diff --git a/_r_e_a_d_m_e_8md.html b/_r_e_a_d_m_e_8md.html index 50cea4e41..27a79d8a6 100644 --- a/_r_e_a_d_m_e_8md.html +++ b/_r_e_a_d_m_e_8md.html @@ -102,7 +102,7 @@ diff --git a/annotated.html b/annotated.html index c111ebe30..5222ed796 100644 --- a/annotated.html +++ b/annotated.html @@ -147,7 +147,7 @@ diff --git a/barray-bones_8hpp.html b/barray-bones_8hpp.html index 8e02a1cfa..7d1fe4b15 100644 --- a/barray-bones_8hpp.html +++ b/barray-bones_8hpp.html @@ -122,7 +122,7 @@ diff --git a/barray-bones_8hpp_source.html b/barray-bones_8hpp_source.html index a70c3f497..d9be1c073 100644 --- a/barray-bones_8hpp_source.html +++ b/barray-bones_8hpp_source.html @@ -328,7 +328,7 @@ diff --git a/barray-iterator_8hpp.html b/barray-iterator_8hpp.html index 79cb99a4e..acc0107e9 100644 --- a/barray-iterator_8hpp.html +++ b/barray-iterator_8hpp.html @@ -112,7 +112,7 @@ diff --git a/barray-iterator_8hpp_source.html b/barray-iterator_8hpp_source.html index 7d2070870..f9811273e 100644 --- a/barray-iterator_8hpp_source.html +++ b/barray-iterator_8hpp_source.html @@ -148,7 +148,7 @@ diff --git a/barray-meat-operators_8hpp.html b/barray-meat-operators_8hpp.html index fe9d2369d..aacfbc663 100644 --- a/barray-meat-operators_8hpp.html +++ b/barray-meat-operators_8hpp.html @@ -576,7 +576,7 @@

diff --git a/barray-meat-operators_8hpp_source.html b/barray-meat-operators_8hpp_source.html index 45c1bfe4c..9f7ad7fc3 100644 --- a/barray-meat-operators_8hpp_source.html +++ b/barray-meat-operators_8hpp_source.html @@ -240,7 +240,7 @@ diff --git a/barray-meat_8hpp.html b/barray-meat_8hpp.html index 8f0a12a23..eaaf8dfa6 100644 --- a/barray-meat_8hpp.html +++ b/barray-meat_8hpp.html @@ -164,7 +164,7 @@

  • include
  • barry
  • barray-meat.hpp
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barray-meat_8hpp_source.html b/barray-meat_8hpp_source.html index d065f0f7b..2fe506633 100644 --- a/barray-meat_8hpp_source.html +++ b/barray-meat_8hpp_source.html @@ -1441,7 +1441,7 @@ diff --git a/barraycell-bones_8hpp.html b/barraycell-bones_8hpp.html index 3808c9281..cf39eb969 100644 --- a/barraycell-bones_8hpp.html +++ b/barraycell-bones_8hpp.html @@ -123,7 +123,7 @@ diff --git a/barraycell-bones_8hpp_source.html b/barraycell-bones_8hpp_source.html index b195d424e..775520f80 100644 --- a/barraycell-bones_8hpp_source.html +++ b/barraycell-bones_8hpp_source.html @@ -204,7 +204,7 @@ diff --git a/barraycell-meat_8hpp.html b/barraycell-meat_8hpp.html index 9798b0bc4..d8f234de6 100644 --- a/barraycell-meat_8hpp.html +++ b/barraycell-meat_8hpp.html @@ -113,7 +113,7 @@ diff --git a/barraycell-meat_8hpp_source.html b/barraycell-meat_8hpp_source.html index 35185cf9a..d65ef5714 100644 --- a/barraycell-meat_8hpp_source.html +++ b/barraycell-meat_8hpp_source.html @@ -220,7 +220,7 @@ diff --git a/barraydense-bones_8hpp.html b/barraydense-bones_8hpp.html index bb3e41293..5719ecf7f 100644 --- a/barraydense-bones_8hpp.html +++ b/barraydense-bones_8hpp.html @@ -122,7 +122,7 @@ diff --git a/barraydense-bones_8hpp_source.html b/barraydense-bones_8hpp_source.html index c87434231..dcfbe9701 100644 --- a/barraydense-bones_8hpp_source.html +++ b/barraydense-bones_8hpp_source.html @@ -340,7 +340,7 @@ diff --git a/barraydense-meat-operators_8hpp.html b/barraydense-meat-operators_8hpp.html index e6ff18d8b..700ee9515 100644 --- a/barraydense-meat-operators_8hpp.html +++ b/barraydense-meat-operators_8hpp.html @@ -481,7 +481,7 @@

  • include
  • barry
  • barraydense-meat-operators.hpp
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barraydense-meat-operators_8hpp_source.html b/barraydense-meat-operators_8hpp_source.html index 4e75ccd68..4226da098 100644 --- a/barraydense-meat-operators_8hpp_source.html +++ b/barraydense-meat-operators_8hpp_source.html @@ -231,7 +231,7 @@ diff --git a/barraydense-meat_8hpp.html b/barraydense-meat_8hpp.html index 7a9174594..6cfe9c334 100644 --- a/barraydense-meat_8hpp.html +++ b/barraydense-meat_8hpp.html @@ -252,7 +252,7 @@

  • include
  • barry
  • barraydense-meat.hpp
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barraydense-meat_8hpp_source.html b/barraydense-meat_8hpp_source.html index ae95cf95d..4c1ce2b1d 100644 --- a/barraydense-meat_8hpp_source.html +++ b/barraydense-meat_8hpp_source.html @@ -1201,7 +1201,7 @@ diff --git a/barraydensecell-bones_8hpp.html b/barraydensecell-bones_8hpp.html index 2b0703147..26a821631 100644 --- a/barraydensecell-bones_8hpp.html +++ b/barraydensecell-bones_8hpp.html @@ -158,7 +158,7 @@

  • include
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    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barraydensecell-bones_8hpp_source.html b/barraydensecell-bones_8hpp_source.html index 0b55a4aa0..ec547e8e2 100644 --- a/barraydensecell-bones_8hpp_source.html +++ b/barraydensecell-bones_8hpp_source.html @@ -189,7 +189,7 @@ diff --git a/barraydensecell-meat_8hpp.html b/barraydensecell-meat_8hpp.html index 957b0840c..4a0e9c45c 100644 --- a/barraydensecell-meat_8hpp.html +++ b/barraydensecell-meat_8hpp.html @@ -152,7 +152,7 @@

  • include
  • barry
  • barraydensecell-meat.hpp
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barraydensecell-meat_8hpp_source.html b/barraydensecell-meat_8hpp_source.html index 80802f599..cbe706668 100644 --- a/barraydensecell-meat_8hpp_source.html +++ b/barraydensecell-meat_8hpp_source.html @@ -235,7 +235,7 @@ diff --git a/barraydensecol-bones_8hpp.html b/barraydensecol-bones_8hpp.html index 1e3152161..f8738c76b 100644 --- a/barraydensecol-bones_8hpp.html +++ b/barraydensecol-bones_8hpp.html @@ -216,7 +216,7 @@

  • include
  • barry
  • barraydensecol-bones.hpp
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barraydensecol-bones_8hpp_source.html b/barraydensecol-bones_8hpp_source.html index de4125f7c..70a612a23 100644 --- a/barraydensecol-bones_8hpp_source.html +++ b/barraydensecol-bones_8hpp_source.html @@ -246,7 +246,7 @@ diff --git a/barraydenserow-bones_8hpp.html b/barraydenserow-bones_8hpp.html index 986794eb2..c7dfad730 100644 --- a/barraydenserow-bones_8hpp.html +++ b/barraydenserow-bones_8hpp.html @@ -216,7 +216,7 @@

  • include
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    • -
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    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barraydenserow-bones_8hpp_source.html b/barraydenserow-bones_8hpp_source.html index b5b7cd037..9db6f1c3e 100644 --- a/barraydenserow-bones_8hpp_source.html +++ b/barraydenserow-bones_8hpp_source.html @@ -257,7 +257,7 @@ diff --git a/barrayrow-bones_8hpp.html b/barrayrow-bones_8hpp.html index bfe2930cf..3e509a4ef 100644 --- a/barrayrow-bones_8hpp.html +++ b/barrayrow-bones_8hpp.html @@ -114,7 +114,7 @@ diff --git a/barrayrow-bones_8hpp_source.html b/barrayrow-bones_8hpp_source.html index cb093d8ba..d1a964a47 100644 --- a/barrayrow-bones_8hpp_source.html +++ b/barrayrow-bones_8hpp_source.html @@ -195,7 +195,7 @@ diff --git a/barrayrow-meat_8hpp.html b/barrayrow-meat_8hpp.html index bbc376187..f7e71bb60 100644 --- a/barrayrow-meat_8hpp.html +++ b/barrayrow-meat_8hpp.html @@ -350,7 +350,7 @@

  • include
  • barry
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    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barrayrow-meat_8hpp_source.html b/barrayrow-meat_8hpp_source.html index c83dbabda..4a1bf2fc0 100644 --- a/barrayrow-meat_8hpp_source.html +++ b/barrayrow-meat_8hpp_source.html @@ -229,7 +229,7 @@ diff --git a/barrayvector-bones_8hpp.html b/barrayvector-bones_8hpp.html index 6303dbee0..0d6a39191 100644 --- a/barrayvector-bones_8hpp.html +++ b/barrayvector-bones_8hpp.html @@ -115,7 +115,7 @@ diff --git a/barrayvector-bones_8hpp_source.html b/barrayvector-bones_8hpp_source.html index eb54883c0..7f8415bdd 100644 --- a/barrayvector-bones_8hpp_source.html +++ b/barrayvector-bones_8hpp_source.html @@ -232,7 +232,7 @@ diff --git a/barrayvector-meat_8hpp.html b/barrayvector-meat_8hpp.html index f73638f7b..b2a430e46 100644 --- a/barrayvector-meat_8hpp.html +++ b/barrayvector-meat_8hpp.html @@ -104,7 +104,7 @@ diff --git a/barrayvector-meat_8hpp_source.html b/barrayvector-meat_8hpp_source.html index 95c507ec9..4b5a76a5b 100644 --- a/barrayvector-meat_8hpp_source.html +++ b/barrayvector-meat_8hpp_source.html @@ -444,7 +444,7 @@ diff --git a/barry-configuration_8hpp.html b/barry-configuration_8hpp.html index c0468efab..4a621010b 100644 --- a/barry-configuration_8hpp.html +++ b/barry-configuration_8hpp.html @@ -257,7 +257,7 @@

  • include
  • barry
  • barry-configuration.hpp
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barry-configuration_8hpp_source.html b/barry-configuration_8hpp_source.html index 8d9bc816c..72a17a50b 100644 --- a/barry-configuration_8hpp_source.html +++ b/barry-configuration_8hpp_source.html @@ -160,7 +160,7 @@ diff --git a/barry-debug_8hpp.html b/barry-debug_8hpp.html index 0d93ca9e9..0c30623fc 100644 --- a/barry-debug_8hpp.html +++ b/barry-debug_8hpp.html @@ -139,7 +139,7 @@

  • include
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    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
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diff --git a/barry-debug_8hpp_source.html b/barry-debug_8hpp_source.html index 777e9f760..9c5c58ee3 100644 --- a/barry-debug_8hpp_source.html +++ b/barry-debug_8hpp_source.html @@ -145,7 +145,7 @@ diff --git a/barry-macros_8hpp.html b/barry-macros_8hpp.html index 85b22c54c..45b3dd429 100644 --- a/barry-macros_8hpp.html +++ b/barry-macros_8hpp.html @@ -122,7 +122,7 @@   #define BARRY_UNUSED(expr)   do { (void)(expr); } while (0);   -#define BARRY_NCORES_ARG(default)   size_t +#define BARRY_NCORES_ARG(default)   size_t ncores default  

Macro Definition Documentation

@@ -137,7 +137,7 @@

  default) -    size_t +    size_t ncores default
@@ -236,7 +236,7 @@

  • include
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    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
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  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1

diff --git a/barry-macros_8hpp_source.html b/barry-macros_8hpp_source.html index f8852c68d..36fbb37b8 100644 --- a/barry-macros_8hpp_source.html +++ b/barry-macros_8hpp_source.html @@ -110,7 +110,7 @@
12 #if defined(_OPENMP) || defined(__OPENMP)
13 #define BARRY_NCORES_ARG(default) size_t ncores default
14 #else
-
15 #define BARRY_NCORES_ARG(default) size_t
+
15 #define BARRY_NCORES_ARG(default) size_t ncores default
16 #endif
17 
18 
@@ -121,7 +121,7 @@ diff --git a/barry_8hpp.html b/barry_8hpp.html index 29539c4a4..5325bfabd 100644 --- a/barry_8hpp.html +++ b/barry_8hpp.html @@ -401,7 +401,7 @@

  • include
  • barry
  • barry.hpp
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
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  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/barry_8hpp_source.html b/barry_8hpp_source.html index b56a2d77c..a785cf295 100644 --- a/barry_8hpp_source.html +++ b/barry_8hpp_source.html @@ -237,7 +237,7 @@ diff --git a/cell-bones_8hpp.html b/cell-bones_8hpp.html index cc9a69154..012a05adf 100644 --- a/cell-bones_8hpp.html +++ b/cell-bones_8hpp.html @@ -122,7 +122,7 @@ diff --git a/cell-bones_8hpp_source.html b/cell-bones_8hpp_source.html index 846236bf7..4983d705b 100644 --- a/cell-bones_8hpp_source.html +++ b/cell-bones_8hpp_source.html @@ -159,7 +159,7 @@ diff --git a/cell-meat_8hpp.html b/cell-meat_8hpp.html index db570ab8e..11983bf3b 100644 --- a/cell-meat_8hpp.html +++ b/cell-meat_8hpp.html @@ -113,7 +113,7 @@ diff --git a/cell-meat_8hpp_source.html b/cell-meat_8hpp_source.html index d337dad1e..1fcef44d8 100644 --- a/cell-meat_8hpp_source.html +++ b/cell-meat_8hpp_source.html @@ -180,7 +180,7 @@ diff --git a/class_b_array-members.html b/class_b_array-members.html index 2429067c0..6516bd085 100644 --- a/class_b_array-members.html +++ b/class_b_array-members.html @@ -165,7 +165,7 @@ diff --git a/class_b_array.html b/class_b_array.html index 740d5fca5..37c843787 100644 --- a/class_b_array.html +++ b/class_b_array.html @@ -2141,7 +2141,7 @@

