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Switch Calloc,Free to R_Calloc,R_Free for STRICT_R_HEADERS #40

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Jan 6, 2022
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Switch Calloc,Free to R_Calloc,R_Free for STRICT_R_HEADERS #40

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102 changes: 51 additions & 51 deletions src/binomial.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -259,21 +259,21 @@ RcppExport SEXP cdfit_binomial_ssr(SEXP X_, SEXP y_, SEXP row_idx_,
}

arma::sp_mat beta = arma::sp_mat(p, L); //beta
double *a = Calloc(p, double); //Beta from previous iteration
double *a = R_Calloc(p, double); //Beta from previous iteration
double a0 = 0.0; //beta0 from previousiteration
double *w = Calloc(n, double);
double *s = Calloc(n, double); //y_i - pi_i
double *eta = Calloc(n, double);
int *e1 = Calloc(p, int); //ever-active set
int *e2 = Calloc(p, int); //strong set
double *w = R_Calloc(n, double);
double *s = R_Calloc(n, double); //y_i - pi_i
double *eta = R_Calloc(n, double);
int *e1 = R_Calloc(p, int); //ever-active set
int *e2 = R_Calloc(p, int); //strong set
double xwr, xwx, pi, u, v, cutoff, l1, l2, shift, si;
double max_update, update, thresh; // for convergence check
int i, j, jj, l, violations, lstart;

double ybar = sum(y, n) / n;
a0 = beta0[0] = log(ybar / (1-ybar));
double nullDev = 0;
double *r = Calloc(n, double);
double *r = R_Calloc(n, double);
for (i = 0; i < n; i++) {
r[i] = y[i];
nullDev = nullDev - y[i]*log(ybar) - (1-y[i])*log(1-ybar);
Expand Down Expand Up @@ -328,7 +328,7 @@ RcppExport SEXP cdfit_binomial_ssr(SEXP X_, SEXP y_, SEXP row_idx_,
}
if (nv > dfmax) {
for (int ll=l; ll<L; ll++) iter[ll] = NA_INTEGER;
Free(s); Free(w); Free(a); Free(r); Free(e1); Free(e2); Free(eta);
R_Free(s); R_Free(w); R_Free(a); R_Free(r); R_Free(e1); R_Free(e2); R_Free(eta);
return List::create(beta0, beta, center, scale, lambda, Dev,
iter, n_reject, Rcpp::wrap(col_idx));
}
Expand Down Expand Up @@ -385,7 +385,7 @@ RcppExport SEXP cdfit_binomial_ssr(SEXP X_, SEXP y_, SEXP row_idx_,
if (Dev[l] / nullDev < .01) {
if (warn) warning("Model saturated; exiting...");
for (int ll=l; ll<L; ll++) iter[ll] = NA_INTEGER;
Free(s); Free(w); Free(a); Free(r); Free(e1); Free(e2); Free(eta);
R_Free(s); R_Free(w); R_Free(a); R_Free(r); R_Free(e1); R_Free(e2); R_Free(eta);
return List::create(beta0, beta, center, scale, lambda, Dev,
iter, n_reject, Rcpp::wrap(col_idx));
}
Expand Down Expand Up @@ -441,7 +441,7 @@ RcppExport SEXP cdfit_binomial_ssr(SEXP X_, SEXP y_, SEXP row_idx_,
if (violations==0) break;
}
}
Free(s); Free(w); Free(a); Free(r); Free(e1); Free(e2); Free(eta);
R_Free(s); R_Free(w); R_Free(a); R_Free(r); R_Free(e1); R_Free(e2); R_Free(eta);
return List::create(beta0, beta, center, scale, lambda, Dev, iter, n_reject, Rcpp::wrap(col_idx));

