Simplex uses Stan's stick breaking transform and fix Dirichlet deriva…

…tive
4ment · Mar 15, 2024 · 9cd695e · 9cd695e
1 parent dade424
commit 9cd695e
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Showing 14 changed files with 318 additions and 247 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -8,7 +8,7 @@ SET( LIBRARY_NAME "PHYC" )
 
 SET( ${LIBRARY_NAME}_MAJOR_VERSION 2 )
 SET( ${LIBRARY_NAME}_MINOR_VERSION 0 )
-SET( ${LIBRARY_NAME}_PATCH_LEVEL 1-dev )
+SET( ${LIBRARY_NAME}_PATCH_LEVEL 0 )
 
 
 #####################################################################
@@ -183,12 +183,21 @@ ENDIF()
 # Config header file
 #####################################################################
 
+execute_process(
+  COMMAND git tag --points-at HEAD
+  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+  OUTPUT_VARIABLE GIT_HEAD_TAG
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+  ERROR_QUIET
+)
+
 # Get the current working branch
 execute_process(
   COMMAND git rev-parse --abbrev-ref HEAD
   WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
   OUTPUT_VARIABLE GIT_BRANCH
   OUTPUT_STRIP_TRAILING_WHITESPACE
+  ERROR_QUIET
 )
 
 # Get the latest abbreviated commit hash of the working branch
@@ -197,6 +206,7 @@ execute_process(
   WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
   OUTPUT_VARIABLE GIT_COMMIT_HASH
   OUTPUT_STRIP_TRAILING_WHITESPACE
+  ERROR_QUIET
 )
 
 configure_file (
@@ -338,7 +348,7 @@ IF(NOT DISABLE_GSL)
 	target_link_libraries(phyc GSL::gsl GSL::gslcblas)
 ENDIF()
 
-IF(NOT LIBRARY_ONLY)	
+IF(NOT LIBRARY_ONLY AND NOT DISABLE_GSL)
 	add_executable(physher src/physher.c)
 	target_link_libraries(physher phyc)
 

diff --git a/examples/fluA/checkpoint.jon b/examples/fluA/checkpoint.jon
diff --git a/src/modelAveraging.c b/src/modelAveraging.c
@@ -61,7 +61,7 @@ int main(int argc, char* argv[]){
 
     if ( args_contains(argc, argv, "-c") ) {
         bool success = false;
-        nclasses = args_get_int(argc, argv, "-c", &success );
+        nclasses = args_get_int2(argc, argv, "-c", &success );
         if( !success || nclasses <= 0 ){
             error("Could not read the number of classes [-c]");
         }

diff --git a/src/phyc/PhyCConfig.h.in b/src/phyc/PhyCConfig.h.in
@@ -31,5 +31,6 @@
 
 #define GIT_BRANCH "@GIT_BRANCH@"
 #define GIT_COMMIT_HASH "@GIT_COMMIT_HASH@"
+#define GIT_HEAD_TAG "@GIT_HEAD_TAG@"
 
 #endif
diff --git a/src/phyc/args.c b/src/phyc/args.c
@@ -420,7 +420,7 @@ int * args_get_pint( int argc, char* argv[], const char flag[] ){
 	return option;
 }
 
-int args_get_int( int argc, char* argv[], const char flag[], bool *success ){
+int args_get_int2( int argc, char* argv[], const char flag[], bool *success ){
     int i = 0;
     char *str = NULL;
 
@@ -446,6 +446,54 @@ int args_get_int( int argc, char* argv[], const char flag[], bool *success ){
 	return 0;
 }
 