  • BArray
    • -
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diff --git a/class_b_array_cell-members.html b/class_b_array_cell-members.html index 5540467de..ca064fc19 100644 --- a/class_b_array_cell-members.html +++ b/class_b_array_cell-members.html @@ -113,7 +113,7 @@ diff --git a/class_b_array_cell.html b/class_b_array_cell.html index 6fb263e36..701c7340b 100644 --- a/class_b_array_cell.html +++ b/class_b_array_cell.html @@ -430,7 +430,7 @@

  • BArrayCell
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
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  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_cell__const-members.html b/class_b_array_cell__const-members.html index 8f0418524..0747f147a 100644 --- a/class_b_array_cell__const-members.html +++ b/class_b_array_cell__const-members.html @@ -113,7 +113,7 @@ diff --git a/class_b_array_cell__const.html b/class_b_array_cell__const.html index 85c316546..ab3bf37a0 100644 --- a/class_b_array_cell__const.html +++ b/class_b_array_cell__const.html @@ -430,7 +430,7 @@

  • BArrayCell_const
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_dense-members.html b/class_b_array_dense-members.html index 15df1b97a..41879d407 100644 --- a/class_b_array_dense-members.html +++ b/class_b_array_dense-members.html @@ -170,7 +170,7 @@ diff --git a/class_b_array_dense.html b/class_b_array_dense.html index 2d8f9100d..c71e4e162 100644 --- a/class_b_array_dense.html +++ b/class_b_array_dense.html @@ -2668,7 +2668,7 @@

  • BArrayDense
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
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diff --git a/class_b_array_dense_cell-members.html b/class_b_array_dense_cell-members.html index 4194a35f6..c6d39064b 100644 --- a/class_b_array_dense_cell-members.html +++ b/class_b_array_dense_cell-members.html @@ -117,7 +117,7 @@ diff --git a/class_b_array_dense_cell.html b/class_b_array_dense_cell.html index 2e79d114c..488424a47 100644 --- a/class_b_array_dense_cell.html +++ b/class_b_array_dense_cell.html @@ -550,7 +550,7 @@

  • BArrayDenseCell
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
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diff --git a/class_b_array_dense_cell__const.html b/class_b_array_dense_cell__const.html index 81a3ee014..8a71fca14 100644 --- a/class_b_array_dense_cell__const.html +++ b/class_b_array_dense_cell__const.html @@ -111,7 +111,7 @@ diff --git a/class_b_array_dense_col-members.html b/class_b_array_dense_col-members.html index f9ba4841f..f149cedd4 100644 --- a/class_b_array_dense_col-members.html +++ b/class_b_array_dense_col-members.html @@ -112,7 +112,7 @@ diff --git a/class_b_array_dense_col.html b/class_b_array_dense_col.html index bb86b48ab..2952f0ce7 100644 --- a/class_b_array_dense_col.html +++ b/class_b_array_dense_col.html @@ -379,7 +379,7 @@

  • BArrayDenseCol
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_dense_col__const-members.html b/class_b_array_dense_col__const-members.html index e63fabcbe..8c7994784 100644 --- a/class_b_array_dense_col__const-members.html +++ b/class_b_array_dense_col__const-members.html @@ -111,7 +111,7 @@ diff --git a/class_b_array_dense_col__const.html b/class_b_array_dense_col__const.html index d932dc4cb..46f1dbbb2 100644 --- a/class_b_array_dense_col__const.html +++ b/class_b_array_dense_col__const.html @@ -351,7 +351,7 @@

  • BArrayDenseCol_const
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
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  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_dense_row-members.html b/class_b_array_dense_row-members.html index 8ed80fdb3..6b3c2d41b 100644 --- a/class_b_array_dense_row-members.html +++ b/class_b_array_dense_row-members.html @@ -112,7 +112,7 @@ diff --git a/class_b_array_dense_row.html b/class_b_array_dense_row.html index 3ccc7c2d1..62be8df45 100644 --- a/class_b_array_dense_row.html +++ b/class_b_array_dense_row.html @@ -379,7 +379,7 @@

  • BArrayDenseRow
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_dense_row__const-members.html b/class_b_array_dense_row__const-members.html index f59659890..d249717f3 100644 --- a/class_b_array_dense_row__const-members.html +++ b/class_b_array_dense_row__const-members.html @@ -111,7 +111,7 @@ diff --git a/class_b_array_dense_row__const.html b/class_b_array_dense_row__const.html index 658251889..b728ce87c 100644 --- a/class_b_array_dense_row__const.html +++ b/class_b_array_dense_row__const.html @@ -351,7 +351,7 @@

  • BArrayDenseRow_const
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
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diff --git a/class_b_array_row-members.html b/class_b_array_row-members.html index f63b9a0a1..bff48f4f5 100644 --- a/class_b_array_row-members.html +++ b/class_b_array_row-members.html @@ -113,7 +113,7 @@ diff --git a/class_b_array_row.html b/class_b_array_row.html index 845458a4b..ca497922d 100644 --- a/class_b_array_row.html +++ b/class_b_array_row.html @@ -354,7 +354,7 @@

  • BArrayRow
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_row__const-members.html b/class_b_array_row__const-members.html index 2a0db2d53..97325aa2a 100644 --- a/class_b_array_row__const-members.html +++ b/class_b_array_row__const-members.html @@ -113,7 +113,7 @@ diff --git a/class_b_array_row__const.html b/class_b_array_row__const.html index 473bb78b7..c97215681 100644 --- a/class_b_array_row__const.html +++ b/class_b_array_row__const.html @@ -354,7 +354,7 @@

  • BArrayRow_const
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_vector-members.html b/class_b_array_vector-members.html index 1c55a7d57..e48f752f6 100644 --- a/class_b_array_vector-members.html +++ b/class_b_array_vector-members.html @@ -118,7 +118,7 @@ diff --git a/class_b_array_vector.html b/class_b_array_vector.html index e475ab8d7..6b94cd317 100644 --- a/class_b_array_vector.html +++ b/class_b_array_vector.html @@ -585,7 +585,7 @@

  • BArrayVector
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_b_array_vector__const-members.html b/class_b_array_vector__const-members.html index db9d39ab8..f369f5010 100644 --- a/class_b_array_vector__const-members.html +++ b/class_b_array_vector__const-members.html @@ -118,7 +118,7 @@ diff --git a/class_b_array_vector__const.html b/class_b_array_vector__const.html index b916d1227..769d37765 100644 --- a/class_b_array_vector__const.html +++ b/class_b_array_vector__const.html @@ -567,7 +567,7 @@

  • BArrayVector_const
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_cell-members.html b/class_cell-members.html index 87ac02089..8c27fece8 100644 --- a/class_cell-members.html +++ b/class_cell-members.html @@ -124,7 +124,7 @@ diff --git a/class_cell.html b/class_cell.html index e2ac2c972..43715cf76 100644 --- a/class_cell.html +++ b/class_cell.html @@ -695,7 +695,7 @@

  • Cell
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_cell__const.html b/class_cell__const.html index 3dd188345..42ca68a7a 100644 --- a/class_cell__const.html +++ b/class_cell__const.html @@ -111,7 +111,7 @@ diff --git a/class_const_b_array_row_iter-members.html b/class_const_b_array_row_iter-members.html index d83ac94d3..b60e49f57 100644 --- a/class_const_b_array_row_iter-members.html +++ b/class_const_b_array_row_iter-members.html @@ -110,7 +110,7 @@ diff --git a/class_const_b_array_row_iter.html b/class_const_b_array_row_iter.html index 8315a535c..7cc86968f 100644 --- a/class_const_b_array_row_iter.html +++ b/class_const_b_array_row_iter.html @@ -278,7 +278,7 @@

  • ConstBArrayRowIter
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_counter-members.html b/class_counter-members.html index cee1cd83f..95f24d755 100644 --- a/class_counter-members.html +++ b/class_counter-members.html @@ -123,7 +123,7 @@ diff --git a/class_counter.html b/class_counter.html index 2b5fc00fa..a6d490a5d 100644 --- a/class_counter.html +++ b/class_counter.html @@ -679,7 +679,7 @@

  • Counter
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  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_counters-members.html b/class_counters-members.html index b4d7b8420..88206f760 100644 --- a/class_counters-members.html +++ b/class_counters-members.html @@ -118,7 +118,7 @@ diff --git a/class_counters.html b/class_counters.html index b18ce14c1..0c8184afe 100644 --- a/class_counters.html +++ b/class_counters.html @@ -573,7 +573,7 @@

  • Counters
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    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_d_e_f_m-members.html b/class_d_e_f_m-members.html index 4644674fb..bbfb23036 100644 --- a/class_d_e_f_m-members.html +++ b/class_d_e_f_m-members.html @@ -124,7 +124,7 @@ diff --git a/class_d_e_f_m.html b/class_d_e_f_m.html index b39b55b63..a42b9c13a 100644 --- a/class_d_e_f_m.html +++ b/class_d_e_f_m.html @@ -811,7 +811,7 @@

  • DEFM
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_d_e_f_m_counter_data-members.html b/class_d_e_f_m_counter_data-members.html index e3cf4a1b3..a1eaae2a4 100644 --- a/class_d_e_f_m_counter_data-members.html +++ b/class_d_e_f_m_counter_data-members.html @@ -114,7 +114,7 @@ diff --git a/class_d_e_f_m_counter_data.html b/class_d_e_f_m_counter_data.html index d926f8aaa..608ce45bd 100644 --- a/class_d_e_f_m_counter_data.html +++ b/class_d_e_f_m_counter_data.html @@ -146,7 +146,7 @@ diff --git a/class_d_e_f_m_data-members.html b/class_d_e_f_m_data-members.html index 061ee3ab5..8f4cfc508 100644 --- a/class_d_e_f_m_data-members.html +++ b/class_d_e_f_m_data-members.html @@ -119,7 +119,7 @@ diff --git a/class_d_e_f_m_data.html b/class_d_e_f_m_data.html index df5db7b7b..15087e89f 100644 --- a/class_d_e_f_m_data.html +++ b/class_d_e_f_m_data.html @@ -164,7 +164,7 @@ diff --git a/class_d_e_f_m_rule_data-members.html b/class_d_e_f_m_rule_data-members.html index 1321cedb3..f1909c65a 100644 --- a/class_d_e_f_m_rule_data-members.html +++ b/class_d_e_f_m_rule_data-members.html @@ -114,7 +114,7 @@ diff --git a/class_d_e_f_m_rule_data.html b/class_d_e_f_m_rule_data.html index 4cc6c747a..4e2b14d7e 100644 --- a/class_d_e_f_m_rule_data.html +++ b/class_d_e_f_m_rule_data.html @@ -150,7 +150,7 @@ diff --git a/class_d_e_f_m_rule_dyn_data-members.html b/class_d_e_f_m_rule_dyn_data-members.html index 4f1276b60..d5585ae74 100644 --- a/class_d_e_f_m_rule_dyn_data-members.html +++ b/class_d_e_f_m_rule_dyn_data-members.html @@ -117,7 +117,7 @@ diff --git a/class_d_e_f_m_rule_dyn_data.html b/class_d_e_f_m_rule_dyn_data.html index 51b8dc58f..b9fc7cf4e 100644 --- a/class_d_e_f_m_rule_dyn_data.html +++ b/class_d_e_f_m_rule_dyn_data.html @@ -167,7 +167,7 @@ diff --git a/class_entries-members.html b/class_entries-members.html index ad0b6d911..1665f94ae 100644 --- a/class_entries-members.html +++ b/class_entries-members.html @@ -111,7 +111,7 @@ diff --git a/class_entries.html b/class_entries.html index 18a5c4c65..d443e438d 100644 --- a/class_entries.html +++ b/class_entries.html @@ -323,7 +323,7 @@

  • Entries
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_flock-members.html b/class_flock-members.html index 6cdaec1de..f7e932dbc 100644 --- a/class_flock-members.html +++ b/class_flock-members.html @@ -110,7 +110,7 @@ get_support_fun()Flockinline init(size_t bar_width=BARRY_PROGRESS_BAR_WIDTH)Flockinline initializedFlock - likelihood_joint(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true,)Flockinline + likelihood_joint(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u)Flockinline modelFlock nfunctionsFlock nfuns() const noexceptFlockinline @@ -130,7 +130,7 @@ diff --git a/class_flock.html b/class_flock.html index eef1f86c5..cc016ef2a 100644 --- a/class_flock.html +++ b/class_flock.html @@ -130,9 +130,9 @@   PhyloModel * get_model ()   -double likelihood_joint (const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true,) - Returns the joint likelihood of the model. More...
-  +double likelihood_joint (const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u) + Returns the joint likelihood of the model. More...
+  Geese * operator() (size_t i, bool check_bounds=true)  Access the i-th geese element. More...
  @@ -483,8 +483,8 @@

-

◆ likelihood_joint()

+ +

◆ likelihood_joint()

@@ -508,7 +508,13 @@

bool  - use_reduced_sequence = true  + use_reduced_sequence = true, + + + + + size_t  + ncores = 1u  @@ -942,7 +948,7 @@

  • Flock
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:59 for barry: Your go-to motif accountant by doxygen 1.9.1

diff --git a/class_flock.js b/class_flock.js index 7b8c81311..aa92ecc85 100644 --- a/class_flock.js +++ b/class_flock.js @@ -10,7 +10,7 @@ var class_flock = [ "get_stats_target", "class_flock.html#a26462201318e4bf34756a2a14e2cc3fb", null ], [ "get_support_fun", "class_flock.html#add876188b5f16af037525e71eaf7fc05", null ], [ "init", "class_flock.html#a5ddef5ec4a7b150a354db11bb6b0c593", null ], - [ "likelihood_joint", "class_flock.html#a7bcad6b3c794cefc1b4bb613d13ddf71", null ], + [ "likelihood_joint", "class_flock.html#add7c442fe0471c790c1945f7abbc2e56", null ], [ "nfuns", "class_flock.html#a55cf3311be1c2129466a666bbe90a3fb", null ], [ "nleafs", "class_flock.html#a68af1602108455f9d339bc4c2994e9ab", null ], [ "nnodes", "class_flock.html#ae1f4eb8ade1c7f369e1f1eddbced3b2b", null ], diff --git a/class_freq_table-members.html b/class_freq_table-members.html index cf10fb7b0..55709ae77 100644 --- a/class_freq_table-members.html +++ b/class_freq_table-members.html @@ -115,7 +115,7 @@ diff --git a/class_freq_table.html b/class_freq_table.html index a34b16a7b..6680164c1 100644 --- a/class_freq_table.html +++ b/class_freq_table.html @@ -491,7 +491,7 @@

