Removed FORCE_FLOAT from vc.h, logistic.h.

2 files changed, 85 insertions, 62 deletions

diff --git a/src/logistic.h b/src/logistic.h
index e951935..7f9e133 100644
--- a/src/logistic.h
+++ b/src/logistic.h
@@ -1,4 +1,4 @@
-#ifndef LOGISTIC_H_   /* Include guard */

+#ifndef LOGISTIC_H_

 #define LOGISTIC_H_

 

 // Mixed interface.

@@ -29,19 +29,21 @@ double fLogit_mixed(gsl_vector *beta,
 		    double lambdaL1,

 		    double lambdaL2);

 

-

 // Categorical-only interface.

-void logistic_cat_pred(gsl_vector *beta,  // Vector of parameters length = 1 + Sum_k(C_k - 1) + Kc

-		       gsl_matrix_int *X,  //Matrix Nobs x K 

-		       gsl_vector_int *nlev, // Vector with number categories

-		       gsl_vector *yhat); //Vector of prob. predicted by the logistic

+void logistic_cat_pred(gsl_vector *beta,     // Vector of parameters

+					     // length = 1+Sum_k(C_k-1)+Kc.

+		       gsl_matrix_int *X,    // Matrix Nobs x K.

+		       gsl_vector_int *nlev, // Vector with number categories.

+		       gsl_vector *yhat);    // Vector of prob. predicted by 

+					     // the logistic.

  

-int logistic_cat_fit(gsl_vector *beta,  // Vector of parameters length = 1 + Sum_k(C_k - 1) + Kc

-		     gsl_matrix_int *X,  //Matrix Nobs x K 

-		     gsl_vector_int *nlev, // Vector with number categories

-		     gsl_vector *y, //Vector of prob. to predict

-		     double lambdaL1, // Regularization L1 0.0 if not used

-		     double lambdaL2); // Regularization L2 0.0 if not used

+int logistic_cat_fit(gsl_vector *beta,     // Vector of parameters

+					   // length = 1+Sum_k(C_k-1)+Kc.

+		     gsl_matrix_int *X,    // Matrix Nobs x K .

+		     gsl_vector_int *nlev, // Vector with number categories.

+		     gsl_vector *y,        // Vector of prob. to predict.

+		     double lambdaL1,      // Regularization L1, 0 if not used

+		     double lambdaL2);     // Regularization L2, 0 if not used

 

 double fLogit_cat(gsl_vector *beta,

 		  gsl_matrix_int *X,

@@ -50,22 +52,24 @@ double fLogit_cat(gsl_vector *beta,
 		  double lambdaL1,

 		  double lambdaL2);

 

-/* Continuous only interface */

-void logistic_cont_pred(gsl_vector *beta  // Vector of parameters length = 1 + Sum_k(C_k - 1) + Kc

-			,gsl_matrix *Xc   // continuous covariates  Matrix Nobs x Kc 

-			,gsl_vector *yhat //Vector of prob. predicted by the logistic

-			);

+// Continuous-only interface.

+void logistic_cont_pred(gsl_vector *beta, // Vector of parameters

+					  // length = 1 + Sum_k(C_k-1) + Kc.

+			gsl_matrix *Xc,   // Continuous cov's matrix Nobs x Kc.

+			gsl_vector *yhat);// Vector of prob. predicted

+					  // by the logistic.

  

-int logistic_cont_fit(gsl_vector *beta  // Vector of parameters length = 1 + Sum_k(C_k - 1) + Kc

-		      ,gsl_matrix *Xc   // continuous covariates  Matrix Nobs x Kc 

-		      ,gsl_vector *y //Vector of prob. to predict

-		      ,double lambdaL1 // Regularization L1 0.0 if not used

-		      ,double lambdaL2); // Regularization L2 0.0 if not used

+int logistic_cont_fit(gsl_vector *beta, // Vector of parameters

+					// length = 1+Sum_k(C_k-1)+Kc.

+		      gsl_matrix *Xc,   // Continuous cov's matrix Nobs x Kc.

+		      gsl_vector *y,    // Vector of prob. to predict.

+		      double lambdaL1,  // Regularization L1, 0 if not used.

+		      double lambdaL2); // Regularization L2, 0 if not used.