+int args_get_int( int argc, char* argv[], const char flag[], int defaultv ){
+    int i = 0;
+    char *str = NULL;
+
+    for ( ; i < argc; i++) {
+        if ( strncmp(argv[i], flag, strlen(flag)) == 0  ) {
+            str = NULL;
+            if( strlen(argv[i]) > strlen(flag) ){
+                str = argv[i]+strlen(flag);
+            }
+            else if( i+1 < argc ){
+                str = argv[i+1];
+            }
+
+            if( str != NULL && isInt(str) ){
+                return atoi( str );
+            }
+            break;
+        }
+
+	}
+	return defaultv;
+}
+
+long args_get_long( int argc, char* argv[], const char flag[], long defaultv ){
+    int i = 0;
+    char *str = NULL;
+
+    for ( ; i < argc; i++) {
+        if ( strncmp(argv[i], flag, strlen(flag)) == 0  ) {
+            str = NULL;
+            if( strlen(argv[i]) > strlen(flag) ){
+                str = argv[i]+strlen(flag);
+            }
+            else if( i+1 < argc ){
+                str = argv[i+1];
+            }
+
+            if( str != NULL && isInt(str) ){
+                return atoi( str );
+            }
+            break;
+        }
+
+	}
+	return defaultv;
+}
+
 double * args_get_pdouble( int argc, char* argv[], const char flag[] ){
 	double *option = NULL;
     char *str = NULL;

diff --git a/src/phyc/args.h b/src/phyc/args.h
@@ -87,7 +87,11 @@ char * args_get_string( int argc, char* argv[], const char flag[] );
 
 int * args_get_pint( int argc, char* argv[], const char flag[] );
 
-int args_get_int( int argc, char* argv[], const char flag[], bool *success );
+int args_get_int2( int argc, char* argv[], const char flag[], bool *success );
+
+int args_get_int( int argc, char* argv[], const char flag[], int defaultv );
+
+long args_get_long( int argc, char* argv[], const char flag[], long defaultv );
 
 double * args_get_pdouble( int argc, char* argv[], const char flag[] );
 

diff --git a/src/phyc/distdirichlet.c b/src/phyc/distdirichlet.c
@@ -35,7 +35,18 @@ double DistributionModel_log_flat_dirichlet_with_values(DistributionModel* dm, c
 }
 
 double DistributionModel_dlog_flat_dirichlet(DistributionModel* dm, const Parameter* p){
-	return 0.0;
+	for (int i = 0; i < Parameters_count(dm->x); i++) {
+        if( p == Parameters_at(dm->x, i)){
+            const double* values = dm->simplex->get_values(dm->simplex);
+            double dlogp = 0;
+            for (size_t j = i; j < Parameters_count(dm->x); j++) {
+                dm->simplex->gradient(dm->simplex, i, dm->tempp);
+                dlogp += dm->tempp[j]/values[j];
+            }
+            return dlogp;
+        }
+    }
+    return 0.0;
 }
 
 double DistributionModel_d2log_flat_dirichlet(DistributionModel* dm, const Parameter* p){
@@ -75,10 +86,25 @@ static double DistributionModel_dirichlet_sample_evaluate(DistributionModel* dm)
 	return logP;
 }
 
+// IMPORTANT: The derivative is wrt unconstrained parameter of the simplex
 double DistributionModel_dlog_dirichlet(DistributionModel* dm, const Parameter* p){
+    /*
+    log pdf(X; \alpha) = \sum_i \alpha_i log(x_i) - log B(\alpha)
+    d log pdf(X)/dz_k = \sum_i \alpha_i d log(x_i)/dz_k
+                     &= \sum_i \alpha_i d log(x_i)/dx_i dx_i/dz_k
+                     &= \sum_i \alpha_i/x_i dx_i/dz_k
+    
+    dx_i/dz_k = 0 for i < k
+    */
 	for (int i = 0; i < Parameters_count(dm->x); i++) {
         if( p == Parameters_at(dm->x, i)){
-            return (Parameters_value(dm->parameters[0], i)-1.0)/Parameter_value(p);
+            const double* values = dm->simplex->get_values(dm->simplex);
+            double dlogp = 0;
+            for (size_t j = i; j < Parameters_count(dm->x); j++) {
+                dm->simplex->gradient(dm->simplex, i, dm->tempp);
+                dlogp += (Parameters_value(dm->parameters[0], j)-1.0)/values[j] * dm->tempp[j];
+            }
+            return dlogp;
         }
     }
 	return 0;