  • FreqTable
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diff --git a/class_geese-members.html b/class_geese-members.html index 043ac5dae..d14586117 100644 --- a/class_geese-members.html +++ b/class_geese-members.html @@ -124,7 +124,7 @@ init(size_t bar_width=BARRY_PROGRESS_BAR_WIDTH)Geeseinline init_node(Node &n)Geeseinline initializedGeese - likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true,)Geeseinline + likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u)Geeseinline likelihood_exhaust(const std::vector< double > &par)Geeseinline map_to_state_idGeese nannotations() const noexceptGeeseinline @@ -159,7 +159,7 @@ diff --git a/class_geese.html b/class_geese.html index a043ee35f..7fc17b718 100644 --- a/class_geese.html +++ b/class_geese.html @@ -118,8 +118,8 @@   void calc_reduced_sequence ()   -double likelihood (const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true,) -  +double likelihood (const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u) +  double likelihood_exhaust (const std::vector< double > &par)   std::vector< double > get_probabilities () const @@ -870,8 +870,8 @@

-

◆ likelihood()

+ +

◆ likelihood()

@@ -895,7 +895,13 @@

bool  - use_reduced_sequence = true  + use_reduced_sequence = true, + + + + + size_t  + ncores = 1u  @@ -1883,7 +1889,7 @@

  • Geese
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:59 for barry: Your go-to motif accountant by doxygen 1.9.1

diff --git a/class_geese.js b/class_geese.js index 62e71b049..24e91ee36 100644 --- a/class_geese.js +++ b/class_geese.js @@ -19,7 +19,7 @@ var class_geese = [ "inherit_support", "class_geese.html#aa95abe540b9977592bcc88e77619d070", null ], [ "init", "class_geese.html#a4eec9d20198fde392b7c5ee0060eff05", null ], [ "init_node", "class_geese.html#a3855898a556e2ac1d30529d3bc35f13a", null ], - [ "likelihood", "class_geese.html#a58fb080f76c71883938b62d5369b6688", null ], + [ "likelihood", "class_geese.html#a557dc9484bbdaf212a6ae2ac8ed3c54c", null ], [ "likelihood_exhaust", "class_geese.html#af2d4bac42cc7c8287fb6853d50882115", null ], [ "nannotations", "class_geese.html#abfec2a7462cc949246a68d540827205f", null ], [ "nfuns", "class_geese.html#ae569fc1b0ade56fc3ccc4d35214fca81", null ], diff --git a/class_model-members.html b/class_model-members.html index 0923bd71d..7652c1db3 100644 --- a/class_model-members.html +++ b/class_model-members.html @@ -181,7 +181,7 @@ diff --git a/class_model.html b/class_model.html index 691403523..940accb7b 100644 --- a/class_model.html +++ b/class_model.html @@ -2785,7 +2785,7 @@

  • Model
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    • +
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diff --git a/class_net_counter_data-members.html b/class_net_counter_data-members.html index d6483b0f4..8485c385b 100644 --- a/class_net_counter_data-members.html +++ b/class_net_counter_data-members.html @@ -109,7 +109,7 @@ diff --git a/class_net_counter_data.html b/class_net_counter_data.html index 9aa575b54..a456dd176 100644 --- a/class_net_counter_data.html +++ b/class_net_counter_data.html @@ -261,7 +261,7 @@

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diff --git a/class_network_data-members.html b/class_network_data-members.html index e31f1b434..d5316d72b 100644 --- a/class_network_data-members.html +++ b/class_network_data-members.html @@ -110,7 +110,7 @@ diff --git a/class_network_data.html b/class_network_data.html index 4e002ae65..c6cdea9a4 100644 --- a/class_network_data.html +++ b/class_network_data.html @@ -323,7 +323,7 @@

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diff --git a/class_node-members.html b/class_node-members.html index 4a804865e..50165e42a 100644 --- a/class_node-members.html +++ b/class_node-members.html @@ -125,7 +125,7 @@ diff --git a/class_node.html b/class_node.html index 87af9bdd0..f5946e97e 100644 --- a/class_node.html +++ b/class_node.html @@ -687,7 +687,7 @@

  • Node
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diff --git a/class_node_data-members.html b/class_node_data-members.html index f939084a8..0a9de2f37 100644 --- a/class_node_data-members.html +++ b/class_node_data-members.html @@ -108,7 +108,7 @@ diff --git a/class_node_data.html b/class_node_data.html index 582895e22..347650507 100644 --- a/class_node_data.html +++ b/class_node_data.html @@ -230,7 +230,7 @@

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diff --git a/class_phylo_counter_data-members.html b/class_phylo_counter_data-members.html index 4688e6f87..6b32ee1a5 100644 --- a/class_phylo_counter_data-members.html +++ b/class_phylo_counter_data-members.html @@ -117,7 +117,7 @@ diff --git a/class_phylo_counter_data.html b/class_phylo_counter_data.html index 4be04debb..16ccad7d5 100644 --- a/class_phylo_counter_data.html +++ b/class_phylo_counter_data.html @@ -512,7 +512,7 @@

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diff --git a/class_phylo_rule_dyn_data-members.html b/class_phylo_rule_dyn_data-members.html index 3192755f3..ff6c1d75f 100644 --- a/class_phylo_rule_dyn_data-members.html +++ b/class_phylo_rule_dyn_data-members.html @@ -112,7 +112,7 @@ diff --git a/class_phylo_rule_dyn_data.html b/class_phylo_rule_dyn_data.html index d0da4ee4d..4c6d287d7 100644 --- a/class_phylo_rule_dyn_data.html +++ b/class_phylo_rule_dyn_data.html @@ -330,7 +330,7 @@

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diff --git a/class_power_set-members.html b/class_power_set-members.html index 459a56545..5ab9ca865 100644 --- a/class_power_set-members.html +++ b/class_power_set-members.html @@ -129,7 +129,7 @@ diff --git a/class_power_set.html b/class_power_set.html index 5a9c403b5..d708a90d3 100644 --- a/class_power_set.html +++ b/class_power_set.html @@ -845,7 +845,7 @@

  • PowerSet
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diff --git a/class_progress-members.html b/class_progress-members.html index 6fe02d610..8f09145ce 100644 --- a/class_progress-members.html +++ b/class_progress-members.html @@ -108,7 +108,7 @@ diff --git a/class_progress.html b/class_progress.html index 6507e1525..8d5b48736 100644 --- a/class_progress.html +++ b/class_progress.html @@ -250,7 +250,7 @@

  • Progress
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diff --git a/class_rule-members.html b/class_rule-members.html index e62e904ae..08a702b00 100644 --- a/class_rule-members.html +++ b/class_rule-members.html @@ -113,7 +113,7 @@ diff --git a/class_rule.html b/class_rule.html index 745b37d30..1bb798cb6 100644 --- a/class_rule.html +++ b/class_rule.html @@ -452,7 +452,7 @@

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diff --git a/class_rules-members.html b/class_rules-members.html index feb8a40b0..dc59f9ac3 100644 --- a/class_rules-members.html +++ b/class_rules-members.html @@ -117,7 +117,7 @@ diff --git a/class_rules.html b/class_rules.html index b1ce28962..9f3d56648 100644 --- a/class_rules.html +++ b/class_rules.html @@ -617,7 +617,7 @@

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diff --git a/class_stats_counter-members.html b/class_stats_counter-members.html index 112f2d790..d98620518 100644 --- a/class_stats_counter-members.html +++ b/class_stats_counter-members.html @@ -118,7 +118,7 @@ diff --git a/class_stats_counter.html b/class_stats_counter.html index 645fbcd81..9e8413938 100644 --- a/class_stats_counter.html +++ b/class_stats_counter.html @@ -519,7 +519,7 @@

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  • Generated on Wed Sep 27 2023 23:39:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_support-members.html b/class_support-members.html index e964b4023..1bc24dac8 100644 --- a/class_support-members.html +++ b/class_support-members.html @@ -143,7 +143,7 @@ diff --git a/class_support.html b/class_support.html index 3a30007e3..fbaa0524e 100644 --- a/class_support.html +++ b/class_support.html @@ -1277,7 +1277,7 @@

  • Support
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/classes.html b/classes.html index 818b76534..d8e196068 100644 --- a/classes.html +++ b/classes.html @@ -140,7 +140,7 @@ diff --git a/col-bones_8hpp.html b/col-bones_8hpp.html index b4fed667f..e76c7a23f 100644 --- a/col-bones_8hpp.html +++ b/col-bones_8hpp.html @@ -104,7 +104,7 @@ diff --git a/col-bones_8hpp_source.html b/col-bones_8hpp_source.html index 3a8bd51cd..df91ff9f0 100644 --- a/col-bones_8hpp_source.html +++ b/col-bones_8hpp_source.html @@ -159,7 +159,7 @@ diff --git a/counters-bones_8hpp.html b/counters-bones_8hpp.html index b94eba140..9e27be696 100644 --- a/counters-bones_8hpp.html +++ b/counters-bones_8hpp.html @@ -125,7 +125,7 @@ diff --git a/counters-bones_8hpp_source.html b/counters-bones_8hpp_source.html index f5a1bd9ab..67f4b6219 100644 --- a/counters-bones_8hpp_source.html +++ b/counters-bones_8hpp_source.html @@ -258,7 +258,7 @@ diff --git a/counters-meat_8hpp.html b/counters-meat_8hpp.html index 79b467a62..ade5f4d12 100644 --- a/counters-meat_8hpp.html +++ b/counters-meat_8hpp.html @@ -1560,7 +1560,7 @@

  • include
  • barry
  • counters-meat.hpp
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/counters-meat_8hpp_source.html b/counters-meat_8hpp_source.html index 18a9cd231..d461ec8dc 100644 --- a/counters-meat_8hpp_source.html +++ b/counters-meat_8hpp_source.html @@ -417,7 +417,7 @@ diff --git a/defm-bones_8hpp.html b/defm-bones_8hpp.html index 74aacc909..3317b6008 100644 --- a/defm-bones_8hpp.html +++ b/defm-bones_8hpp.html @@ -121,7 +121,7 @@ diff --git a/defm-bones_8hpp_source.html b/defm-bones_8hpp_source.html index 4f6eca7ca..45b1060fc 100644 --- a/defm-bones_8hpp_source.html +++ b/defm-bones_8hpp_source.html @@ -216,7 +216,7 @@ diff --git a/defm-meat_8hpp.html b/defm-meat_8hpp.html index cfa675f3c..9cd4f2681 100644 --- a/defm-meat_8hpp.html +++ b/defm-meat_8hpp.html @@ -212,7 +212,7 @@

  • include
  • barry
  • models
  • defm
  • defm-meat.hpp
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/defm-meat_8hpp_source.html b/defm-meat_8hpp_source.html index a40d28e55..15004b5d1 100644 --- a/defm-meat_8hpp_source.html +++ b/defm-meat_8hpp_source.html @@ -592,7 +592,7 @@ diff --git a/defm-types_8hpp.html b/defm-types_8hpp.html index 199e5d566..cce7f8f26 100644 --- a/defm-types_8hpp.html +++ b/defm-types_8hpp.html @@ -171,7 +171,7 @@

  • include
  • barry
  • models
  • defm
  • defm-types.hpp
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/defm-types_8hpp_source.html b/defm-types_8hpp_source.html index 7a8338402..87626d03a 100644 --- a/defm-types_8hpp_source.html +++ b/defm-types_8hpp_source.html @@ -305,7 +305,7 @@ diff --git a/defm_2counters_8hpp.html b/defm_2counters_8hpp.html index bbd82d21b..b798315a9 100644 --- a/defm_2counters_8hpp.html +++ b/defm_2counters_8hpp.html @@ -326,7 +326,7 @@

  • include
  • barry
  • models
  • defm
  • counters.hpp
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/defm_2counters_8hpp_source.html b/defm_2counters_8hpp_source.html index 1590a444c..2d9cbda8f 100644 --- a/defm_2counters_8hpp_source.html +++ b/defm_2counters_8hpp_source.html @@ -794,7 +794,7 @@ diff --git a/defm_8hpp.html b/defm_8hpp.html index 9a6e07121..8fc8b9ebe 100644 --- a/defm_8hpp.html +++ b/defm_8hpp.html @@ -133,7 +133,7 @@ diff --git a/defm_8hpp_source.html b/defm_8hpp_source.html index a9c41466c..0e8c204aa 100644 --- a/defm_8hpp_source.html +++ b/defm_8hpp_source.html @@ -126,7 +126,7 @@ diff --git a/dir_000001_000002.html b/dir_000001_000002.html index 70e3e355a..be6dd063a 100644 --- a/dir_000001_000002.html +++ b/dir_000001_000002.html @@ -98,7 +98,7 @@

barry → counters Relation

diff --git a/dir_000003_000004.html b/dir_000003_000004.html index 811c368a4..1f16da617 100644 --- a/dir_000003_000004.html +++ b/dir_000003_000004.html @@ -98,7 +98,7 @@

models → defm Relation

  • include
  • barry
  • models
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/dir_000003_000005.html b/dir_000003_000005.html index bf6353358..85fe56417 100644 --- a/dir_000003_000005.html +++ b/dir_000003_000005.html @@ -98,7 +98,7 @@

