Add files via upload

1 files changed, 291 insertions, 0 deletions

diff --git a/sourcecodes/localscore/Applic.h b/sourcecodes/localscore/Applic.h
new file mode 100644
index 00000000..0ae5e981
--- /dev/null
+++ b/sourcecodes/localscore/Applic.h
@@ -0,0 +1,291 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1998-2012   Robert Gentleman, Ross Ihaka
+ *                             and the R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ *
+ *
+ * Application Routines, typically implemented in  ../appl/
+ * ----------------------------------------------  ========
+ */
+
+/* This header file contains routines which are in the R API and ones which
+   are not.
+
+   Those which are not can be used only at the user's risk and may change
+   or disappear in a future release of R.
+*/
+
+
+#ifndef R_APPLIC_H_
+#define R_APPLIC_H_
+
+#include <R_ext/Boolean.h>
+#include <R_ext/RS.h>		/* F77_... */
+#include <R_ext/BLAS.h>
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+/* Entry points in the R API */
+
+/* appl/integrate.c */
+typedef void integr_fn(double *x, int n, void *ex);
+/* vectorizing function   f(x[1:n], ...) -> x[]  {overwriting x[]}. */
+
+void Rdqags(integr_fn f, void *ex, double *a, double *b,
+	    double *epsabs, double *epsrel,
+	    double *result, double *abserr, int *neval, int *ier,
+	    int *limit, int *lenw, int *last, int *iwork, double *work);
+
+void Rdqagi(integr_fn f, void *ex, double *bound, int *inf,
+	    double *epsabs, double *epsrel,
+	    double *result, double *abserr, int *neval, int *ier,
+	    int *limit, int *lenw, int *last,
+	    int *iwork, double *work);
+
+/* main/optim.c */
+typedef double optimfn(int, double *, void *);
+typedef void optimgr(int, double *, double *, void *);
+
+void vmmin(int n, double *b, double *Fmin,
+	   optimfn fn, optimgr gr, int maxit, int trace,
+	   int *mask, double abstol, double reltol, int nREPORT,
+	   void *ex, int *fncount, int *grcount, int *fail);
+void nmmin(int n, double *Bvec, double *X, double *Fmin, optimfn fn,
+	   int *fail, double abstol, double intol, void *ex,
+	   double alpha, double bet, double gamm, int trace,
+	   int *fncount, int maxit);
+void cgmin(int n, double *Bvec, double *X, double *Fmin,
+	   optimfn fn, optimgr gr,
+	   int *fail, double abstol, double intol, void *ex,
+	   int type, int trace, int *fncount, int *grcount, int maxit);
+void lbfgsb(int n, int m, double *x, double *l, double *u, int *nbd,
+	    double *Fmin, optimfn fn, optimgr gr, int *fail, void *ex,
+	    double factr, double pgtol, int *fncount, int *grcount,
+	    int maxit, char *msg, int trace, int nREPORT);
+void samin(int n, double *pb, double *yb, optimfn fn, int maxit,
+	   int tmax, double ti, int trace, void *ex);
+
+
+
+/* Entry points NOT in the R API */
+
+/* appl/bakslv.c : hidden */
+void bakslv(double *, int *, int *,
+	    double *, int *, int *,
+	    double *, int *, int *);
+
+/* appl/binning.c : hidden */
+void bincode (double *x, int *n, double *breaks, int *nb,
+	      int *code, int *right, int *include_border, int *naok);
+void bincount(double *x, int *n, double *breaks, int *nb, int *count,
+	      int *right, int *include_border, int *naok);
+
+/* appl/ch2inv.f */
+void F77_NAME(ch2inv)(double *x, int *ldx, int *n, double *v, int *info);
+
+/* appl/chol.f Used in nlme */
+void F77_NAME(chol)(double *a, int *lda, int *n, double *v, int *info);
+
+/* appl/cpoly.c : hidden */
+void R_cpolyroot(double *opr, double *opi, int *degree,
+		 double *zeror, double *zeroi, Rboolean *fail);
+/* More `Complex Polynomial Utilities' could be exported:
+
+   polyev(...)
+   errev(...)
+   cpoly_cauchy(...)
+   cpoly_scale(...)
+   cdivid(...)