 

 double fLogit_cont(gsl_vector *beta,

-		   gsl_matrix *Xc, // Continuous covariates matrix Nobs x Kc .

+		   gsl_matrix *Xc, // Continuous covariates matrix Nobs x Kc.

 		   gsl_vector *y,

 		   double lambdaL1,

 		   double lambdaL2);

 

-#endif // LOGISTIC_H_

+#endif

diff --git a/src/vc.h b/src/vc.h
index 3358433..43c6979 100644
--- a/src/vc.h
+++ b/src/vc.h
@@ -1,6 +1,6 @@
 /*
-	Genome-wide Efficient Mixed Model Association (GEMMA)
-    Copyright (C) 2011  Xiang Zhou
+    Genome-wide Efficient Mixed Model Association (GEMMA)
+    Copyright (C) 2011-2017, Xiang Zhou
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -13,7 +13,7 @@
     GNU General Public License for more details.
 
     You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+    along with this program. If not, see <http://www.gnu.org/licenses/>.
 */
 
 #ifndef __VC_H__
@@ -21,22 +21,12 @@
 
 #include "gsl/gsl_vector.h"
 #include "gsl/gsl_matrix.h"
-
-
-#ifdef FORCE_FLOAT
-#include "param_float.h"
-#include "io_float.h"
-#else
 #include "param.h"
 #include "io.h"
-#endif
 
 using namespace std;
 
-
-
-class VC_PARAM
-{
+class VC_PARAM {
 
 public:
 	const gsl_matrix *K;
@@ -50,14 +40,10 @@ public:
 	bool noconstrain;
 };
 
-
-
-
-
 class VC {
 
 public:
-	// IO related parameters
+  // IO-related parameters
   size_t a_mode;
 	string file_cat;
 	string file_beta;
@@ -89,28 +75,61 @@ public:
 	double time_UtX;
 	double time_opt;
 
-	// Main functions
+	// Main functions.
 	void CopyFromParam (PARAM &cPar);
 	void CopyToParam (PARAM &cPar);
-	void WriteFile_qs (const gsl_vector *s_vec, const gsl_vector *q_vec, const gsl_vector *qvar_vec, const gsl_matrix *S_mat, const gsl_matrix *Svar_mat);
-	void CalcVChe (const gsl_matrix *K, const gsl_matrix *W, const gsl_vector *y);
-	void CalcVCreml (const bool noconstrain, const gsl_matrix *K, const gsl_matrix *W, const gsl_vector *y);
-	void CalcVCacl (const gsl_matrix *K, const gsl_matrix *W, const gsl_vector *y);
+	void WriteFile_qs (const gsl_vector *s_vec, const gsl_vector *q_vec,
+			   const gsl_vector *qvar_vec, const gsl_matrix *S_mat,
+			   const gsl_matrix *Svar_mat);
+	void CalcVChe (const gsl_matrix *K, const gsl_matrix *W,
+		       const gsl_vector *y);
+	void CalcVCreml (const bool noconstrain, const gsl_matrix *K,
+			 const gsl_matrix *W, const gsl_vector *y);
+	void CalcVCacl (const gsl_matrix *K, const gsl_matrix *W,
+			const gsl_vector *y);
 };
 