models → geese Relation

  • include
  • barry
  • models
    • -
  • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Wed Sep 27 2023 23:39:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/dir_488ec4010567cc6d95c62bdcb57a6d3e.html b/dir_488ec4010567cc6d95c62bdcb57a6d3e.html index df90a2f47..850df949c 100644 --- a/dir_488ec4010567cc6d95c62bdcb57a6d3e.html +++ b/dir_488ec4010567cc6d95c62bdcb57a6d3e.html @@ -130,7 +130,7 @@ diff --git a/dir_6e63e3665115632dc5d61b2d6d6c3354.html b/dir_6e63e3665115632dc5d61b2d6d6c3354.html index e67abc60f..83443eefa 100644 --- a/dir_6e63e3665115632dc5d61b2d6d6c3354.html +++ b/dir_6e63e3665115632dc5d61b2d6d6c3354.html @@ -203,7 +203,7 @@ diff --git a/dir_b3150c389b0f5b078392750f1ae70361.html b/dir_b3150c389b0f5b078392750f1ae70361.html index 153261529..a650a345e 100644 --- a/dir_b3150c389b0f5b078392750f1ae70361.html +++ b/dir_b3150c389b0f5b078392750f1ae70361.html @@ -110,7 +110,7 @@ diff --git a/dir_c5954a04c87570f0664da134464d5428.html b/dir_c5954a04c87570f0664da134464d5428.html index 54abdb87e..68cc9c071 100644 --- a/dir_c5954a04c87570f0664da134464d5428.html +++ b/dir_c5954a04c87570f0664da134464d5428.html @@ -134,7 +134,7 @@ diff --git a/dir_d44c64559bbebec7f509842c48db8b23.html b/dir_d44c64559bbebec7f509842c48db8b23.html index 6d98f286b..a17198154 100644 --- a/dir_d44c64559bbebec7f509842c48db8b23.html +++ b/dir_d44c64559bbebec7f509842c48db8b23.html @@ -117,7 +117,7 @@ diff --git a/dir_d7a554d3e09ed8456d56450fe8436947.html b/dir_d7a554d3e09ed8456d56450fe8436947.html index a05122342..0c5dc85ab 100644 --- a/dir_d7a554d3e09ed8456d56450fe8436947.html +++ b/dir_d7a554d3e09ed8456d56450fe8436947.html @@ -116,7 +116,7 @@ diff --git a/files.html b/files.html index 100729f42..a1842bf19 100644 --- a/files.html +++ b/files.html @@ -173,7 +173,7 @@ diff --git a/flock-bones_8hpp.html b/flock-bones_8hpp.html index b4272fabd..e1e41c600 100644 --- a/flock-bones_8hpp.html +++ b/flock-bones_8hpp.html @@ -122,7 +122,7 @@ diff --git a/flock-bones_8hpp_source.html b/flock-bones_8hpp_source.html index f3b3b49ea..0c24708b5 100644 --- a/flock-bones_8hpp_source.html +++ b/flock-bones_8hpp_source.html @@ -133,11 +133,11 @@
57  std::vector< std::vector< double > > * get_stats_target();
58  PhyloModel * get_model();
59 
-
69  double likelihood_joint(
+
69  double likelihood_joint(
70  const std::vector< double > & par,
71  bool as_log = false,
72  bool use_reduced_sequence = true,
-
73  BARRY_NCORES_ARG(=1)
+
73  size_t ncores = 1u
74  );
75 
80  size_t nfuns() const noexcept;
@@ -158,7 +158,6 @@
103 };
104 
105 #endif
-
BARRY_NCORES_ARG
#define BARRY_NCORES_ARG(default)
Definition: barry-macros.hpp:15
Flock
A Flock is a group of Geese.
Definition: flock-bones.hpp:14
Flock::model
PhyloModel model
Definition: flock-bones.hpp:23
Flock::rengine
std::mt19937 rengine
Definition: flock-bones.hpp:22
@@ -174,12 +173,12 @@
Flock::add_data
size_t add_data(std::vector< std::vector< size_t > > &annotations, std::vector< size_t > &geneid, std::vector< int > &parent, std::vector< bool > &duplication)
Add a tree to the flock.
Definition: flock-meat.hpp:6
Flock::nleafs
std::vector< size_t > nleafs() const noexcept
Definition: flock-meat.hpp:196
Flock::nterms
size_t nterms() const
Definition: flock-meat.hpp:210
-
Flock::likelihood_joint
double likelihood_joint(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true,)
Returns the joint likelihood of the model.
Definition: flock-meat.hpp:138
Flock::get_model
PhyloModel * get_model()
Definition: flock-meat.hpp:131
Flock::initialized
bool initialized
Definition: flock-bones.hpp:19
Flock::get_stats_support
std::vector< std::vector< double > > * get_stats_support()
Definition: flock-meat.hpp:117
Flock::support_size
size_t support_size() const noexcept
Definition: flock-meat.hpp:218
+
Flock::likelihood_joint
double likelihood_joint(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u)
Returns the joint likelihood of the model.
Definition: flock-meat.hpp:138
Flock::get_support_fun
PhyloSupport * get_support_fun()
Definition: flock-meat.hpp:110
Flock::nnodes
std::vector< size_t > nnodes() const noexcept
Definition: flock-meat.hpp:182
Flock::ntrees
size_t ntrees() const noexcept
Definition: flock-meat.hpp:175
@@ -198,7 +197,7 @@ diff --git a/flock-meat_8hpp.html b/flock-meat_8hpp.html index 60e3c4bd8..b7b210ea8 100644 --- a/flock-meat_8hpp.html +++ b/flock-meat_8hpp.html @@ -113,7 +113,7 @@ diff --git a/flock-meat_8hpp_source.html b/flock-meat_8hpp_source.html index 4075c7131..dc34d411e 100644 --- a/flock-meat_8hpp_source.html +++ b/flock-meat_8hpp_source.html @@ -233,11 +233,11 @@
135 
136 }
137 
-
138 inline double Flock::likelihood_joint(
+
138 inline double Flock::likelihood_joint(
139  const std::vector< double > & par,
140  bool as_log,
141  bool use_reduced_sequence,
-
142  BARRY_NCORES_ARG()
+
142  size_t ncores
143 )
144 {
145 
@@ -248,14 +248,14 @@
150  if (as_log) {
151 
152  for (auto& d : this->dat)
-
153  ans += d.likelihood(par, as_log, use_reduced_sequence);
+
153  ans += d.likelihood(par, as_log, use_reduced_sequence, ncores);
154 
155  }
156  else
157  {
158 
159  for (auto& d : this->dat)
-
160  ans *= d.likelihood(par, as_log, use_reduced_sequence);
+
160  ans *= d.likelihood(par, as_log, use_reduced_sequence, ncores);
161 
162  }
163 
@@ -410,7 +410,6 @@
312 
313 #endif
printf_barry
#define printf_barry
Definition: barry-configuration.hpp:51
-
BARRY_NCORES_ARG
#define BARRY_NCORES_ARG(default)
Definition: barry-macros.hpp:15
Flock::operator()
Geese * operator()(size_t i, bool check_bounds=true)
Access the i-th geese element.
Definition: flock-meat.hpp:303
Flock::model
PhyloModel model
Definition: flock-bones.hpp:23
Flock::rengine
std::mt19937 rengine
Definition: flock-bones.hpp:22
@@ -425,11 +424,11 @@
Flock::add_data
size_t add_data(std::vector< std::vector< size_t > > &annotations, std::vector< size_t > &geneid, std::vector< int > &parent, std::vector< bool > &duplication)
Add a tree to the flock.
Definition: flock-meat.hpp:6
Flock::nleafs
std::vector< size_t > nleafs() const noexcept
Definition: flock-meat.hpp:196
Flock::nterms
size_t nterms() const
Definition: flock-meat.hpp:210
-
Flock::likelihood_joint
double likelihood_joint(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true,)
Returns the joint likelihood of the model.
Definition: flock-meat.hpp:138
Flock::get_model
PhyloModel * get_model()
Definition: flock-meat.hpp:131
Flock::initialized
bool initialized
Definition: flock-bones.hpp:19
Flock::get_stats_support
std::vector< std::vector< double > > * get_stats_support()
Definition: flock-meat.hpp:117
Flock::support_size
size_t support_size() const noexcept
Definition: flock-meat.hpp:218
+
Flock::likelihood_joint
double likelihood_joint(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u)
Returns the joint likelihood of the model.
Definition: flock-meat.hpp:138
Flock::get_support_fun
PhyloSupport * get_support_fun()
Definition: flock-meat.hpp:110
Flock::nnodes
std::vector< size_t > nnodes() const noexcept
Definition: flock-meat.hpp:182
Flock::ntrees
size_t ntrees() const noexcept
Definition: flock-meat.hpp:175
@@ -450,7 +449,7 @@ diff --git a/formula_8hpp.html b/formula_8hpp.html index f384fc4df..b6ecaa593 100644 --- a/formula_8hpp.html +++ b/formula_8hpp.html @@ -206,7 +206,7 @@

Transition effects

diff --git a/formula_8hpp_source.html b/formula_8hpp_source.html index 5c561a96c..e83874a2a 100644 --- a/formula_8hpp_source.html +++ b/formula_8hpp_source.html @@ -288,7 +288,7 @@ diff --git a/freqtable_8hpp.html b/freqtable_8hpp.html index 7b02628c4..e8e8a13fa 100644 --- a/freqtable_8hpp.html +++ b/freqtable_8hpp.html @@ -122,7 +122,7 @@ diff --git a/freqtable_8hpp_source.html b/freqtable_8hpp_source.html index 0f651126b..be1eeabfa 100644 --- a/freqtable_8hpp_source.html +++ b/freqtable_8hpp_source.html @@ -356,7 +356,7 @@ diff --git a/functions.html b/functions.html index b899defa6..92fe6f629 100644 --- a/functions.html +++ b/functions.html @@ -159,7 +159,7 @@

- a -

    diff --git a/functions_b.html b/functions_b.html index a3deca7e6..e268b8247 100644 --- a/functions_b.html +++ b/functions_b.html @@ -192,7 +192,7 @@

    - b -

      diff --git a/functions_c.html b/functions_c.html index ffec996ac..80da83e7f 100644 --- a/functions_c.html +++ b/functions_c.html @@ -203,7 +203,7 @@

      - c -

        diff --git a/functions_d.html b/functions_d.html index a55440fbb..60e6e10f9 100644 --- a/functions_d.html +++ b/functions_d.html @@ -166,7 +166,7 @@

        - d -

          diff --git a/functions_e.html b/functions_e.html index 2d921c395..3eadca658 100644 --- a/functions_e.html +++ b/functions_e.html @@ -137,7 +137,7 @@

          - e -

            diff --git a/functions_f.html b/functions_f.html index a91824fd6..63b5cff1d 100644 --- a/functions_f.html +++ b/functions_f.html @@ -113,7 +113,7 @@

            - f -

              diff --git a/functions_func.html b/functions_func.html index 3ec10a048..56cc6c00e 100644 --- a/functions_func.html +++ b/functions_func.html @@ -140,7 +140,7 @@

              - a -

                diff --git a/functions_func_b.html b/functions_func_b.html index 0a0040c99..f9aa7037e 100644 --- a/functions_func_b.html +++ b/functions_func_b.html @@ -151,7 +151,7 @@

                - b -

                  diff --git a/functions_func_c.html b/functions_func_c.html index 66b3c88b3..753396bf2 100644 --- a/functions_func_c.html +++ b/functions_func_c.html @@ -155,7 +155,7 @@

                  - c -

                    diff --git a/functions_func_d.html b/functions_func_d.html index 05db25f1a..1aff41dd9 100644 --- a/functions_func_d.html +++ b/functions_func_d.html @@ -129,7 +129,7 @@

                    - d -

                      diff --git a/functions_func_e.html b/functions_func_e.html index d704ec06f..60d348e83 100644 --- a/functions_func_e.html +++ b/functions_func_e.html @@ -122,7 +122,7 @@

                      - e -

                        diff --git a/functions_func_f.html b/functions_func_f.html index 3089dfeed..30b227a6a 100644 --- a/functions_func_f.html +++ b/functions_func_f.html @@ -110,7 +110,7 @@

                        - f -

                          diff --git a/functions_func_g.html b/functions_func_g.html index 60f96391d..e60d0f0dd 100644 --- a/functions_func_g.html +++ b/functions_func_g.html @@ -272,7 +272,7 @@

                          - g -

                            diff --git a/functions_func_i.html b/functions_func_i.html index 550af06ac..a69b839fc 100644 --- a/functions_func_i.html +++ b/functions_func_i.html @@ -151,7 +151,7 @@

                            - i -

                              diff --git a/functions_func_l.html b/functions_func_l.html index 415a146d9..3758c8792 100644 --- a/functions_func_l.html +++ b/functions_func_l.html @@ -96,14 +96,14 @@

                              - l -

                              • likelihood() -: Geese +: Geese , Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
                              • likelihood_exhaust() : Geese
                              • likelihood_joint() -: Flock +: Flock
                              • likelihood_total() : Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type > @@ -117,7 +117,7 @@

                                - l -

                                  diff --git a/functions_func_m.html b/functions_func_m.html index 6ab71594b..c7af8a577 100644 --- a/functions_func_m.html +++ b/functions_func_m.html @@ -110,7 +110,7 @@

                                  - m -

                                    diff --git a/functions_func_n.html b/functions_func_n.html index c61696c9e..75020c280 100644 --- a/functions_func_n.html +++ b/functions_func_n.html @@ -166,7 +166,7 @@

                                    - n -

                                      diff --git a/functions_func_o.html b/functions_func_o.html index 08212d1c6..c99930062 100644 --- a/functions_func_o.html +++ b/functions_func_o.html @@ -228,7 +228,7 @@

                                      - o -

                                        diff --git a/functions_func_p.html b/functions_func_p.html index 8ed15f1a5..ab9b84ffc 100644 --- a/functions_func_p.html +++ b/functions_func_p.html @@ -158,7 +158,7 @@

                                        - p -

                                          diff --git a/functions_func_r.html b/functions_func_r.html index caea25b50..0490f306d 100644 --- a/functions_func_r.html +++ b/functions_func_r.html @@ -136,7 +136,7 @@

                                          - r -

                                            diff --git a/functions_func_s.html b/functions_func_s.html index d6cefade0..34deb9541 100644 --- a/functions_func_s.html +++ b/functions_func_s.html @@ -189,7 +189,7 @@

                                            - s -

                                              diff --git a/functions_func_t.html b/functions_func_t.html index 0e321e59d..1c1a9464d 100644 --- a/functions_func_t.html +++ b/functions_func_t.html @@ -116,7 +116,7 @@

                                              - t -

                                                diff --git a/functions_func_u.html b/functions_func_u.html index 35387f823..272e0ce70 100644 --- a/functions_func_u.html +++ b/functions_func_u.html @@ -104,7 +104,7 @@

                                                - u -

                                                  diff --git a/functions_func_z.html b/functions_func_z.html index d6399c1a8..122525fbe 100644 --- a/functions_func_z.html +++ b/functions_func_z.html @@ -109,7 +109,7 @@

