function.\n");
return wrap(-1);
}
}
else if (type=="stpm2_normal_frailty") {
if (link == "PH")
return stpm2_model_output_<NormalSharedFrailty<Stpm2<LogLogLink> > >(args);
else if (link == "PO")
return stpm2_model_output_<NormalSharedFrailty<Stpm2<LogitLink> > >(args);
else if (link == "AH")
return stpm2_model_output_<NormalSharedFrailty<Stpm2<LogLink> > >(args);
else if (link == "probit")
return stpm2_model_output_<NormalSharedFrailty<Stpm2<ProbitLink> > >(args);
else {
REprintf("Unknown link function.\n");
return wrap(-1);
}
}
else if (type=="pstpm2_normal_frailty") {
if (link == "PH")
return pstpm2_model_output_<Pstpm2<NormalSharedFrailty<Stpm2<LogLogLink> >,SmoothLogH> >(args);
else if (link == "PO")
return pstpm2_model_output_<Pstpm2<NormalSharedFrailty<Stpm2<LogitLink> >,SmoothLogH> >(args);
else if (link == "AH")
return pstpm2_model_output_<Pstpm2<NormalSharedFrailty<Stpm2<LogLink> >,SmoothLogH> >(args);
else if (link == "probit")
return pstpm2_model_output_<Pstpm2<NormalSharedFrailty<Stpm2<ProbitLink> >,SmoothLogH> >(args);
else {
REprintf("Unknown link function.\n");
return wrap(-1);
}
}
else {
REprintf("Unknown model type.\n");
return wrap(-1);
}
}
// Proof of concept for a Weibull cure model
struct CureModel {
int n0, n1, n2;
mat Xshape, Xscale, Xcure;
vec time, status;
};
double fminfn_cureModel(int n, double * beta, void *ex) {
double ll = 0.0;
CureModel * data = (CureModel *) ex;
vec vbeta(&beta[0],n);
vec shape = exp(data->Xshape * vbeta(span(0,data->n0-1)));
vec scale = exp(data->Xscale * vbeta(span(data->n0,data->n1-1)));
vec cure = 1.0/(1.0+exp(-data->Xcure * vbeta(span(data->n1,data->n2-1))));
for (size_t i=0; i < data->time.size(); ++i) {
ll += data->status(i)==1.0 ?
log(1.0-cure(i)) + R::dweibull(data->time(i),shape(i),scale(i),1) :
log(cure(i)+(1.0-cure(i)) * R::pweibull(data->time(i),shape(i),scale(i),0,0));
}
R_CheckUserInterrupt(); /* be polite -- did the user hit ctrl-C? */
return -ll;
}
RcppExport SEXP fitCureModel(SEXP stime, SEXP sstatus, SEXP sXshape,
SEXP sXscale, SEXP sXcure, SEXP sbeta) {
mat Xshape = as<mat>(sXshape);
mat Xscale = as<mat>(sXscale);
mat Xcure = as<mat>(sXcure);
vec time = as<vec>(stime);
vec status = as<vec>(sstatus);
NumericVector init = as<NumericVector>(sbeta);
int n0=Xshape.n_cols;
int n1=n0+Xscale.n_cols;
int n2=n1+Xcure.n_cols;
CureModel data = {n0,n1,n2,Xshape,Xscale,Xcure,time,status};
NelderMead nm;
nm.reltol = 1.0e-8;
nm.maxit = 1000;
nm.optim(& fminfn_cureModel, init, (void *) &data);
for (int i = 0; i<nm.coef.size(); ++i)
init[i] = nm.coef[i]; // clone
return List::create(_("Fmin")=nm.Fmin,
_("coef")=wrap(init),
_("fail")=nm.fail,
_("hessian")=wrap(nm.hessian));
}
// R CMD INSTALL ~/src/R/microsimulation
// R -q -e "require(microsimulation); .Call('test_nmmin',1:2,PACKAGE='microsimulation')"
} // anonymous namespace