-void CalcVCss(const gsl_matrix *Vq, const gsl_matrix *S_mat, const gsl_matrix *Svar_mat, const gsl_vector *q_vec, const gsl_vector *s_vec, const double df, vector<double> &v_pve, vector<double> &v_se_pve, double &pve_total, double &se_pve_total, vector<double> &v_sigma2, vector<double> &v_se_sigma2, vector<double> &v_enrich, vector<double> &v_se_enrich);
-
-
-bool BimbamXwz (const string &file_geno, const int display_pace, vector<int> &indicator_idv, vector<int> &indicator_snp, const vector<size_t> &vec_cat, const gsl_vector *w, const gsl_vector *z, size_t ns_test, gsl_matrix *XWz);
-bool PlinkXwz (const string &file_bed, const int display_pace, vector<int> &indicator_idv, vector<int> &indicator_snp, const vector<size_t> &vec_cat, const gsl_vector *w, const gsl_vector *z, size_t ns_test, gsl_matrix *XWz);
-bool MFILEXwz (const size_t mfile_mode, const string &file_mfile, const int display_pace, vector<int> &indicator_idv, vector<vector<int> > &mindicator_snp, const vector<size_t> &vec_cat, const gsl_vector *w, const gsl_vector *z, gsl_matrix *XWz);
-
-bool BimbamXtXwz (const string &file_geno, const int display_pace, vector<int> &indicator_idv, vector<int> &indicator_snp, const gsl_matrix *XWz, size_t ns_test, gsl_matrix *XtXWz);
-bool PlinkXtXwz (const string &file_bed, const int display_pace, vector<int> &indicator_idv, vector<int> &indicator_snp, const gsl_matrix *XWz, size_t ns_test, gsl_matrix *XtXWz);
-bool MFILEXtXwz (const size_t mfile_mode, const string &file_mfile, const int display_pace, vector<int> &indicator_idv, vector<vector<int> > &mindicator_snp, const gsl_matrix *XWz, gsl_matrix *XtXWz);
-
-void CalcCIss(const gsl_matrix *Xz, const gsl_matrix *XWz, const gsl_matrix *XtXWz, const gsl_matrix *S_mat, const gsl_matrix *Svar_mat, const gsl_vector *w, const gsl_vector *z, const gsl_vector *s_vec, const vector<size_t> &vec_cat, const vector<double> &v_pve, vector<double> &v_se_pve, double &pve_total, double &se_pve_total, vector<double> &v_sigma2, vector<double> &v_se_sigma2, vector<double> &v_enrich, vector<double> &v_se_enrich);
+void CalcVCss(const gsl_matrix *Vq, const gsl_matrix *S_mat,
+	      const gsl_matrix *Svar_mat, const gsl_vector *q_vec,
+	      const gsl_vector *s_vec, const double df, vector<double> &v_pve,
+	      vector<double> &v_se_pve, double &pve_total,
+	      double &se_pve_total, vector<double> &v_sigma2,
+	      vector<double> &v_se_sigma2, vector<double> &v_enrich,
+	      vector<double> &v_se_enrich);
+
+bool BimbamXwz (const string &file_geno, const int display_pace,
+		vector<int> &indicator_idv, vector<int> &indicator_snp,
+		const vector<size_t> &vec_cat, const gsl_vector *w,
+		const gsl_vector *z, size_t ns_test, gsl_matrix *XWz);
+bool PlinkXwz (const string &file_bed, const int display_pace,
+	       vector<int> &indicator_idv, vector<int> &indicator_snp,
+	       const vector<size_t> &vec_cat, const gsl_vector *w,
+	       const gsl_vector *z, size_t ns_test, gsl_matrix *XWz);
+bool MFILEXwz (const size_t mfile_mode, const string &file_mfile,
+	       const int display_pace, vector<int> &indicator_idv,
+	       vector<vector<int> > &mindicator_snp,
+	       const vector<size_t> &vec_cat, const gsl_vector *w,
+	       const gsl_vector *z, gsl_matrix *XWz);
+
+bool BimbamXtXwz (const string &file_geno, const int display_pace,
+		  vector<int> &indicator_idv, vector<int> &indicator_snp,
+		  const gsl_matrix *XWz, size_t ns_test, gsl_matrix *XtXWz);
+bool PlinkXtXwz (const string &file_bed, const int display_pace,
+		 vector<int> &indicator_idv, vector<int> &indicator_snp,
+		 const gsl_matrix *XWz, size_t ns_test, gsl_matrix *XtXWz);
+bool MFILEXtXwz (const size_t mfile_mode, const string &file_mfile,
+		 const int display_pace, vector<int> &indicator_idv,
+		 vector<vector<int> > &mindicator_snp, const gsl_matrix *XWz,
+		 gsl_matrix *XtXWz);
+
+void CalcCIss(const gsl_matrix *Xz, const gsl_matrix *XWz,
+	      const gsl_matrix *XtXWz, const gsl_matrix *S_mat,
+	      const gsl_matrix *Svar_mat, const gsl_vector *w,
+	      const gsl_vector *z, const gsl_vector *s_vec,
+	      const vector<size_t> &vec_cat, const vector<double> &v_pve,
+	      vector<double> &v_se_pve, double &pve_total,
+	      double &se_pve_total, vector<double> &v_sigma2,
+	      vector<double> &v_se_sigma2, vector<double> &v_enrich,
+	      vector<double> &v_se_enrich);
 
 #endif
-
-