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diff --git a/barraydense-meat_8hpp_source.html b/barraydense-meat_8hpp_source.html index ee8e279f5..b08873707 100644 --- a/barraydense-meat_8hpp_source.html +++ b/barraydense-meat_8hpp_source.html @@ -1186,7 +1186,7 @@ diff --git a/barraydensecell-bones_8hpp.html b/barraydensecell-bones_8hpp.html index 141eb414c..549c6c508 100644 --- a/barraydensecell-bones_8hpp.html +++ b/barraydensecell-bones_8hpp.html @@ -158,7 +158,7 @@

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diff --git a/barraydensecell-bones_8hpp_source.html b/barraydensecell-bones_8hpp_source.html index 8b91dbf8d..bf40c3d89 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 bf317b1c8..062c0dc40 100644 --- a/barraydensecell-meat_8hpp.html +++ b/barraydensecell-meat_8hpp.html @@ -152,7 +152,7 @@

  • include
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diff --git a/barraydensecell-meat_8hpp_source.html b/barraydensecell-meat_8hpp_source.html index b8e889654..7716959a0 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 a60879c8e..147c78020 100644 --- a/barraydensecol-bones_8hpp.html +++ b/barraydensecol-bones_8hpp.html @@ -216,7 +216,7 @@

  • include
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diff --git a/barraydensecol-bones_8hpp_source.html b/barraydensecol-bones_8hpp_source.html index e469cdca3..f9bd3715f 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 f5f28153b..24c182a4a 100644 --- a/barraydenserow-bones_8hpp.html +++ b/barraydenserow-bones_8hpp.html @@ -216,7 +216,7 @@

  • include
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diff --git a/barraydenserow-bones_8hpp_source.html b/barraydenserow-bones_8hpp_source.html index b36cfa9ef..3344537fd 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 17ae2300e..f2583e566 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 360a540d8..70e710a37 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 d00fd8ab4..e3609db5b 100644 --- a/barrayrow-meat_8hpp.html +++ b/barrayrow-meat_8hpp.html @@ -350,7 +350,7 @@

  • include
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  • barrayrow-meat.hpp
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diff --git a/barrayrow-meat_8hpp_source.html b/barrayrow-meat_8hpp_source.html index 0138f39ba..ab4a34db3 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 695258888..2ec76bed4 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 0d2e1c53b..6ea7ee124 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 c4efed6d9..937faa684 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 ce6a3e50f..a1b773991 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 0ca8a9ec3..7c40bb826 100644 --- a/barry-configuration_8hpp.html +++ b/barry-configuration_8hpp.html @@ -257,7 +257,7 @@

  • include
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diff --git a/barry-configuration_8hpp_source.html b/barry-configuration_8hpp_source.html index 6f3cdfdc7..c8414faf2 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 2c4d8b8e1..cba81163e 100644 --- a/barry-debug_8hpp.html +++ b/barry-debug_8hpp.html @@ -139,7 +139,7 @@

  • include
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diff --git a/barry-debug_8hpp_source.html b/barry-debug_8hpp_source.html index 4248a6082..c816dbd6f 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 40d2b9fea..611ac10d3 100644 --- a/barry-macros_8hpp.html +++ b/barry-macros_8hpp.html @@ -236,7 +236,7 @@

  • include
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diff --git a/barry-macros_8hpp_source.html b/barry-macros_8hpp_source.html index 20cb38844..8f6714ad3 100644 --- a/barry-macros_8hpp_source.html +++ b/barry-macros_8hpp_source.html @@ -121,7 +121,7 @@ diff --git a/barry_8hpp.html b/barry_8hpp.html index de9e38365..8869fea92 100644 --- a/barry_8hpp.html +++ b/barry_8hpp.html @@ -401,7 +401,7 @@

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diff --git a/barry_8hpp_source.html b/barry_8hpp_source.html index 18ded020c..074919ccb 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 f8e55f015..d79961621 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 69e597925..f72f9317d 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 949ff93b5..b30e05933 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 a0361ab48..8a5f3ba8b 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 4fae78a44..fe4c06fcc 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 f67366259..6e9208174 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 e77183d2e..ed6e18029 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 e788fdcf6..7eb286ca8 100644 --- a/class_b_array_cell.html +++ b/class_b_array_cell.html @@ -430,7 +430,7 @@