                                                  - z -

                                                    diff --git a/functions_func_~.html b/functions_func_~.html index cc5016e87..62d165149 100644 --- a/functions_func_~.html +++ b/functions_func_~.html @@ -194,7 +194,7 @@

                                                    - ~ -

                                                      diff --git a/functions_g.html b/functions_g.html index e8e5da2c4..603fa8a09 100644 --- a/functions_g.html +++ b/functions_g.html @@ -272,7 +272,7 @@

                                                      - g -

                                                        diff --git a/functions_h.html b/functions_h.html index c8d371a20..2cabab189 100644 --- a/functions_h.html +++ b/functions_h.html @@ -110,7 +110,7 @@

                                                        - h -

                                                          diff --git a/functions_i.html b/functions_i.html index 76bfb0434..4b3f39c24 100644 --- a/functions_i.html +++ b/functions_i.html @@ -171,7 +171,7 @@

                                                          - i -

                                                            diff --git a/functions_k.html b/functions_k.html index 5bd3815c7..cc433e931 100644 --- a/functions_k.html +++ b/functions_k.html @@ -104,7 +104,7 @@

                                                            - k -

                                                              diff --git a/functions_l.html b/functions_l.html index 98775318a..65b1c54fc 100644 --- a/functions_l.html +++ b/functions_l.html @@ -99,14 +99,14 @@

                                                              - l -

                                                                : PhyloRuleDynData
                                                              • likelihood() -: Geese +: Geese , Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
                                                              • likelihood_exhaust() : Geese
                                                              • likelihood_joint() -: Flock +: Flock
                                                              • likelihood_total() : Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type > @@ -124,7 +124,7 @@

                                                                - l -

                                                                  diff --git a/functions_m.html b/functions_m.html index 2eb7c5bff..90fbc93fb 100644 --- a/functions_m.html +++ b/functions_m.html @@ -123,7 +123,7 @@

                                                                  - m -

                                                                    diff --git a/functions_n.html b/functions_n.html index 27e2aad50..f61eef6d1 100644 --- a/functions_n.html +++ b/functions_n.html @@ -200,7 +200,7 @@

                                                                    - n -

                                                                      diff --git a/functions_o.html b/functions_o.html index e9fdd8f2b..6badc37db 100644 --- a/functions_o.html +++ b/functions_o.html @@ -237,7 +237,7 @@

                                                                      - o -

                                                                        diff --git a/functions_p.html b/functions_p.html index 6f751e1b0..121353397 100644 --- a/functions_p.html +++ b/functions_p.html @@ -182,7 +182,7 @@

                                                                        - p -

                                                                          diff --git a/functions_r.html b/functions_r.html index fa02e0974..e85d0fb7c 100644 --- a/functions_r.html +++ b/functions_r.html @@ -153,7 +153,7 @@

                                                                          - r -

                                                                            diff --git a/functions_rela.html b/functions_rela.html index 86dd02f2d..51be2b1f3 100644 --- a/functions_rela.html +++ b/functions_rela.html @@ -137,7 +137,7 @@ diff --git a/functions_s.html b/functions_s.html index 8b49104db..9c99c2bc0 100644 --- a/functions_s.html +++ b/functions_s.html @@ -213,7 +213,7 @@

                                                                            - s -

                                                                              diff --git a/functions_t.html b/functions_t.html index 42ca649e8..6a6c059e1 100644 --- a/functions_t.html +++ b/functions_t.html @@ -125,7 +125,7 @@

                                                                              - t -

                                                                                diff --git a/functions_u.html b/functions_u.html index 1a67decee..df41443d3 100644 --- a/functions_u.html +++ b/functions_u.html @@ -107,7 +107,7 @@

                                                                                - u -

                                                                                  diff --git a/functions_v.html b/functions_v.html index 159083846..c56c71b8f 100644 --- a/functions_v.html +++ b/functions_v.html @@ -116,7 +116,7 @@

                                                                                  - v -

                                                                                    diff --git a/functions_vars.html b/functions_vars.html index 147dea8f8..ced1f300e 100644 --- a/functions_vars.html +++ b/functions_vars.html @@ -506,7 +506,7 @@

                                                                                    - x -

                                                                                      diff --git a/functions_w.html b/functions_w.html index a139fddde..f4c024ef1 100644 --- a/functions_w.html +++ b/functions_w.html @@ -104,7 +104,7 @@

                                                                                      - w -

                                                                                        diff --git a/functions_x.html b/functions_x.html index 8b7579343..df57c023e 100644 --- a/functions_x.html +++ b/functions_x.html @@ -107,7 +107,7 @@

                                                                                        - x -

                                                                                          diff --git a/functions_z.html b/functions_z.html index 6e88efc8e..d89145512 100644 --- a/functions_z.html +++ b/functions_z.html @@ -109,7 +109,7 @@

                                                                                          - z -

                                                                                            diff --git a/functions_~.html b/functions_~.html index 9ba156b81..fb7bba78e 100644 --- a/functions_~.html +++ b/functions_~.html @@ -194,7 +194,7 @@

                                                                                            - ~ -

                                                                                              diff --git a/geese-bones_8hpp.html b/geese-bones_8hpp.html index 1c181ed02..ddcd67ea7 100644 --- a/geese-bones_8hpp.html +++ b/geese-bones_8hpp.html @@ -291,7 +291,7 @@