}
Expand Down Expand Up @@ -518,21 +518,21 @@ RcppExport SEXP cdfit_binomial_ssr_approx(SEXP X_, SEXP y_, SEXP row_idx_,
}

arma::sp_mat beta = arma::sp_mat(p, L); //beta
double *a = Calloc(p, double); //Beta from previous iteration
double *a = R_Calloc(p, double); //Beta from previous iteration
double a0 = 0.0; //beta0 from previousiteration
double *w = Calloc(n, double);
double *s = Calloc(n, double); //y_i - pi_i
double *eta = Calloc(n, double);
int *e1 = Calloc(p, int); //ever-active set
int *e2 = Calloc(p, int); //strong set
double *w = R_Calloc(n, double);
double *s = R_Calloc(n, double); //y_i - pi_i
double *eta = R_Calloc(n, double);
int *e1 = R_Calloc(p, int); //ever-active set
int *e2 = R_Calloc(p, int); //strong set
double xwr, xwx, pi, u, v, cutoff, l1, l2, shift, si;
double max_update, update, thresh; // for convergence check
int i, j, jj, l, violations, lstart; // temp index

double ybar = sum(y, n)/n;
a0 = beta0[0] = log(ybar/(1-ybar));
double nullDev = 0;
double *r = Calloc(n, double);
double *r = R_Calloc(n, double);
for (i = 0; i < n; i++) {
r[i] = y[i];
nullDev = nullDev - y[i] * log(ybar) - (1 - y[i]) * log(1 - ybar);
Expand Down Expand Up @@ -580,7 +580,7 @@ RcppExport SEXP cdfit_binomial_ssr_approx(SEXP X_, SEXP y_, SEXP row_idx_,
}
if (nv > dfmax) {
for (int ll=l; ll<L; ll++) iter[ll] = NA_INTEGER;
Free(s); Free(w); Free(a); Free(r); Free(e1); Free(e2); Free(eta);
R_Free(s); R_Free(w); R_Free(a); R_Free(r); R_Free(e1); R_Free(e2); R_Free(eta);
return List::create(beta0, beta, center, scale, lambda, Dev,
iter, n_reject, Rcpp::wrap(col_idx));
}
Expand Down Expand Up @@ -634,7 +634,7 @@ RcppExport SEXP cdfit_binomial_ssr_approx(SEXP X_, SEXP y_, SEXP row_idx_,
if (Dev[l] / nullDev < .01) {
if (warn) warning("Model saturated; exiting...");
for (int ll = l; ll < L; ll++) iter[ll] = NA_INTEGER;
Free(s); Free(w); Free(a); Free(r); Free(e1); Free(e2); Free(eta);
R_Free(s); R_Free(w); R_Free(a); R_Free(r); R_Free(e1); R_Free(e2); R_Free(eta);
return List::create(beta0, beta, center, scale, lambda, Dev,
iter, n_reject, Rcpp::wrap(col_idx));
}
Expand Down Expand Up @@ -696,7 +696,7 @@ RcppExport SEXP cdfit_binomial_ssr_approx(SEXP X_, SEXP y_, SEXP row_idx_,
}
}

Free(s); Free(w); Free(a); Free(r); Free(e1); Free(e2); Free(eta);
R_Free(s); R_Free(w); R_Free(a); R_Free(r); R_Free(e1); R_Free(e2); R_Free(eta);
return List::create(beta0, beta, center, scale, lambda, Dev, iter, n_reject, Rcpp::wrap(col_idx));
}

Expand Down Expand Up @@ -778,21 +778,21 @@ RcppExport SEXP cdfit_binomial_slores_ssr(SEXP X_, SEXP y_, SEXP n_pos_, SEXP yl
}

arma::sp_mat beta = arma::sp_mat(p, L); //beta
double *a = Calloc(p, double); //Beta from previous iteration
double *a = R_Calloc(p, double); //Beta from previous iteration
double a0 = 0.0; //beta0 from previousiteration
double *w = Calloc(n, double);
double *s = Calloc(n, double); //y_i - pi_i
double *eta = Calloc(n, double);
int *e1 = Calloc(p, int); //ever-active set
int *e2 = Calloc(p, int); //strong set
double *w = R_Calloc(n, double);
double *s = R_Calloc(n, double); //y_i - pi_i
double *eta = R_Calloc(n, double);
int *e1 = R_Calloc(p, int); //ever-active set
int *e2 = R_Calloc(p, int); //strong set
double xwr, xwx, pi, u, v, cutoff, l1, l2, shift, si;
double max_update, update, thresh; // for convergence check
int i, j, jj, l, violations, lstart;