  • BArrayCell
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diff --git a/class_b_array_cell__const-members.html b/class_b_array_cell__const-members.html index 62642a046..f05fab10f 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 6b0a4e435..ab46c2c9c 100644 --- a/class_b_array_cell__const.html +++ b/class_b_array_cell__const.html @@ -430,7 +430,7 @@

  • BArrayCell_const
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diff --git a/class_b_array_dense-members.html b/class_b_array_dense-members.html index 02e5fb983..ce41e45db 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 ee9e07988..819bc3682 100644 --- a/class_b_array_dense.html +++ b/class_b_array_dense.html @@ -2668,7 +2668,7 @@

  • BArrayDense
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diff --git a/class_b_array_dense_cell-members.html b/class_b_array_dense_cell-members.html index 88818cbc6..054dfb622 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 d63591c26..1f7ef0a35 100644 --- a/class_b_array_dense_cell.html +++ b/class_b_array_dense_cell.html @@ -550,7 +550,7 @@

  • BArrayDenseCell
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diff --git a/class_b_array_dense_cell__const.html b/class_b_array_dense_cell__const.html index 8779eb73d..ac75f3e1a 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 c47a59a6b..da0785d68 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 31f78a867..54fd6ee11 100644 --- a/class_b_array_dense_col.html +++ b/class_b_array_dense_col.html @@ -379,7 +379,7 @@

  • BArrayDenseCol
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diff --git a/class_b_array_dense_col__const-members.html b/class_b_array_dense_col__const-members.html index c71f7481b..38f00eba3 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 a6a7e377c..d6a94ec30 100644 --- a/class_b_array_dense_col__const.html +++ b/class_b_array_dense_col__const.html @@ -351,7 +351,7 @@

  • BArrayDenseCol_const
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diff --git a/class_b_array_dense_row-members.html b/class_b_array_dense_row-members.html index fcaae78f2..3901617a6 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 5da91b397..807a4c891 100644 --- a/class_b_array_dense_row.html +++ b/class_b_array_dense_row.html @@ -379,7 +379,7 @@

  • BArrayDenseRow
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diff --git a/class_b_array_dense_row__const-members.html b/class_b_array_dense_row__const-members.html index 33d407629..803c80df0 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 5d1e4c375..e6a9fbf05 100644 --- a/class_b_array_dense_row__const.html +++ b/class_b_array_dense_row__const.html @@ -351,7 +351,7 @@

  • BArrayDenseRow_const
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diff --git a/class_b_array_row-members.html b/class_b_array_row-members.html index e37026ea4..6c7ce9b4c 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 30aad574b..b78910516 100644 --- a/class_b_array_row.html +++ b/class_b_array_row.html @@ -354,7 +354,7 @@

  • BArrayRow
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diff --git a/class_b_array_row__const-members.html b/class_b_array_row__const-members.html index 321466bfb..62b41f712 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 7f76f208b..d76033b63 100644 --- a/class_b_array_row__const.html +++ b/class_b_array_row__const.html @@ -354,7 +354,7 @@

  • BArrayRow_const
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diff --git a/class_b_array_vector-members.html b/class_b_array_vector-members.html index d8d400845..f2b806e05 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 7d6342975..3e4758be5 100644 --- a/class_b_array_vector.html +++ b/class_b_array_vector.html @@ -585,7 +585,7 @@

  • BArrayVector
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diff --git a/class_b_array_vector__const-members.html b/class_b_array_vector__const-members.html index 116f2cb1c..29bf45411 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 c58f8f468..8994639ec 100644 --- a/class_b_array_vector__const.html +++ b/class_b_array_vector__const.html @@ -567,7 +567,7 @@

  • BArrayVector_const
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diff --git a/class_cell-members.html b/class_cell-members.html index a3c29b91d..7d25b9dcf 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 4592aef92..fe938db21 100644 --- a/class_cell.html +++ b/class_cell.html @@ -695,7 +695,7 @@

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diff --git a/class_cell__const.html b/class_cell__const.html index d8261b9a5..f7553ff65 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 7b5f4537b..d260227ea 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 92703ac68..e4426dd8f 100644 --- a/class_const_b_array_row_iter.html +++ b/class_const_b_array_row_iter.html @@ -278,7 +278,7 @@