                                                                                              • include
                                                                                              • barry
                                                                                              • models
                                                                                              • geese
                                                                                              • geese-bones.hpp
                                                                                                • -
                                                                                              • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                • +
                                                                                              • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                              diff --git a/geese-bones_8hpp_source.html b/geese-bones_8hpp_source.html index 700ab0cfe..2148d80e7 100644 --- a/geese-bones_8hpp_source.html +++ b/geese-bones_8hpp_source.html @@ -246,11 +246,11 @@
                                                                                              212  void calc_sequence(Node * n = nullptr);
                                                                                              213  void calc_reduced_sequence();
                                                                                              214 
                                                                                              -
                                                                                              215  double likelihood(
                                                                                              +
                                                                                              215  double likelihood(
                                                                                              216  const std::vector< double > & par,
                                                                                              217  bool as_log = false,
                                                                                              218  bool use_reduced_sequence = true,
                                                                                              -
                                                                                              219  BARRY_NCORES_ARG(= 1)
                                                                                              +
                                                                                              219  size_t ncores = 1u
                                                                                              220  );
                                                                                              221 
                                                                                              222  double likelihood_exhaust(const std::vector< double > & par);
                                                                                              @@ -329,7 +329,6 @@
                                                                                              348 };
                                                                                              349 
                                                                                              350 #endif
                                                                                              -
                                                                                              BARRY_NCORES_ARG
                                                                                              #define BARRY_NCORES_ARG(default)
                                                                                              Definition: barry-macros.hpp:15
                                                                                              Flock
                                                                                              A Flock is a group of Geese.
                                                                                              Definition: flock-bones.hpp:14
                                                                                              Geese
                                                                                              Annotated Phylo Model.
                                                                                              Definition: geese-bones.hpp:103
                                                                                              Geese::reduced_sequence
                                                                                              std::vector< size_t > reduced_sequence
                                                                                              Definition: geese-bones.hpp:138
                                                                                              @@ -353,7 +352,7 @@
                                                                                              Geese::colnames
                                                                                              std::vector< std::string > colnames() const
                                                                                              Names of the terms in the model.
                                                                                              Definition: geese-meat.hpp:480
                                                                                              Geese::init
                                                                                              void init(size_t bar_width=BARRY_PROGRESS_BAR_WIDTH)
                                                                                              Definition: geese-meat.hpp:131
                                                                                              Geese::nnodes
                                                                                              size_t nnodes() const noexcept
                                                                                              Number of nodes (interior + leaf)
                                                                                              Definition: geese-meat.hpp:434
                                                                                              -
                                                                                              Geese::likelihood
                                                                                              double likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true,)
                                                                                              Definition: geese-meat-likelihood.hpp:6
                                                                                              +
                                                                                              Geese::likelihood
                                                                                              double likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u)
                                                                                              Definition: geese-meat-likelihood.hpp:6
                                                                                              Geese::operator=
                                                                                              Geese & operator=(Geese &&model_) noexcept=delete
                                                                                              Geese::get_probabilities
                                                                                              std::vector< double > get_probabilities() const
                                                                                              Definition: geese-meat.hpp:406
                                                                                              Geese::predict_sim
                                                                                              std::vector< std::vector< double > > predict_sim(const std::vector< double > &par, bool only_annotated=false, size_t nsims=10000u)
                                                                                              Definition: geese-meat-predict_sim.hpp:6
                                                                                              @@ -404,7 +403,7 @@ diff --git a/geese-meat-constructors_8hpp.html b/geese-meat-constructors_8hpp.html index 4795aac54..5281a78df 100644 --- a/geese-meat-constructors_8hpp.html +++ b/geese-meat-constructors_8hpp.html @@ -113,7 +113,7 @@ diff --git a/geese-meat-constructors_8hpp_source.html b/geese-meat-constructors_8hpp_source.html index 1047316c1..6bd65f361 100644 --- a/geese-meat-constructors_8hpp_source.html +++ b/geese-meat-constructors_8hpp_source.html @@ -484,7 +484,7 @@ diff --git a/geese-meat-likelihood_8hpp.html b/geese-meat-likelihood_8hpp.html index f57124e38..b1a8f341f 100644 --- a/geese-meat-likelihood_8hpp.html +++ b/geese-meat-likelihood_8hpp.html @@ -123,7 +123,7 @@ diff --git a/geese-meat-likelihood_8hpp_source.html b/geese-meat-likelihood_8hpp_source.html index 596f966c8..3dcc8800d 100644 --- a/geese-meat-likelihood_8hpp_source.html +++ b/geese-meat-likelihood_8hpp_source.html @@ -101,11 +101,11 @@
                                                                                              3 
                                                                                              4 #include "geese-bones.hpp"
                                                                                              5 
                                                                                              -
                                                                                              6 inline double Geese::likelihood(
                                                                                              +
                                                                                              6 inline double Geese::likelihood(
                                                                                              7  const std::vector< double > & par,
                                                                                              8  bool as_log,
                                                                                              9  bool use_reduced_sequence,
                                                                                              -
                                                                                              10  BARRY_NCORES_ARG()
                                                                                              +
                                                                                              10  size_t ncores
                                                                                              11 ) {
                                                                                              12 
                                                                                              13  INITIALIZED()
                                                                                              @@ -248,75 +248,75 @@
                                                                                              150  par0,
                                                                                              151  temp_stats,
                                                                                              152  node.narray[s],
                                                                                              -
                                                                                              153  ncores
                                                                                              -
                                                                                              154  );
                                                                                              -
                                                                                              155  } catch (std::exception & e) {
                                                                                              -
                                                                                              156 
                                                                                              -
                                                                                              157  auto err = std::string(e.what());
                                                                                              -
                                                                                              158 
                                                                                              -
                                                                                              159  std::string state_str = "";
                                                                                              -
                                                                                              160  for (const auto & ss : states[s])
                                                                                              -
                                                                                              161  state_str += std::to_string(ss) + " ";
                                                                                              -
                                                                                              162 
                                                                                              -
                                                                                              163  err = "Error computing the likelihood at node " +
                                                                                              -
                                                                                              164  std::to_string(node.id) + " with state " + state_str +
                                                                                              -
                                                                                              165  ". Error message:\n" +
                                                                                              -
                                                                                              166  err;
                                                                                              -
                                                                                              167 
                                                                                              -
                                                                                              168  throw std::runtime_error(err);
                                                                                              -
                                                                                              169 
                                                                                              -
                                                                                              170  }
                                                                                              -
                                                                                              171 
                                                                                              -
                                                                                              172  // Adding to the total probabilities
                                                                                              -
                                                                                              173  totprob += off_mult;
                                                                                              -
                                                                                              174 
                                                                                              -
                                                                                              175  }
                                                                                              -
                                                                                              176 
                                                                                              -
                                                                                              177  // Setting the probability at the node
                                                                                              -
                                                                                              178  node.subtree_prob[s] = totprob;
                                                                                              -
                                                                                              179 
                                                                                              -
                                                                                              180  }
                                                                                              -
                                                                                              181 
                                                                                              -
                                                                                              182  // All probabilities should be completed at this point
                                                                                              -
                                                                                              183  if (node.parent == nullptr)
                                                                                              -
                                                                                              184  {
                                                                                              -
                                                                                              185 
                                                                                              -
                                                                                              186  for (size_t s = 0u; s < states.size(); ++s)
                                                                                              -
                                                                                              187  {
                                                                                              -
                                                                                              188 
                                                                                              -
                                                                                              189  double tmpll = 1.0;
                                                                                              -
                                                                                              190 
                                                                                              -
                                                                                              191  for (auto k = 0u; k < nfunctions; ++k)
                                                                                              -
                                                                                              192  {
                                                                                              -
                                                                                              193 
                                                                                              -
                                                                                              194  tmpll *= states[s][k] ? par_root[k] : (1 - par_root[k]);
                                                                                              -
                                                                                              195 
                                                                                              -
                                                                                              196  }
                                                                                              -
                                                                                              197 
                                                                                              -
                                                                                              198  ll += tmpll * node.subtree_prob[s];
                                                                                              -
                                                                                              199 
                                                                                              -
                                                                                              200  }
                                                                                              -
                                                                                              201  }
                                                                                              -
                                                                                              202 
                                                                                              -
                                                                                              203  }
                                                                                              -
                                                                                              204 
                                                                                              -
                                                                                              205  // In the case that the sequence is empty, then it means
                                                                                              -
                                                                                              206  // that we are looking at a completely unnanotated tree,
                                                                                              -
                                                                                              207  // thus the likelihood should be one
                                                                                              -
                                                                                              208  if (preseq->size() == 0u)
                                                                                              -
                                                                                              209  return as_log ? -std::numeric_limits<double>::infinity() : 1.0;
                                                                                              -
                                                                                              210 
                                                                                              +
                                                                                              153  as_log,
                                                                                              +
                                                                                              154  ncores
                                                                                              +
                                                                                              155  );
                                                                                              +
                                                                                              156  } catch (std::exception & e) {
                                                                                              +
                                                                                              157 
                                                                                              +
                                                                                              158  auto err = std::string(e.what());
                                                                                              +
                                                                                              159 
                                                                                              +
                                                                                              160  std::string state_str = "";
                                                                                              +
                                                                                              161  for (const auto & ss : states[s])
                                                                                              +
                                                                                              162  state_str += std::to_string(ss) + " ";
                                                                                              +
                                                                                              163 
                                                                                              +
                                                                                              164  err = "Error computing the likelihood at node " +
                                                                                              +
                                                                                              165  std::to_string(node.id) + " with state " + state_str +
                                                                                              +
                                                                                              166  ". Error message:\n" +
                                                                                              +
                                                                                              167  err;
                                                                                              +
                                                                                              168 
                                                                                              +
                                                                                              169  throw std::runtime_error(err);
                                                                                              +
                                                                                              170 
                                                                                              +
                                                                                              171  }
                                                                                              +
                                                                                              172 
                                                                                              +
                                                                                              173  // Adding to the total probabilities
                                                                                              +
                                                                                              174  totprob += off_mult;
                                                                                              +
                                                                                              175 
                                                                                              +
                                                                                              176  }
                                                                                              +
                                                                                              177 
                                                                                              +
                                                                                              178  // Setting the probability at the node
                                                                                              +
                                                                                              179  node.subtree_prob[s] = totprob;
                                                                                              +
                                                                                              180 
                                                                                              +
                                                                                              181  }
                                                                                              +
                                                                                              182 
                                                                                              +
                                                                                              183  // All probabilities should be completed at this point
                                                                                              +
                                                                                              184  if (node.parent == nullptr)
                                                                                              +
                                                                                              185  {
                                                                                              +
                                                                                              186 
                                                                                              +
                                                                                              187  for (size_t s = 0u; s < states.size(); ++s)
                                                                                              +
                                                                                              188  {
                                                                                              +
                                                                                              189 
                                                                                              +
                                                                                              190  double tmpll = 1.0;
                                                                                              +
                                                                                              191 
                                                                                              +
                                                                                              192  for (auto k = 0u; k < nfunctions; ++k)
                                                                                              +
                                                                                              193  {
                                                                                              +
                                                                                              194 
                                                                                              +
                                                                                              195  tmpll *= states[s][k] ? par_root[k] : (1 - par_root[k]);
                                                                                              +
                                                                                              196 
                                                                                              +
                                                                                              197  }
                                                                                              +
                                                                                              198 
                                                                                              +
                                                                                              199  ll += tmpll * node.subtree_prob[s];
                                                                                              +
                                                                                              200 
                                                                                              +
                                                                                              201  }
                                                                                              +
                                                                                              202  }
                                                                                              +
                                                                                              203 
                                                                                              +
                                                                                              204  }
                                                                                              +
                                                                                              205 
                                                                                              +
                                                                                              206  // In the case that the sequence is empty, then it means
                                                                                              +
                                                                                              207  // that we are looking at a completely unnanotated tree,
                                                                                              +
                                                                                              208  // thus the likelihood should be one
                                                                                              +
                                                                                              209  if (preseq->size() == 0u)
                                                                                              +
                                                                                              210  return as_log ? -std::numeric_limits<double>::infinity() : 1.0;
                                                                                              211 
                                                                                              -
                                                                                              212  return as_log ? std::log(ll) : ll;
                                                                                              -
                                                                                              213 
                                                                                              -
                                                                                              214 }
                                                                                              -
                                                                                              215 #endif
                                                                                              -
                                                                                              BARRY_NCORES_ARG
                                                                                              #define BARRY_NCORES_ARG(default)
                                                                                              Definition: barry-macros.hpp:15
                                                                                              +
                                                                                              212 
                                                                                              +
                                                                                              213  return as_log ? std::log(ll) : ll;
                                                                                              +
                                                                                              214 
                                                                                              +
                                                                                              215 }
                                                                                              +
                                                                                              216 #endif
                                                                                              Geese::reduced_sequence
                                                                                              std::vector< size_t > reduced_sequence
                                                                                              Definition: geese-bones.hpp:138
                                                                                              Geese::sequence
                                                                                              std::vector< size_t > sequence
                                                                                              Definition: geese-bones.hpp:137
                                                                                              Geese::pset_loc
                                                                                              std::vector< std::vector< std::vector< size_t > > > pset_loc
                                                                                              Locations of columns.
                                                                                              Definition: geese-bones.hpp:134
                                                                                              Geese::nfunctions
                                                                                              size_t nfunctions
                                                                                              Definition: geese-bones.hpp:130
                                                                                              -
                                                                                              Geese::likelihood
                                                                                              double likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true,)
                                                                                              Definition: geese-meat-likelihood.hpp:6
                                                                                              +
                                                                                              Geese::likelihood
                                                                                              double likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u)
                                                                                              Definition: geese-meat-likelihood.hpp:6
                                                                                              Geese::nodes
                                                                                              std::map< size_t, Node > nodes
                                                                                              Definition: geese-bones.hpp:131
                                                                                              Node
                                                                                              A single node for the model.
                                                                                              Definition: geese-node-bones.hpp:11
                                                                                              Node::annotations
                                                                                              std::vector< size_t > annotations
                                                                                              Observed annotations (only defined for Geese)
                                                                                              Definition: geese-node-bones.hpp:18
                                                                                              @@ -335,7 +335,7 @@ diff --git a/geese-meat-likelihood__exhaust_8hpp.html b/geese-meat-likelihood__exhaust_8hpp.html index ee60ceafd..353bc9472 100644 --- a/geese-meat-likelihood__exhaust_8hpp.html +++ b/geese-meat-likelihood__exhaust_8hpp.html @@ -113,7 +113,7 @@ diff --git a/geese-meat-likelihood__exhaust_8hpp_source.html b/geese-meat-likelihood__exhaust_8hpp_source.html index 9dd2cc09b..7f6ffeb9a 100644 --- a/geese-meat-likelihood__exhaust_8hpp_source.html +++ b/geese-meat-likelihood__exhaust_8hpp_source.html @@ -247,7 +247,7 @@ diff --git a/geese-meat-predict_8hpp.html b/geese-meat-predict_8hpp.html index be4f5dbef..88581edca 100644 --- a/geese-meat-predict_8hpp.html +++ b/geese-meat-predict_8hpp.html @@ -113,7 +113,7 @@ diff --git a/geese-meat-predict_8hpp_source.html b/geese-meat-predict_8hpp_source.html index e4d222367..67c3c4168 100644 --- a/geese-meat-predict_8hpp_source.html +++ b/geese-meat-predict_8hpp_source.html @@ -136,7 +136,7 @@
                                                                                              38  size_t root_id = preorder[0u];
                                                                                              39  Node * tmp_node = &nodes[root_id];
                                                                                              40  tmp_node->probability.resize(states.size(), 0.0);
                                                                                              -
                                                                                              41  double tmp_likelihood = likelihood(par, false, use_reduced_sequence);
                                                                                              +
                                                                                              41  double tmp_likelihood = likelihood(par, false, use_reduced_sequence);
                                                                                              42 
                                                                                              43  if (!std::isfinite(tmp_likelihood))
                                                                                              44  {
                                                                                              @@ -480,7 +480,7 @@
                                                                                              Geese::sequence
                                                                                              std::vector< size_t > sequence
                                                                                              Definition: geese-bones.hpp:137
                                                                                              Geese::predict
                                                                                              std::vector< std::vector< double > > predict(const std::vector< double > &par, std::vector< std::vector< double > > *res_prob=nullptr, bool leave_one_out=false, bool only_annotated=false, bool use_reduced_sequence=true)
                                                                                              Definition: geese-meat-predict.hpp:287
                                                                                              Geese::nnodes
                                                                                              size_t nnodes() const noexcept
                                                                                              Number of nodes (interior + leaf)
                                                                                              Definition: geese-meat.hpp:434
                                                                                              -
                                                                                              Geese::likelihood
                                                                                              double likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true,)
                                                                                              Definition: geese-meat-likelihood.hpp:6
                                                                                              +
                                                                                              Geese::likelihood
                                                                                              double likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u)
                                                                                              Definition: geese-meat-likelihood.hpp:6
                                                                                              Geese::update_annotations
                                                                                              void update_annotations(size_t nodeid, std::vector< size_t > newann)
                                                                                              Definition: geese-meat.hpp:285
                                                                                              Geese::nodes
                                                                                              std::map< size_t, Node > nodes
                                                                                              Definition: geese-bones.hpp:131
                                                                                              Geese::predict_backend
                                                                                              std::vector< std::vector< double > > predict_backend(const std::vector< double > &par, bool use_reduced_sequence, const std::vector< size_t > &preorder)
                                                                                              Definition: geese-meat-predict.hpp:6
                                                                                              @@ -505,7 +505,7 @@ diff --git a/geese-meat-predict__exhaust_8hpp.html b/geese-meat-predict__exhaust_8hpp.html index 91ade0a46..490b0013a 100644 --- a/geese-meat-predict__exhaust_8hpp.html +++ b/geese-meat-predict__exhaust_8hpp.html @@ -113,7 +113,7 @@ diff --git a/geese-meat-predict__exhaust_8hpp_source.html b/geese-meat-predict__exhaust_8hpp_source.html index 5579f98d8..33ffcc887 100644 --- a/geese-meat-predict__exhaust_8hpp_source.html +++ b/geese-meat-predict__exhaust_8hpp_source.html @@ -156,7 +156,7 @@
                                                                                              58  for (auto& p : par_root)
                                                                                              59  p = std::exp(p)/(std::exp(p) + 1);
                                                                                              60 
                                                                                              -
                                                                                              61  double baseline_likelihood = this->likelihood(par);
                                                                                              +
                                                                                              61  double baseline_likelihood = this->likelihood(par);
                                                                                              62 
                                                                                              63  // Computing all combinations ----------------------------------------------
                                                                                              64  // The base PhyloArray will store the original set of annotations.
                                                                                              @@ -267,7 +267,7 @@
                                                                                              169 #endif
                                                                                              Geese::sequence
                                                                                              std::vector< size_t > sequence
                                                                                              Definition: geese-bones.hpp:137
                                                                                              Geese::nnodes
                                                                                              size_t nnodes() const noexcept
                                                                                              Number of nodes (interior + leaf)
                                                                                              Definition: geese-meat.hpp:434
                                                                                              -
                                                                                              Geese::likelihood
                                                                                              double likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true,)
                                                                                              Definition: geese-meat-likelihood.hpp:6
                                                                                              +
                                                                                              Geese::likelihood
                                                                                              double likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u)
                                                                                              Definition: geese-meat-likelihood.hpp:6
                                                                                              Geese::predict_exhaust_backend
                                                                                              std::vector< std::vector< double > > predict_exhaust_backend(const std::vector< double > &par, const std::vector< size_t > &preorder)
                                                                                              Definition: geese-meat-predict_exhaust.hpp:47
                                                                                              Geese::get_annotated_nodes
                                                                                              std::vector< size_t > get_annotated_nodes() const
                                                                                              Returns the ids of the nodes with at least one annotation.
                                                                                              Definition: geese-meat.hpp:769
                                                                                              Geese::update_annotations
                                                                                              void update_annotations(size_t nodeid, std::vector< size_t > newann)
                                                                                              Definition: geese-meat.hpp:285
                                                                                              @@ -294,7 +294,7 @@ diff --git a/geese-meat-predict__sim_8hpp.html b/geese-meat-predict__sim_8hpp.html index eea2f894e..6eb2eb7d8 100644 --- a/geese-meat-predict__sim_8hpp.html +++ b/geese-meat-predict__sim_8hpp.html @@ -113,7 +113,7 @@ diff --git a/geese-meat-predict__sim_8hpp_source.html b/geese-meat-predict__sim_8hpp_source.html index 372e0118e..9cebb8b56 100644 --- a/geese-meat-predict__sim_8hpp_source.html +++ b/geese-meat-predict__sim_8hpp_source.html @@ -218,7 +218,7 @@ diff --git a/geese-meat-simulate_8hpp.html b/geese-meat-simulate_8hpp.html index 4ccc78ab9..35511881b 100644 --- a/geese-meat-simulate_8hpp.html +++ b/geese-meat-simulate_8hpp.html @@ -113,7 +113,7 @@ diff --git a/geese-meat-simulate_8hpp_source.html b/geese-meat-simulate_8hpp_source.html index 523f758db..c9174a4f6 100644 --- a/geese-meat-simulate_8hpp_source.html +++ b/geese-meat-simulate_8hpp_source.html @@ -207,7 +207,7 @@ diff --git a/geese-meat_8hpp.html b/geese-meat_8hpp.html index c29785ae1..2d91105ac 100644 --- a/geese-meat_8hpp.html +++ b/geese-meat_8hpp.html @@ -113,7 +113,7 @@ diff --git a/geese-meat_8hpp_source.html b/geese-meat_8hpp_source.html index 11de2b8a3..17e4bc8c3 100644 --- a/geese-meat_8hpp_source.html +++ b/geese-meat_8hpp_source.html @@ -987,7 +987,7 @@ diff --git a/geese-node-bones_8hpp.html b/geese-node-bones_8hpp.html index 7cacfdb83..873c806f2 100644 --- a/geese-node-bones_8hpp.html +++ b/geese-node-bones_8hpp.html @@ -122,7 +122,7 @@ diff --git a/geese-node-bones_8hpp_source.html b/geese-node-bones_8hpp_source.html index 087b08a8a..5c2a3152f 100644 --- a/geese-node-bones_8hpp_source.html +++ b/geese-node-bones_8hpp_source.html @@ -225,7 +225,7 @@ diff --git a/geese-types_8hpp.html b/geese-types_8hpp.html index 4c6294b63..668a14be4 100644 --- a/geese-types_8hpp.html +++ b/geese-types_8hpp.html @@ -384,7 +384,7 @@

                                                                                              • include
                                                                                              • barry
                                                                                              • models
                                                                                              • geese
                                                                                              • geese-types.hpp
                                                                                                • -
                                                                                              • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                • +
                                                                                              • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
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                                                                                                                                                diff --git a/group__counters-phylo.html b/group__counters-phylo.html index 02ecc98f5..c77bbc4fb 100644 --- a/group__counters-phylo.html +++ b/group__counters-phylo.html @@ -1334,7 +1334,7 @@

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                                                                                                                                                diff --git a/group__rules-phylo.html b/group__rules-phylo.html index 31553c850..1c5e67d50 100644 --- a/group__rules-phylo.html +++ b/group__rules-phylo.html @@ -1465,7 +1465,7 @@