double ybar = sum(y, n) / n;
a0 = beta0[0] = log(ybar / (1-ybar));
double nullDev = 0;
double *r = Calloc(n, double);
double *r = R_Calloc(n, double);
for (i = 0; i < n; i++) {
r[i] = y[i];
nullDev = nullDev - y[i]*log(ybar) - (1-y[i])*log(1-ybar);
Expand Down Expand Up @@ -836,8 +836,8 @@ RcppExport SEXP cdfit_binomial_slores_ssr(SEXP X_, SEXP y_, SEXP n_pos_, SEXP yl
vector<double> X_theta_lam_xi_pos;
vector<double> prod_PX_Pxmax_xi_pos;
vector<double> cutoff_xi_pos;
int *slores_reject = Calloc(p, int);
int *slores_reject_old = Calloc(p, int);
int *slores_reject = R_Calloc(p, int);
int *slores_reject_old = R_Calloc(p, int);
for (int j = 0; j < p; j++) slores_reject_old[j] = 1;

int slores; // if 0, don't perform Slores rule
Expand Down Expand Up @@ -877,8 +877,8 @@ RcppExport SEXP cdfit_binomial_slores_ssr(SEXP X_, SEXP y_, SEXP n_pos_, SEXP yl
}
if (nv > dfmax) {
for (int ll=l; ll<L; ll++) iter[ll] = NA_INTEGER;
Free(slores_reject); Free(slores_reject_old);
Free(s); Free(w); Free(a); Free(r); Free(e1); Free(e2); Free(eta);
R_Free(slores_reject); R_Free(slores_reject_old);
R_Free(s); R_Free(w); R_Free(a); R_Free(r); R_Free(e1); R_Free(e2); R_Free(eta);
//ProfilerStop();
return List::create(beta0, beta, center, scale, lambda, Dev,
iter, n_reject, Rcpp::wrap(col_idx));
Expand Down Expand Up @@ -952,8 +952,8 @@ RcppExport SEXP cdfit_binomial_slores_ssr(SEXP X_, SEXP y_, SEXP n_pos_, SEXP yl
if (Dev[l] / nullDev < .01) {
if (warn) warning("Model saturated; exiting...");
for (int ll=l; ll<L; ll++) iter[ll] = NA_INTEGER;
Free(slores_reject); Free(slores_reject_old);
Free(s); Free(w); Free(a); Free(r); Free(e1); Free(e2); Free(eta);
R_Free(slores_reject); R_Free(slores_reject_old);
R_Free(s); R_Free(w); R_Free(a); R_Free(r); R_Free(e1); R_Free(e2); R_Free(eta);
return List::create(beta0, beta, center, scale, lambda, Dev, iter, n_reject, n_slores_reject, Rcpp::wrap(col_idx));
}
// Intercept
Expand Down Expand Up @@ -1012,8 +1012,8 @@ RcppExport SEXP cdfit_binomial_slores_ssr(SEXP X_, SEXP y_, SEXP n_pos_, SEXP yl
}
}
}
Free(slores_reject); Free(slores_reject_old);
Free(s); Free(w); Free(a); Free(r); Free(e1); Free(e2); Free(eta);
R_Free(slores_reject); R_Free(slores_reject_old);
R_Free(s); R_Free(w); R_Free(a); R_Free(r); R_Free(e1); R_Free(e2); R_Free(eta);
//ProfilerStop();
return List::create(beta0, beta, center, scale, lambda, Dev, iter, n_reject, n_slores_reject, Rcpp::wrap(col_idx));
}
Expand Down Expand Up @@ -1097,21 +1097,21 @@ RcppExport SEXP cdfit_binomial_ada_slores_ssr(SEXP X_, SEXP y_, SEXP n_pos_, SEX
}