  • ConstBArrayRowIter
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diff --git a/class_counter-members.html b/class_counter-members.html index 39a115365..e7ff06cfb 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 6bbe09afd..59f6e543e 100644 --- a/class_counter.html +++ b/class_counter.html @@ -679,7 +679,7 @@

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diff --git a/class_counters-members.html b/class_counters-members.html index eebd3e29f..44647de8b 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 30e6b9273..2327d246a 100644 --- a/class_counters.html +++ b/class_counters.html @@ -573,7 +573,7 @@

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diff --git a/class_d_e_f_m-members.html b/class_d_e_f_m-members.html index 0c3eef775..7b5e0b318 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 2312cdd9d..a33cb4303 100644 --- a/class_d_e_f_m.html +++ b/class_d_e_f_m.html @@ -811,7 +811,7 @@

  • DEFM
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    • +
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diff --git a/class_d_e_f_m_counter_data-members.html b/class_d_e_f_m_counter_data-members.html index f2da697d4..6fd37aa8e 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 c2c73b196..43a7c6cb4 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 b992b4c36..ea61daed7 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 04f3c8599..a6f45f35e 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 177286537..c4e329201 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 0a08ddb38..d86c61879 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 6ea4bb831..ebb7c75e8 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 6c4ad2299..72acc3c2d 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 1ece24e1a..7330d695f 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 31bfb89fd..e6ee13e92 100644 --- a/class_entries.html +++ b/class_entries.html @@ -323,7 +323,7 @@

  • Entries
    • -
  • Generated on Mon Oct 2 2023 21:11:12 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 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 16498fe3a..e7e3de4a8 100644 --- a/class_flock-members.html +++ b/class_flock-members.html @@ -130,7 +130,7 @@ diff --git a/class_flock.html b/class_flock.html index a8c17da30..8867f6eed 100644 --- a/class_flock.html +++ b/class_flock.html @@ -948,7 +948,7 @@

  • Flock
    • -
  • Generated on Mon Oct 2 2023 21:11:12 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_freq_table-members.html b/class_freq_table-members.html index 5df6310c7..2857371f0 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 dd7526567..c90721315 100644 --- a/class_freq_table.html +++ b/class_freq_table.html @@ -491,7 +491,7 @@

  • FreqTable
    • -
  • Generated on Mon Oct 2 2023 21:11:12 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_geese-members.html b/class_geese-members.html index 080b4e364..e99911e07 100644 --- a/class_geese-members.html +++ b/class_geese-members.html @@ -159,7 +159,7 @@ diff --git a/class_geese.html b/class_geese.html index a34264c87..f39f5691a 100644 --- a/class_geese.html +++ b/class_geese.html @@ -922,7 +922,7 @@

-

Definition at line 115 of file geese-meat-likelihood.hpp.

+

Definition at line 109 of file geese-meat-likelihood.hpp.

@@ -1895,7 +1895,7 @@

  • Geese
    • -
  • Generated on Mon Oct 2 2023 21:11:12 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_model-members.html b/class_model-members.html index 789d04671..9b0d73098 100644 --- a/class_model-members.html +++ b/class_model-members.html @@ -182,7 +182,7 @@ diff --git a/class_model.html b/class_model.html index b5526a377..10fee5fd2 100644 --- a/class_model.html +++ b/class_model.html @@ -2837,7 +2837,7 @@

  • Model
    • -
  • Generated on Mon Oct 2 2023 21:11:13 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_net_counter_data-members.html b/class_net_counter_data-members.html index 60478ec8c..68dee23a6 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 1e238730b..852c2f603 100644 --- a/class_net_counter_data.html +++ b/class_net_counter_data.html @@ -261,7 +261,7 @@

  • NetCounterData
    • -
  • Generated on Mon Oct 2 2023 21:11:13 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_network_data-members.html b/class_network_data-members.html index beaea16cc..9535605b8 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 6e9d2eaf8..75c2be892 100644 --- a/class_network_data.html +++ b/class_network_data.html @@ -323,7 +323,7 @@

  • NetworkData
    • -
  • Generated on Mon Oct 2 2023 21:11:13 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_node-members.html b/class_node-members.html index 7899e84fb..a9c85ad18 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 e84d3211b..e6c5fbb99 100644 --- a/class_node.html +++ b/class_node.html @@ -687,7 +687,7 @@