+*/
+
+
+/* appl/cumsum.c : non-API, used in package DCluster */
+void R_cumsum(double *, int *, double *, double *);
+
+/* appl/eigen.f */
+int F77_NAME(cg)(int *nm, int *n, double *ar, double *ai,
+		 double *wr, double *wi, int *matz, double *zr, double *zi,
+		 double *fv1, double *fv2, double *fv3, int *ierr);
+int F77_NAME(ch)(int *nm, int *n, double *ar, double *ai,
+		 double *w, int *matz, double *zr, double *zi,
+		 double *fv1, double *fv2, double *fm1, int *ierr);
+int F77_NAME(rg)(int *nm, int *n, double *a, double *wr, double *wi,
+		 int *matz, double *z, int *iv1, double *fv1, int *ierr);
+/* used in nlme */
+int F77_NAME(rs)(int *nm, int *n, double *a, double *w,
+		 int *matz, double *z, double *fv1, double *fv2, int *ierr);
+
+/* appl/fft.c */
+/* NOTE:  The following functions use GLOBAL (static) variables !!
+ * ----   some of R-core think that this should be changed,
+ *        which will INEVITABLY extend the argument lists ...!
+ */
+/* non-API, but used by package RandomFields */
+void fft_factor(int n, int *pmaxf, int *pmaxp);
+Rboolean fft_work(double *a, double *b, int nseg, int n, int nspn,
+/* TRUE: success */ int isn, double *work, int *iwork);
+
+/* appl/fmin.c : */
+double Brent_fmin(double ax, double bx, double (*f)(double, void *),
+		  void *info, double tol);
+
+/* appl/interv.c: also in Utils.h */
+/* used in packages gam and mda */
+int F77_SUB(interv)(double *xt, int *n, double *x,
+		    Rboolean *rightmost_closed, Rboolean *all_inside,
+		    int *ilo, int *mflag);
+/* Non-API No longer used */
+void find_interv_vec(double *xt, int *n, double *x, int *nx,
+		     int *rightmost_closed, int *all_inside, int *indx);
+/* API, used in package eco */
+int findInterval(double *xt, int n, double x,
+		 Rboolean rightmost_closed,  Rboolean all_inside, int ilo,
+		 int *mflag);
+
+/* appl/lbfgsb.c */
+void setulb(int n, int m, double *x, double *l, double *u, int *nbd,
+	    double *f, double *g, double factr, double *pgtol,
+	    double *wa, int * iwa, char *task, int iprint,
+	    int *lsave, int *isave, double *dsave);
+
+/* appl/machar.c */
+void machar(int *ibeta, int *it, int *irnd, int *ngrd, int *machep,
+	    int *negep, int *iexp, int *minexp, int *maxexp,
+	    double *eps, double *epsneg, double *xmin, double *xmax);
+
+/* appl/maxcol.c: also in Utils.h  Used in package MNP */
+void R_max_col(double *matrix, int *nr, int *nc, int *maxes, int *ties_meth);
+
+
+/* appl/pretty.c */
+double R_pretty0(double *lo, double *up, int *ndiv, int min_n,
+		 double shrink_sml, double high_u_fact[],
+		 int eps_correction, int return_bounds);
+void R_pretty(double *lo, double *up, int *ndiv, int *min_n,
+	      double *shrink_sml, double *high_u_fact,
+	      int *eps_correction);
+
+/* appl/rcont.c: API prior to R 2.15.2 */
+void rcont2(int *nrow, int *ncol, int *nrowt, int *ncolt, int *ntotal,
+	    double *fact, int *jwork, int *matrix);
+
+/* appl/rowsum.c */
+void R_rowsum(int *dim, double *na_x, double *x, double *group);
+
+/* appl/stem.c */
+Rboolean stemleaf(double *x, int *n, double *scale, int *width, double *atom);
+
+/* appl/strsignif.c */
+void str_signif(char *x, int *n, const char **type, int *width, int *digits,
+		const char **format, const char **flag, char **result);
+
+/* appl/tabulate.c : non-API, used in package ape, phangorn, pcaPA */
+void R_tabulate(int *x, int *n, int *nbin, int *ans);
+
+/* appl/uncmin.c : */
+
+/* type of pointer to the target and gradient functions */
+typedef void (*fcn_p)(int, double *, double *, void *);
+
+/* type of pointer to the hessian functions */