                                                                                                                                                diff --git a/group__stat-models.html b/group__stat-models.html index 8c648fabb..93807e09c 100644 --- a/group__stat-models.html +++ b/group__stat-models.html @@ -121,7 +121,7 @@ diff --git a/group__stat-models.js b/group__stat-models.js index 1f535d540..056f06552 100644 --- a/group__stat-models.js +++ b/group__stat-models.js @@ -90,7 +90,7 @@ var group__stat_models = [ "get_stats_target", "class_flock.html#a26462201318e4bf34756a2a14e2cc3fb", null ], [ "get_support_fun", "class_flock.html#add876188b5f16af037525e71eaf7fc05", null ], [ "init", "class_flock.html#a5ddef5ec4a7b150a354db11bb6b0c593", null ], - [ "likelihood_joint", "class_flock.html#a7bcad6b3c794cefc1b4bb613d13ddf71", null ], + [ "likelihood_joint", "class_flock.html#add7c442fe0471c790c1945f7abbc2e56", null ], [ "nfuns", "class_flock.html#a55cf3311be1c2129466a666bbe90a3fb", null ], [ "nleafs", "class_flock.html#a68af1602108455f9d339bc4c2994e9ab", null ], [ "nnodes", "class_flock.html#ae1f4eb8ade1c7f369e1f1eddbced3b2b", null ], @@ -127,7 +127,7 @@ var group__stat_models = [ "inherit_support", "class_geese.html#aa95abe540b9977592bcc88e77619d070", null ], [ "init", "class_geese.html#a4eec9d20198fde392b7c5ee0060eff05", null ], [ "init_node", "class_geese.html#a3855898a556e2ac1d30529d3bc35f13a", null ], - [ "likelihood", "class_geese.html#a58fb080f76c71883938b62d5369b6688", null ], + [ "likelihood", "class_geese.html#a557dc9484bbdaf212a6ae2ac8ed3c54c", null ], [ "likelihood_exhaust", "class_geese.html#af2d4bac42cc7c8287fb6853d50882115", null ], [ "nannotations", "class_geese.html#abfec2a7462cc949246a68d540827205f", null ], [ "nfuns", "class_geese.html#ae569fc1b0ade56fc3ccc4d35214fca81", null ], diff --git a/hierarchy.html b/hierarchy.html index 84410d43f..684a75507 100644 --- a/hierarchy.html +++ b/hierarchy.html @@ -161,7 +161,7 @@ diff --git a/index.html b/index.html index 8f161026d..88a236895 100644 --- a/index.html +++ b/index.html @@ -206,7 +206,7 @@

                                                                                                                                                Code of Conduct

                                                                                                                                                diff --git a/inherits.html b/inherits.html index 64e2c7c0c..f17c370f1 100644 --- a/inherits.html +++ b/inherits.html @@ -367,7 +367,7 @@ diff --git a/latex/barray-bones_8hpp__dep__incl.pdf b/latex/barray-bones_8hpp__dep__incl.pdf index bc0811b2a..4c98119bc 100644 Binary files a/latex/barray-bones_8hpp__dep__incl.pdf and b/latex/barray-bones_8hpp__dep__incl.pdf differ diff --git a/latex/barray-meat-operators_8hpp__dep__incl.pdf b/latex/barray-meat-operators_8hpp__dep__incl.pdf index e36797548..23d01694c 100644 Binary files a/latex/barray-meat-operators_8hpp__dep__incl.pdf and b/latex/barray-meat-operators_8hpp__dep__incl.pdf differ diff --git a/latex/barray-meat_8hpp__dep__incl.pdf b/latex/barray-meat_8hpp__dep__incl.pdf index 3ef10c2e6..046da7df8 100644 Binary files a/latex/barray-meat_8hpp__dep__incl.pdf and 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b/latex/barry-macros_8hpp.tex index ac08f23d7..86030e641 100644 --- a/latex/barry-macros_8hpp.tex +++ b/latex/barry-macros_8hpp.tex @@ -21,7 +21,7 @@ \item \#define \mbox{\hyperlink{barry-macros_8hpp_abdbb6194e397040509635a85186d0d23}{BARRY\+\_\+\+UNUSED}}(expr)~do \{ (void)(expr); \} while (0); \item -\#define \mbox{\hyperlink{barry-macros_8hpp_a1ca54136450bf509406c9def89692fc6}{BARRY\+\_\+\+NCORES\+\_\+\+ARG}}(default)~size\+\_\+t +\#define \mbox{\hyperlink{barry-macros_8hpp_a1ca54136450bf509406c9def89692fc6}{BARRY\+\_\+\+NCORES\+\_\+\+ARG}}(default)~size\+\_\+t ncores default \end{DoxyCompactItemize} @@ -30,7 +30,7 @@ \index{barry-\/macros.hpp@{barry-\/macros.hpp}!BARRY\_NCORES\_ARG@{BARRY\_NCORES\_ARG}} \index{BARRY\_NCORES\_ARG@{BARRY\_NCORES\_ARG}!barry-\/macros.hpp@{barry-\/macros.hpp}} \doxysubsubsection{\texorpdfstring{BARRY\_NCORES\_ARG}{BARRY\_NCORES\_ARG}} -{\footnotesize\ttfamily \#define BARRY\+\_\+\+NCORES\+\_\+\+ARG(\begin{DoxyParamCaption}\item[{}]{default }\end{DoxyParamCaption})~size\+\_\+t} +{\footnotesize\ttfamily \#define BARRY\+\_\+\+NCORES\+\_\+\+ARG(\begin{DoxyParamCaption}\item[{}]{default }\end{DoxyParamCaption})~size\+\_\+t ncores default} diff --git a/latex/barry-macros_8hpp__dep__incl.pdf b/latex/barry-macros_8hpp__dep__incl.pdf index 10a754be4..64747d99f 100644 Binary files a/latex/barry-macros_8hpp__dep__incl.pdf and b/latex/barry-macros_8hpp__dep__incl.pdf differ diff --git a/latex/barry_8hpp__incl.pdf b/latex/barry_8hpp__incl.pdf index 83fe52d7a..ba7ad8570 100644 Binary files a/latex/barry_8hpp__incl.pdf and b/latex/barry_8hpp__incl.pdf differ diff --git a/latex/cell-bones_8hpp__dep__incl.pdf b/latex/cell-bones_8hpp__dep__incl.pdf index a409d53c9..772fb89e7 100644 Binary files a/latex/cell-bones_8hpp__dep__incl.pdf and b/latex/cell-bones_8hpp__dep__incl.pdf differ diff --git a/latex/cell-meat_8hpp__dep__incl.pdf b/latex/cell-meat_8hpp__dep__incl.pdf index e75c39c9c..eafeee1c3 100644 Binary files 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\mbox{\hyperlink{class_flock_a9692be014117ae093ce160462dbde0d2}{get\+\_\+model}} () \item -double \mbox{\hyperlink{class_flock_a7bcad6b3c794cefc1b4bb613d13ddf71}{likelihood\+\_\+joint}} (const std\+::vector$<$ double $>$ \&par, bool as\+\_\+log=false, bool use\+\_\+reduced\+\_\+sequence=true,) +double \mbox{\hyperlink{class_flock_add7c442fe0471c790c1945f7abbc2e56}{likelihood\+\_\+joint}} (const std\+::vector$<$ double $>$ \&par, bool as\+\_\+log=false, bool use\+\_\+reduced\+\_\+sequence=true, size\+\_\+t ncores=1u) \begin{DoxyCompactList}\small\item\em Returns the joint likelihood of the model. \end{DoxyCompactList}\item \mbox{\hyperlink{class_geese}{Geese}} $\ast$ \mbox{\hyperlink{class_flock_a00fde307995418d36deeedbc78f29a7a}{operator()}} (size\+\_\+t \mbox{\hyperlink{counters-meat_8hpp_ae46bd26d7133dfe98f8cec7c5ac5c7a1}{i}}, bool check\+\_\+bounds=true) \begin{DoxyCompactList}\small\item\em Access the i-\/th geese element. \end{DoxyCompactList}\end{DoxyCompactItemize} @@ -204,11 +204,11 @@ Definition at line 49 of file flock-\/meat.\+hpp. -\mbox{\Hypertarget{class_flock_a7bcad6b3c794cefc1b4bb613d13ddf71}\label{class_flock_a7bcad6b3c794cefc1b4bb613d13ddf71}} +\mbox{\Hypertarget{class_flock_add7c442fe0471c790c1945f7abbc2e56}\label{class_flock_add7c442fe0471c790c1945f7abbc2e56}} \index{Flock@{Flock}!likelihood\_joint@{likelihood\_joint}} \index{likelihood\_joint@{likelihood\_joint}!Flock@{Flock}} \doxysubsubsection{\texorpdfstring{likelihood\_joint()}{likelihood\_joint()}} -{\footnotesize\ttfamily double Flock\+::likelihood\+\_\+joint (\begin{DoxyParamCaption}\item[{const std\+::vector$<$ double $>$ \&}]{par, }\item[{bool}]{as\+\_\+log = {\ttfamily false}, }\item[{bool}]{use\+\_\+reduced\+\_\+sequence = {\ttfamily true} }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} +{\footnotesize\ttfamily double Flock\+::likelihood\+\_\+joint (\begin{DoxyParamCaption}\item[{const std\+::vector$<$ double $>$ \&}]{par, }\item[{bool}]{as\+\_\+log = {\ttfamily false}, }\item[{bool}]{use\+\_\+reduced\+\_\+sequence = {\ttfamily true}, }\item[{size\+\_\+t}]{ncores = {\ttfamily 1u} }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} diff --git a/latex/class_geese.tex b/latex/class_geese.tex index 0c033c846..7d6cb0d9a 100644 --- a/latex/class_geese.tex +++ b/latex/class_geese.tex @@ -22,7 +22,7 @@ \item void \mbox{\hyperlink{class_geese_a0a460414624fd1b7013ce3b1a09150d1}{calc\+\_\+reduced\+\_\+sequence}} () \item -double \mbox{\hyperlink{class_geese_a58fb080f76c71883938b62d5369b6688}{likelihood}} (const std\+::vector$<$ double $>$ \&par, bool as\+\_\+log=false, bool use\+\_\+reduced\+\_\+sequence=true,) +double \mbox{\hyperlink{class_geese_a557dc9484bbdaf212a6ae2ac8ed3c54c}{likelihood}} (const std\+::vector$<$ double $>$ \&par, bool as\+\_\+log=false, bool use\+\_\+reduced\+\_\+sequence=true, size\+\_\+t ncores=1u) \item double \mbox{\hyperlink{class_geese_af2d4bac42cc7c8287fb6853d50882115}{likelihood\+\_\+exhaust}} (const std\+::vector$<$ double $>$ \&par) \item @@ -436,11 +436,11 @@ Definition at line 6 of file geese-\/meat.\+hpp. -\mbox{\Hypertarget{class_geese_a58fb080f76c71883938b62d5369b6688}\label{class_geese_a58fb080f76c71883938b62d5369b6688}} +\mbox{\Hypertarget{class_geese_a557dc9484bbdaf212a6ae2ac8ed3c54c}\label{class_geese_a557dc9484bbdaf212a6ae2ac8ed3c54c}} \index{Geese@{Geese}!likelihood@{likelihood}} \index{likelihood@{likelihood}!Geese@{Geese}} \doxysubsubsection{\texorpdfstring{likelihood()}{likelihood()}} -{\footnotesize\ttfamily double Geese\+::likelihood (\begin{DoxyParamCaption}\item[{const std\+::vector$<$ double $>$ \&}]{par, }\item[{bool}]{as\+\_\+log = {\ttfamily false}, }\item[{bool}]{use\+\_\+reduced\+\_\+sequence = {\ttfamily true} }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} +{\footnotesize\ttfamily double Geese\+::likelihood (\begin{DoxyParamCaption}\item[{const std\+::vector$<$ double $>$ \&}]{par, }\item[{bool}]{as\+\_\+log = {\ttfamily false}, }\item[{bool}]{use\+\_\+reduced\+\_\+sequence = {\ttfamily true}, }\item[{size\+\_\+t}]{ncores = {\ttfamily 1u} }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} diff --git a/latex/class_model__coll__graph.pdf b/latex/class_model__coll__graph.pdf index 5a2dd89b9..d072865d1 100644 Binary files a/latex/class_model__coll__graph.pdf and b/latex/class_model__coll__graph.pdf differ diff --git a/latex/class_node__coll__graph.pdf b/latex/class_node__coll__graph.pdf index 9ff173659..9e59726c8 100644 Binary files a/latex/class_node__coll__graph.pdf and b/latex/class_node__coll__graph.pdf differ diff --git a/latex/class_power_set__coll__graph.pdf b/latex/class_power_set__coll__graph.pdf index c24ffee08..6065f90d3 100644 Binary files a/latex/class_power_set__coll__graph.pdf and b/latex/class_power_set__coll__graph.pdf differ diff --git a/latex/counters-bones_8hpp__dep__incl.pdf b/latex/counters-bones_8hpp__dep__incl.pdf index 0a3425c68..cca98a8cd 100644 Binary files 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                                                                                                                                                • include
                                                                                                                                                • barry
                                                                                                                                                • model-meat.hpp
                                                                                                                                                  • -
                                                                                                                                                • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                  • +
                                                                                                                                                • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                diff --git a/model-meat_8hpp_source.html b/model-meat_8hpp_source.html index 6d4bdbc92..1df7c8e64 100644 --- a/model-meat_8hpp_source.html +++ b/model-meat_8hpp_source.html @@ -1002,7 +1002,7 @@
                                                                                                                                                914  params.size()
                                                                                                                                                915  ) BARRY_SAFE_EXP;
                                                                                                                                                916 
                                                                                                                                                -
                                                                                                                                                917  #ifdef __OPENM
                                                                                                                                                +
                                                                                                                                                917  #if defined(__OPENMP) || defined(_OPENMP)
                                                                                                                                                918  #pragma omp simd reduction(-:res)
                                                                                                                                                919  #endif
                                                                                                                                                920  for (size_t i = 0u; i < params_last_size; ++i)
                                                                                                                                                @@ -1012,7 +1012,7 @@
                                                                                                                                                924 
                                                                                                                                                925  res = 1.0;
                                                                                                                                                926  size_t stats_target_size = stats_target.size();
                                                                                                                                                -
                                                                                                                                                927  #ifdef __OPENM
                                                                                                                                                +
                                                                                                                                                927  #if defined(__OPENMP) || defined(_OPENMP)
                                                                                                                                                928  #pragma omp simd reduction(*:res)
                                                                                                                                                929  #endif
                                                                                                                                                930  for (size_t i = 0; i < stats_target_size; ++i)
                                                                                                                                                @@ -1781,7 +1781,7 @@ diff --git a/modules.html b/modules.html index 4766c8fbe..311bb9942 100644 --- a/modules.html +++ b/modules.html @@ -110,7 +110,7 @@ diff --git a/namespace_c_h_e_c_k.html b/namespace_c_h_e_c_k.html index 7fc7ab0eb..12aa880b5 100644 --- a/namespace_c_h_e_c_k.html +++ b/namespace_c_h_e_c_k.html @@ -186,7 +186,7 @@