  • Node
    • -
  • Generated on Mon Oct 2 2023 21:11:13 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_node_data-members.html b/class_node_data-members.html index 6ded1e79e..27b8ddf29 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 0b2549012..73247a2d7 100644 --- a/class_node_data.html +++ b/class_node_data.html @@ -230,7 +230,7 @@

  • NodeData
    • -
  • Generated on Mon Oct 2 2023 21:11:13 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_phylo_counter_data-members.html b/class_phylo_counter_data-members.html index 0c4cedfae..23794f31c 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 be3c30968..895c4f7dc 100644 --- a/class_phylo_counter_data.html +++ b/class_phylo_counter_data.html @@ -512,7 +512,7 @@

  • PhyloCounterData
    • -
  • Generated on Mon Oct 2 2023 21:11:13 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_phylo_rule_dyn_data-members.html b/class_phylo_rule_dyn_data-members.html index a9a13d3d8..a45ec1a56 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 1b91ec9a5..981c85435 100644 --- a/class_phylo_rule_dyn_data.html +++ b/class_phylo_rule_dyn_data.html @@ -330,7 +330,7 @@

  • PhyloRuleDynData
    • -
  • Generated on Mon Oct 2 2023 21:11:13 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_power_set-members.html b/class_power_set-members.html index c9457458b..4f9d8e7ea 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 d1de61eba..838c4dbcf 100644 --- a/class_power_set.html +++ b/class_power_set.html @@ -845,7 +845,7 @@

  • PowerSet
    • -
  • Generated on Mon Oct 2 2023 21:11:13 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_progress-members.html b/class_progress-members.html index e8acda764..6ff734b72 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 99278c5a6..cd15eed7d 100644 --- a/class_progress.html +++ b/class_progress.html @@ -250,7 +250,7 @@

  • Progress
    • -
  • Generated on Mon Oct 2 2023 21:11:13 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_rule-members.html b/class_rule-members.html index dd649c197..acf7601f4 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 2dd8b2300..5327e1ff0 100644 --- a/class_rule.html +++ b/class_rule.html @@ -452,7 +452,7 @@

  • Rule
    • -
  • Generated on Mon Oct 2 2023 21:11:13 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_rules-members.html b/class_rules-members.html index cedbd3086..657e6b8b0 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 30fda7115..de71b3e26 100644 --- a/class_rules.html +++ b/class_rules.html @@ -617,7 +617,7 @@

  • Rules
    • -
  • Generated on Mon Oct 2 2023 21:11:13 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/class_stats_counter-members.html b/class_stats_counter-members.html index 06749a20b..47a9a2d72 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 1227a28f5..4e854ce9b 100644 --- a/class_stats_counter.html +++ b/class_stats_counter.html @@ -519,7 +519,7 @@

  • StatsCounter
    • -
  • Generated on Mon Oct 2 2023 21:11:13 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 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 a09d20ff2..5682959e1 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 6417e31df..2795f5eeb 100644 --- a/class_support.html +++ b/class_support.html @@ -1277,7 +1277,7 @@

  • Support
    • -
  • Generated on Mon Oct 2 2023 21:11:13 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/classes.html b/classes.html index 6a96de6cd..4294e4fcc 100644 --- a/classes.html +++ b/classes.html @@ -140,7 +140,7 @@ diff --git a/col-bones_8hpp.html b/col-bones_8hpp.html index fe8cc330f..b1fe9d524 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 98560cd1b..33b8134dd 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 62a8e6591..be60111f5 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 6a57f1048..7ea313a8e 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 cc568bab1..ff219e923 100644 --- a/counters-meat_8hpp.html +++ b/counters-meat_8hpp.html @@ -1560,7 +1560,7 @@

  • include
  • barry
  • counters-meat.hpp
    • -
  • Generated on Mon Oct 2 2023 21:11:12 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:58 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 f3494d508..0513eeb6e 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 1246bb6b9..aad941e3e 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 048d5992a..2ac4ec70a 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 aa1d02c8d..1b67cd361 100644 --- a/defm-meat_8hpp.html +++ b/defm-meat_8hpp.html @@ -212,7 +212,7 @@