arma::sp_mat beta = arma::sp_mat(p, L); //beta
double *a = Calloc(p, double); //Beta from previous iteration
double *a = R_Calloc(p, double); //Beta from previous iteration
double a0 = 0.0; //beta0 from previousiteration
double *w = Calloc(n, double);
double *s = Calloc(n, double); //y_i - pi_i
double *eta = Calloc(n, double);
int *e1 = Calloc(p, int); //ever-active set
int *e2 = Calloc(p, int); //strong set
double *w = R_Calloc(n, double);
double *s = R_Calloc(n, double); //y_i - pi_i
double *eta = R_Calloc(n, double);
int *e1 = R_Calloc(p, int); //ever-active set
int *e2 = R_Calloc(p, int); //strong set
double xwr, xwx, pi, u, v, cutoff, l1, l2, shift, si;
double max_update, update, thresh; // for convergence check
int i, j, jj, l, violations, lstart;

double ybar = sum(y, n) / n;
a0 = beta0[0] = log(ybar / (1-ybar));
double nullDev = 0;
double *r = Calloc(n, double);
double *r = R_Calloc(n, double);
for (i = 0; i < n; i++) {
r[i] = y[i];
nullDev = nullDev - y[i]*log(ybar) - (1-y[i])*log(1-ybar);
Expand Down Expand Up @@ -1155,8 +1155,8 @@ RcppExport SEXP cdfit_binomial_ada_slores_ssr(SEXP X_, SEXP y_, SEXP n_pos_, SEX
vector<double> X_theta_lam_xi_pos;
vector<double> prod_PX_Pxmax_xi_pos;
vector<double> cutoff_xi_pos;
int *slores_reject = Calloc(p, int);
int *slores_reject_old = Calloc(p, int);
int *slores_reject = R_Calloc(p, int);
int *slores_reject_old = R_Calloc(p, int);
for (int j = 0; j < p; j++) slores_reject_old[j] = 1;
int l_prev = lstart;
double gain = 0.0;
Expand Down Expand Up @@ -1201,8 +1201,8 @@ RcppExport SEXP cdfit_binomial_ada_slores_ssr(SEXP X_, SEXP y_, SEXP n_pos_, SEX
}
if (nv > dfmax) {
for (int ll=l; ll<L; ll++) iter[ll] = NA_INTEGER;
Free(slores_reject); Free(slores_reject_old);
Free(s); Free(w); Free(a); Free(r); Free(e1); Free(e2); Free(eta);
R_Free(slores_reject); R_Free(slores_reject_old);
R_Free(s); R_Free(w); R_Free(a); R_Free(r); R_Free(e1); R_Free(e2); R_Free(eta);
//ProfilerStop();
return List::create(beta0, beta, center, scale, lambda, Dev,
iter, n_reject, Rcpp::wrap(col_idx));
Expand Down Expand Up @@ -1301,8 +1301,8 @@ RcppExport SEXP cdfit_binomial_ada_slores_ssr(SEXP X_, SEXP y_, SEXP n_pos_, SEX
if (Dev[l] / nullDev < .01) {
if (warn) warning("Model saturated; exiting...");
for (int ll=l; ll<L; ll++) iter[ll] = NA_INTEGER;
Free(slores_reject); Free(slores_reject_old);
Free(s); Free(w); Free(a); Free(r); Free(e1); Free(e2); Free(eta);
R_Free(slores_reject); R_Free(slores_reject_old);
R_Free(s); R_Free(w); R_Free(a); R_Free(r); R_Free(e1); R_Free(e2); R_Free(eta);
return List::create(beta0, beta, center, scale, lambda, Dev, iter, n_reject, n_slores_reject, Rcpp::wrap(col_idx));
}
// Intercept
Expand Down Expand Up @@ -1373,8 +1373,8 @@ RcppExport SEXP cdfit_binomial_ada_slores_ssr(SEXP X_, SEXP y_, SEXP n_pos_, SEX
}*/
}
}
Free(slores_reject); Free(slores_reject_old);
Free(s); Free(w); Free(a); Free(r); Free(e1); Free(e2); Free(eta);
R_Free(slores_reject); R_Free(slores_reject_old);
R_Free(s); R_Free(w); R_Free(a); R_Free(r); R_Free(e1); R_Free(e2); R_Free(eta);
//ProfilerStop();
return List::create(beta0, beta, center, scale, lambda, Dev, iter, n_reject, n_slores_reject, Rcpp::wrap(col_idx));
}
}
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