                                                                                                                                                • CHECK
                                                                                                                                                  • -
                                                                                                                                                • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                  • +
                                                                                                                                                • Generated on Wed Sep 27 2023 23:39:59 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                diff --git a/namespace_e_x_i_s_t_s.html b/namespace_e_x_i_s_t_s.html index 774bb8099..010269a49 100644 --- a/namespace_e_x_i_s_t_s.html +++ b/namespace_e_x_i_s_t_s.html @@ -240,7 +240,7 @@

                                                                                                                                                • EXISTS
                                                                                                                                                  • -
                                                                                                                                                • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                  • +
                                                                                                                                                • Generated on Wed Sep 27 2023 23:39:59 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                diff --git a/namespacebarry.html b/namespacebarry.html index f87f24c8b..0a096641b 100644 --- a/namespacebarry.html +++ b/namespacebarry.html @@ -116,7 +116,7 @@ diff --git a/namespacebarry_1_1counters.html b/namespacebarry_1_1counters.html index eceaca2cd..6afa093bd 100644 --- a/namespacebarry_1_1counters.html +++ b/namespacebarry_1_1counters.html @@ -115,7 +115,7 @@ diff --git a/namespacebarry_1_1counters_1_1network.html b/namespacebarry_1_1counters_1_1network.html index 00b315bc9..f72b0af3f 100644 --- a/namespacebarry_1_1counters_1_1network.html +++ b/namespacebarry_1_1counters_1_1network.html @@ -102,7 +102,7 @@ diff --git a/namespacedefm.html b/namespacedefm.html index 0db6ec95a..26030c46a 100644 --- a/namespacedefm.html +++ b/namespacedefm.html @@ -102,7 +102,7 @@ diff --git a/namespacegeese.html b/namespacegeese.html index ebe17925f..7e418b06e 100644 --- a/namespacegeese.html +++ b/namespacegeese.html @@ -102,7 +102,7 @@ diff --git a/namespacemembers.html b/namespacemembers.html index 0106ef07a..112a1a212 100644 --- a/namespacemembers.html +++ b/namespacemembers.html @@ -124,7 +124,7 @@ diff --git a/namespacemembers_vars.html b/namespacemembers_vars.html index e52f4adab..54d30f511 100644 --- a/namespacemembers_vars.html +++ b/namespacemembers_vars.html @@ -124,7 +124,7 @@ diff --git a/navtreeindex1.js b/navtreeindex1.js index d8fbf260a..a388b06f7 100644 --- a/navtreeindex1.js +++ b/navtreeindex1.js @@ -232,12 +232,12 @@ var NAVTREEINDEX1 = "class_flock.html#a5e882cb60a36398180557662731d3c11":[0,1,1,2], "class_flock.html#a68af1602108455f9d339bc4c2994e9ab":[0,1,1,12], "class_flock.html#a71d5966ea3fda9e2baedf76be6c837c6":[0,1,1,14], -"class_flock.html#a7bcad6b3c794cefc1b4bb613d13ddf71":[0,1,1,10], "class_flock.html#a9692be014117ae093ce160462dbde0d2":[0,1,1,5], "class_flock.html#aad9b90040d349a23b33e09292bb964db":[0,1,1,22], "class_flock.html#ab5ed0567a8721dd114763267f9fa3bdf":[0,1,1,1], "class_flock.html#ab5f4c94b0484772321b3856debdf3a58":[0,1,1,6], "class_flock.html#ad0f1cd362bc6a2dfbb81fa2abeff59cc":[0,1,1,20], +"class_flock.html#add7c442fe0471c790c1945f7abbc2e56":[0,1,1,10], "class_flock.html#add876188b5f16af037525e71eaf7fc05":[0,1,1,8], "class_flock.html#ae1f4eb8ade1c7f369e1f1eddbced3b2b":[0,1,1,13], "class_flock.html#ae47e9d235c3e3e6f3bb574772f2463d0":[0,1,1,15], diff --git a/navtreeindex2.js b/navtreeindex2.js index 4ecb96e20..6d259014e 100644 --- a/navtreeindex2.js +++ b/navtreeindex2.js @@ -27,7 +27,7 @@ var NAVTREEINDEX2 = "class_geese.html#a4d9127f67eea16500650cca49be58018":[0,1,2,7], "class_geese.html#a4eec9d20198fde392b7c5ee0060eff05":[0,1,2,17], "class_geese.html#a50453216e1b1968c19c3da0a703bffcf":[0,1,2,24], -"class_geese.html#a58fb080f76c71883938b62d5369b6688":[0,1,2,19], +"class_geese.html#a557dc9484bbdaf212a6ae2ac8ed3c54c":[0,1,2,19], "class_geese.html#a5a56d129d383ca8648e6ddf9b845b05a":[0,1,2,28], "class_geese.html#a5c9cf28a69270fe4d3f48984fe2c5723":[0,1,2,12], "class_geese.html#a65ea8253e72213a0e44e534d408b95dc":[0,1,2,34], diff --git a/network-css_8hpp.html b/network-css_8hpp.html index 6dfce319e..d52a11c18 100644 --- a/network-css_8hpp.html +++ b/network-css_8hpp.html @@ -1259,7 +1259,7 @@

                                                                                                                                                • include
                                                                                                                                                • barry
                                                                                                                                                • counters
                                                                                                                                                • network-css.hpp
                                                                                                                                                  • -
                                                                                                                                                • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                  • +
                                                                                                                                                • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                diff --git a/network-css_8hpp_source.html b/network-css_8hpp_source.html index 8efacc3c7..5caa27c47 100644 --- a/network-css_8hpp_source.html +++ b/network-css_8hpp_source.html @@ -874,7 +874,7 @@ diff --git a/network_8hpp.html b/network_8hpp.html index 23829c6bf..2625448ea 100644 --- a/network_8hpp.html +++ b/network_8hpp.html @@ -682,7 +682,7 @@

                                                                                                                                                • include
                                                                                                                                                • barry
                                                                                                                                                • counters
                                                                                                                                                • network.hpp
                                                                                                                                                  • -
                                                                                                                                                • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                  • +
                                                                                                                                                • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                diff --git a/network_8hpp_source.html b/network_8hpp_source.html index 9450c7f0a..b495a6263 100644 --- a/network_8hpp_source.html +++ b/network_8hpp_source.html @@ -718,7 +718,7 @@
                                                                                                                                                673 
                                                                                                                                                674  // i->j->k->i
                                                                                                                                                675  double ans = 0.0;
                                                                                                                                                -
                                                                                                                                                676  #ifdef __OPENM
                                                                                                                                                +
                                                                                                                                                676  #if defined(__OPENMP) || defined(_OPENMP)
                                                                                                                                                677  #pragma omp simd reduction(+:ans)
                                                                                                                                                678  #endif
                                                                                                                                                679  for (size_t k = 0u; k < Array.nrow(); ++k)
                                                                                                                                                @@ -1496,7 +1496,7 @@ diff --git a/powerset-bones_8hpp.html b/powerset-bones_8hpp.html index c188be031..90bf29915 100644 --- a/powerset-bones_8hpp.html +++ b/powerset-bones_8hpp.html @@ -122,7 +122,7 @@ diff --git a/powerset-bones_8hpp_source.html b/powerset-bones_8hpp_source.html index d56c49abc..79418ac1f 100644 --- a/powerset-bones_8hpp_source.html +++ b/powerset-bones_8hpp_source.html @@ -187,7 +187,7 @@ diff --git a/powerset-meat_8hpp.html b/powerset-meat_8hpp.html index 0a0dbdbf1..9d8930313 100644 --- a/powerset-meat_8hpp.html +++ b/powerset-meat_8hpp.html @@ -113,7 +113,7 @@ diff --git a/powerset-meat_8hpp_source.html b/powerset-meat_8hpp_source.html index ee58e0dc5..caaaebe6b 100644 --- a/powerset-meat_8hpp_source.html +++ b/powerset-meat_8hpp_source.html @@ -319,7 +319,7 @@ diff --git a/progress_8hpp.html b/progress_8hpp.html index b3b54ac7e..69f5c4848 100644 --- a/progress_8hpp.html +++ b/progress_8hpp.html @@ -146,7 +146,7 @@

                                                                                                                                                • include
                                                                                                                                                • barry
                                                                                                                                                • progress.hpp
                                                                                                                                                  • -
                                                                                                                                                • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                  • +
                                                                                                                                                • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                diff --git a/progress_8hpp_source.html b/progress_8hpp_source.html index 99fe2314d..e97c25b82 100644 --- a/progress_8hpp_source.html +++ b/progress_8hpp_source.html @@ -164,7 +164,7 @@ diff --git a/rules-bones_8hpp.html b/rules-bones_8hpp.html index 769b99ba9..01b4a54ce 100644 --- a/rules-bones_8hpp.html +++ b/rules-bones_8hpp.html @@ -177,7 +177,7 @@

                                                                                                                                                • include
                                                                                                                                                • barry
                                                                                                                                                • rules-bones.hpp
                                                                                                                                                  • -
                                                                                                                                                • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                  • +
                                                                                                                                                • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
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                                                                                                                                                • include
                                                                                                                                                • barry
                                                                                                                                                • statscounter-meat.hpp
                                                                                                                                                  • -
                                                                                                                                                • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                  • +
                                                                                                                                                • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                diff --git a/statscounter-meat_8hpp_source.html b/statscounter-meat_8hpp_source.html index d50cb1197..cb4f85474 100644 --- a/statscounter-meat_8hpp_source.html +++ b/statscounter-meat_8hpp_source.html @@ -384,7 +384,7 @@ diff --git a/structvec_hasher-members.html b/structvec_hasher-members.html index 1f62626e3..ad1f770f3 100644 --- a/structvec_hasher-members.html +++ b/structvec_hasher-members.html @@ -105,7 +105,7 @@ diff --git a/structvec_hasher.html b/structvec_hasher.html index a20798e6b..4dc4a0290 100644 --- a/structvec_hasher.html +++ b/structvec_hasher.html @@ -153,7 +153,7 @@

                                                                                                                                                • vecHasher
                                                                                                                                                  • -
                                                                                                                                                • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                  • +
                                                                                                                                                • Generated on Wed Sep 27 2023 23:39:59 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                diff --git a/support-bones_8hpp.html b/support-bones_8hpp.html index 4b2f7c692..c0189ad56 100644 --- a/support-bones_8hpp.html +++ b/support-bones_8hpp.html @@ -122,7 +122,7 @@ diff --git a/support-bones_8hpp_source.html b/support-bones_8hpp_source.html index 1c901a3d5..47b5f6007 100644 --- a/support-bones_8hpp_source.html +++ b/support-bones_8hpp_source.html @@ -289,7 +289,7 @@ diff --git a/support-meat_8hpp.html b/support-meat_8hpp.html index f9fd4fa05..61130e6e8 100644 --- a/support-meat_8hpp.html +++ b/support-meat_8hpp.html @@ -138,7 +138,7 @@

                                                                                                                                                • include
                                                                                                                                                • barry
                                                                                                                                                • support-meat.hpp
                                                                                                                                                  • -
                                                                                                                                                • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                  • +
                                                                                                                                                • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                diff --git a/support-meat_8hpp_source.html b/support-meat_8hpp_source.html index 091d34f26..baa153d41 100644 --- a/support-meat_8hpp_source.html +++ b/support-meat_8hpp_source.html @@ -746,7 +746,7 @@ diff --git a/typedefs_8hpp.html b/typedefs_8hpp.html index 37dd79b96..59d712ff0 100644 --- a/typedefs_8hpp.html +++ b/typedefs_8hpp.html @@ -624,7 +624,7 @@

                                                                                                                                                • include
                                                                                                                                                • barry
                                                                                                                                                • typedefs.hpp
                                                                                                                                                  • -
                                                                                                                                                • Generated on Wed Sep 27 2023 22:53:07 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                  • +
                                                                                                                                                • Generated on Wed Sep 27 2023 23:39:58 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                                                                                diff --git a/typedefs_8hpp_source.html b/typedefs_8hpp_source.html index eb7370214..ac1724517 100644 --- a/typedefs_8hpp_source.html +++ b/typedefs_8hpp_source.html @@ -306,7 +306,7 @@
                                                                                                                                                255  return false;
                                                                                                                                                256 }
                                                                                                                                                258 
                                                                                                                                                -
                                                                                                                                                259 #ifdef __OPENM
                                                                                                                                                +
                                                                                                                                                259 #if defined(__OPENMP) || defined(_OPENMP)
                                                                                                                                                260 #pragma omp declare simd
                                                                                                                                                261 #endif
                                                                                                                                                262 template <typename T>
                                                                                                                                                @@ -317,7 +317,7 @@
                                                                                                                                                267 ) {
                                                                                                                                                268 
                                                                                                                                                269  double res = 0.0;
                                                                                                                                                -
                                                                                                                                                270  #ifdef __OPENM
                                                                                                                                                +
                                                                                                                                                270  #if defined(__OPENMP) || defined(_OPENMP)
                                                                                                                                                271  #pragma omp simd reduction(+:res)
                                                                                                                                                272  #else
                                                                                                                                                273  #ifdef __GNUC__
                                                                                                                                                @@ -333,7 +333,7 @@
                                                                                                                                                283 
                                                                                                                                                284 }
                                                                                                                                                285 
                                                                                                                                                -
                                                                                                                                                286 #ifdef __OPENM
                                                                                                                                                +
                                                                                                                                                286 #if defined(__OPENMP) || defined(_OPENMP)
                                                                                                                                                287 #pragma omp declare simd
                                                                                                                                                288 #endif
                                                                                                                                                289 template <>
                                                                                                                                                @@ -414,7 +414,7 @@