  • include
  • barry
  • models
  • defm
  • defm-meat.hpp
    • -
  • Generated on Mon Oct 2 2023 21:11:12 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:58 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 75682c685..8c293fbc8 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 66da03904..824468263 100644 --- a/defm-types_8hpp.html +++ b/defm-types_8hpp.html @@ -171,7 +171,7 @@

  • include
  • barry
  • models
  • defm
  • defm-types.hpp
    • -
  • Generated on Mon Oct 2 2023 21:11:12 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:58 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 8265954a9..81a17119b 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 c86c5be2a..d44f52098 100644 --- a/defm_2counters_8hpp.html +++ b/defm_2counters_8hpp.html @@ -326,7 +326,7 @@

  • include
  • barry
  • models
  • defm
  • counters.hpp
    • -
  • Generated on Mon Oct 2 2023 21:11:12 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:58 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 7c0138d00..5a0fefb58 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 f328b0f14..8117fb5a7 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 2c024bbed..2a4486c5f 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 1f4fa1d32..f699c87d3 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 0a80aad3c..9958b1e0b 100644 --- a/dir_000003_000004.html +++ b/dir_000003_000004.html @@ -98,7 +98,7 @@

models → defm Relation

- + @@ -230,7 +230,7 @@

diff --git a/geese-meat-likelihood_8hpp.js b/geese-meat-likelihood_8hpp.js index 52305ee89..997448e9e 100644 --- a/geese-meat-likelihood_8hpp.js +++ b/geese-meat-likelihood_8hpp.js @@ -1,4 +1,4 @@ var geese_meat_likelihood_8hpp = [ - [ "pset_loop", "geese-meat-likelihood_8hpp.html#a8f076f3f2817ecf61ebfbd307062e6b2", null ] + [ "pset_loop", "geese-meat-likelihood_8hpp.html#a226e3a40afafec1f83caf7183e8f97af", null ] ]; \ No newline at end of file diff --git a/geese-meat-likelihood_8hpp_source.html b/geese-meat-likelihood_8hpp_source.html index b7530abe4..de80e0cab 100644 --- a/geese-meat-likelihood_8hpp_source.html +++ b/geese-meat-likelihood_8hpp_source.html @@ -101,7 +101,7 @@
3 
4 #include "geese-bones.hpp"
5 
-
6 inline void pset_loop(
+
6 inline void pset_loop(
7  size_t n,
8  size_t s,
9  size_t nfunctions,
@@ -112,7 +112,7 @@
14  const std::vector<std::vector<bool>> & states,
15  const std::vector< PhyloArray > & psets,
16  const std::vector<double> & psets_stats,
-
17  std::vector< std::vector< size_t > > & locations,
+
17  const std::vector< std::vector< size_t > > & locations,
18  const std::vector<geese::Node *> & node_offspring
19 )
20 {
@@ -171,200 +171,199 @@
73  if (off_mult < 0.0)
74  return;
75 
-
76  // Multiplying by P(x|x_n), the transition probability
-
77  std::vector< double > temp_stats;
-
78  temp_stats.reserve(par0.size());
-
79  for (auto p = 0u; p < par0.size(); ++p)
-
80  temp_stats.push_back(psets_stats[par0.size() * n + p]);
-
81 
-
82  // Use try catch in the following line
-
83  try {
-
84 
-
85  off_mult *= barry::likelihood_(
-
86  &temp_stats[0u],
-
87  par0,
-
88  norm_const_i,
-
89  par0.size(),
-
90  false
-
91  );
-
92 
-
93  } catch (std::exception & e) {
+
76  // Use try catch in the following line
+
77  try {
+
78 
+
79  off_mult *= barry::likelihood_(
+
80  &psets_stats[par0.size() * n],
+
81  par0,
+
82  norm_const_i,
+
83  par0.size(),
+
84  false
+
85  );
+
86 
+
87  } catch (std::exception & e) {
+
88 
+
89  auto err = std::string(e.what());
+
90 
+
91  std::string state_str = "";
+
92  for (const auto & ss : states[s])
+
93  state_str += std::to_string(ss) + " ";
94 
-
95  auto err = std::string(e.what());
-
96 
-
97  std::string state_str = "";