+typedef void (*d2fcn_p)(int, int, double *, double *, void *);
+
+void fdhess(int n, double *x, double fval, fcn_p fun, void *state,
+	    double *h, int nfd, double *step, double *f, int ndigit,
+	    double *typx);
+
+/* used in nlme */
+void optif9(int nr, int n, double *x,
+	    fcn_p fcn, fcn_p d1fcn, d2fcn_p d2fcn,
+	    void *state, double *typsiz, double fscale, int method,
+	    int iexp, int *msg, int ndigit, int itnlim, int iagflg,
+	    int iahflg, double dlt, double gradtl, double stepmx,
+	    double steptl, double *xpls, double *fpls, double *gpls,
+	    int *itrmcd, double *a, double *wrk, int *itncnt);
+
+void optif0(int nr, int n, double *x, fcn_p fcn, void *state,
+	    double *xpls, double *fpls, double *gpls, int *itrmcd,
+	    double *a, double *wrk);
+
+/* appl/zeroin.c : non API, but used in package qtl */
+double R_zeroin(double ax, double bx, double (*f)(double, void *), void *info,
+		double *Tol, int *Maxit);
+/* R_zeroin2() is faster for "expensive" f(), in those typical cases where
+ *             f(ax) and f(bx) are available anyway : */
+double R_zeroin2(double ax, double bx, double fa, double fb,
+		 double (*f)(double, void *), void *info, double *Tol, int *Maxit);
+
+
+/* ALL appl/<foobar>.f	[semi-automatically by
+ *				 f2c -A -P *.f; cat *.P > all.h	 and editing]
+ */
+
+/* This is not in the applications but in the BLAS, and defined in Lapack.h
+extern int F77_NAME(lsame)(const char *, const char *);
+*/
+
+/* LINPACK routines also declared in Linpack.h
+void F77_NAME(dpoco)(double *a, int *lda, int *n, double *rcond,
+		     double *z__, int *info);
+void F77_NAME(dpodi)(double *a, int *lda, int *n, double *det, int *job);
+void F77_NAME(dpofa)(double *a, int *lda, int *n, int *info);
+void F77_NAME(dposl)(double *a, int *lda, int *n, double *b);
+void F77_NAME(dqrdc)(double *x, int *ldx, int *n, int *p,
+		     double *qraux, int *jpvt, double *work, int *job);
+void F77_NAME(dqrsl)(double *x, int *ldx, int *n, int *k,
+		     double *qraux, double *y,
+		     double *qy, double *qty, double *b,
+		     double *rsd, double *xb, int *job, int *info);
+void F77_NAME(dsvdc)(double *x, int *ldx, int *n, int *p,
+		     double *s, double *e,
+		     double *u, int *ldu, double *v, int *ldv,
+		     double *work, int *job, int *info);
+void F77_NAME(dtrco)(double *t, int *ldt, int *n, double *rcond,
+		     double *z__, int *job);
+void F77_NAME(dtrsl)(double *t, int *ldt, int *n, double *b, int *job,
+		     int *info);
+*/
+
+/* find qr decomposition, dqrdc2() is basis of R's qr(), also used by nlme */
+void F77_NAME(dqrdc2)(double *x, int *ldx, int *n, int *p,
+		      double *tol, int *rank,
+		      double *qraux, int *pivot, double *work);
+void F77_NAME(dqrls)(double *x, int *n, int *p, double *y, int *ny,
+		     double *tol, double *b, double *rsd,
+		     double *qty, int *k,
+		     int *jpvt, double *qraux, double *work);
+
+/* appl/dqrutl.f: interfaces to dqrsl */
+void F77_NAME(dqrqty)(double *x, int *n, int *k, double *qraux,
+		      double *y, int *ny, double *qty);
+void F77_NAME(dqrqy)(double *x, int *n, int *k, double *qraux,
+		     double *y, int *ny, double *qy);
+void F77_NAME(dqrcf)(double *x, int *n, int *k, double *qraux,
+		     double *y, int *ny, double *b, int *info);
+void F77_NAME(dqrrsd)(double *x, int *n, int *k, double *qraux,
+		     double *y, int *ny, double *rsd);
+void F77_NAME(dqrxb)(double *x, int *n, int *k, double *qraux,
+		     double *y, int *ny, double *xb);
+
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* R_APPLIC_H_ */