-
98  for (const auto & ss : states[s])
-
99  state_str += std::to_string(ss) + " ";
-
100 
-
101  err = "Error computing the likelihood at node " +
-
102  std::to_string(node_id) + " with state " + state_str +
-
103  ". Error message:\n" +
-
104  err;
-
105 
-
106  throw std::runtime_error(err);
-
107 
-
108  }
-
109 
-
110  // Adding to the total probabilities
-
111  totprob_n[n] = off_mult;
-
112 
-
113 }
-
114 
-
115 inline double Geese::likelihood(
-
116  const std::vector< double > & par,
-
117  bool as_log,
-
118  bool use_reduced_sequence,
-
119  size_t ncores,
-
120  bool no_update_normalizing_constant
-
121 ) {
-
122 
-
123  // Checking whether the model is initialized
-
124  INITIALIZED()
-
125 
-
126  // Splitting the probabilities
-
127  std::vector< double > par0(par.begin(), par.end() - nfunctions);
-
128  std::vector< double > par_root(par.end() - nfunctions, par.end());
+
95  err = "Error computing the likelihood at node " +
+
96  std::to_string(node_id) + " with state " + state_str +
+
97  ". Error message:\n" +
+
98  err;
+
99 
+
100  throw std::runtime_error(err);
+
101 
+
102  }
+
103 
+
104  // Adding to the total probabilities
+
105  totprob_n[n] = off_mult;
+
106 
+
107 }
+
108 
+
109 inline double Geese::likelihood(
+
110  const std::vector< double > & par,
+
111  bool as_log,
+
112  bool use_reduced_sequence,
+
113  size_t ncores,
+
114  bool no_update_normalizing_constant
+
115 ) {
+
116 
+
117  // Checking whether the model is initialized
+
118  INITIALIZED()
+
119 
+
120  // Splitting the probabilities
+
121  std::vector< double > par0(par.begin(), par.end() - nfunctions);
+
122  std::vector< double > par_root(par.end() - nfunctions, par.end());
+
123 
+
124  // Scaling root
+
125  for (auto& p : par_root)
+
126  p = std::exp(p)/(std::exp(p) + 1);
+
127 
+
128  double ll = 0.0;
129 
-
130  // Scaling root
-
131  for (auto& p : par_root)
-
132  p = std::exp(p)/(std::exp(p) + 1);
+
130  // Updating normalizing constants
+
131  if (!no_update_normalizing_constant)
+
132  model->update_normalizing_constants(par0, ncores);
133 
-
134  double ll = 0.0;
-
135 
-
136  // Updating normalizing constants
-
137  if (!no_update_normalizing_constant)
-
138  model->update_normalizing_constants(par0, ncores);
-
139 
-
140  // Following the prunning sequence
-
141  const std::vector< size_t > & preseq = use_reduced_sequence ?
-
142  this->reduced_sequence : this->sequence;
+
134  // Following the prunning sequence
+
135  const std::vector< size_t > & preseq = use_reduced_sequence ?
+
136  this->reduced_sequence : this->sequence;
+
137 
+
138  // The first time it is called, it need to generate the corresponding
+
139  // hashes of the columns so it is fast to access then (saves time
+
140  // hashing and looking in the map.)
+
141  const auto & arrays2support = *(model->get_arrays2support());
+
142  const auto & normconst = model->get_normalizing_constants();
143 
-
144  // The first time it is called, it need to generate the corresponding
-
145  // hashes of the columns so it is fast to access then (saves time
-
146  // hashing and looking in the map.)
-
147  const auto & arrays2support = *(model->get_arrays2support());
-
148  const auto & normconst = model->get_normalizing_constants();
-
149 
-
150  for (auto& i : preseq)
-
151  {
-
152 
-
153  // We cannot compute probability at the leaf, we need to continue
-
154  if (this->nodes[i].is_leaf())
-
155  continue;
-
156 
-
157  // Since we are using this a lot...
-
158  Node & node = nodes[i];
-
159  const size_t node_id = node.id;
-
160 
-
161  // Iterating through states
-
162  for (size_t s = 0u; s < states.size(); ++s)
-
163  {
-
164 
-
165  // Starting the prob
-
166  size_t array_id = node.narray[s];
-
167  size_t support_id = arrays2support[array_id];
-
168  double norm_const_i = normconst[support_id];
-
169 
-
170  // Retrieving the sets of arrays
-
171  const std::vector< PhyloArray > & psets =
-
172  *(model->get_pset(array_id));
-
173 
-
174  const std::vector<double> & psets_stats =
-
175  *(model->get_pset_stats(array_id));
-
176 
-
177  std::vector< std::vector< size_t > > & locations = pset_loc[support_id];
-
178 
-
179  // Making sure parallelization makes sense
-
180  if (psets.size() < 1000)
-
181  ncores = 1u;
-
182 
-
183  // Summation over all possible values of X
-
184  const auto & node_offspring = node.offspring;
-
185  std::vector< double > totprob_n(psets.size(), 0.0);
-
186  #if defined(_OPENMP) || defined(__OPENMP)
-
187  if (ncores > 1u)
-
188  {
-
189  #pragma omp parallel for num_threads(ncores) \
-
190  shared(\
-
191  locations, psets, psets_stats, totprob_n, node, states,\
-
192  par0, node_offspring, nfunctions, array_id, norm_const_i, \
-
193  s, node_id) default(none)
-
194  for (size_t n = 0u; n < psets.size(); ++n)
-
195  {
-
196  pset_loop(
-
197  n, s, nfunctions, node_id, norm_const_i, totprob_n,
-
198  par0, states, psets, psets_stats, locations,
-
199  node_offspring
-
200  );
-
201  }
-
202  } else {
-
203  for (size_t n = 0u; n < psets.size(); ++n)
-
204  {
-
205  pset_loop(
-
206  n, s, nfunctions, node_id, norm_const_i, totprob_n,
-
207  par0, states, psets, psets_stats, locations,
-
208  node_offspring
-
209  );
-
210  }
-
211  }
-
212  #else
-
213  for (size_t n = 0u; n < psets.size(); ++n)
-
214  {
-
215  pset_loop(
-
216  n, s, nfunctions, node_id, norm_const_i, totprob_n,
-
217  par0, states, psets, psets_stats, locations,
-
218  node_offspring
-
219  );
-
220  }
-
221  #endif
-
222 
-
223 
-
224  // Setting the probability at the node
-
225  node.subtree_prob[s] = 0.0;
-
226  for (size_t n = 0u; n < psets.size(); ++n)
-
227  node.subtree_prob[s] += totprob_n[n];
-
228 
-
229  }
-
230 
-
231  // All probabilities should be completed at this point
-
232  if (node.parent == nullptr)
-
233  {
-
234 
-
235  for (size_t s = 0u; s < states.size(); ++s)
-
236  {
-
237 
-
238  double tmpll = 1.0;
-
239 
-
240  for (auto k = 0u; k < nfunctions; ++k)
-
241  {
-
242 
-
243  tmpll *= states[s][k] ? par_root[k] : (1 - par_root[k]);
-
244 
-
245  }
-
246 
-
247  ll += tmpll * node.subtree_prob[s];
-
248 
-
249  }
-
250  }
-
251 
-
252  }
-
253 
-
254  // In the case that the sequence is empty, then it means
-
255  // that we are looking at a completely unnanotated tree,
-
256  // thus the likelihood should be one
-
257  if (preseq.size() == 0u)
-
258  return as_log ? -std::numeric_limits<double>::infinity() : 1.0;
+
144  for (auto& i : preseq)
+
145  {
+
146 
+
147  // We cannot compute probability at the leaf, we need to continue
+
148  if (this->nodes[i].is_leaf())
+
149  continue;
+
150 
+
151  // Since we are using this a lot...
+
152  Node & node = nodes[i];
+
153  const size_t node_id = node.id;
+
154 
+
155  // Iterating through states
+
156  for (size_t s = 0u; s < states.size(); ++s)
+
157  {
+
158 
+
159  // Starting the prob
+
160  size_t array_id = node.narray[s];
+
161  size_t support_id = arrays2support[array_id];
+
162  double norm_const_i = normconst[support_id];
+
163 
+
164  // Retrieving the sets of arrays
+
165  const std::vector< PhyloArray > & psets =
+
166  *(model->get_pset(array_id));
+
167 
+
168  const std::vector<double> & psets_stats =
+
169  *(model->get_pset_stats(array_id));
+
170 
+
171  std::vector< std::vector< size_t > > & locations = pset_loc[support_id];
+
172 
+
173  // Making sure parallelization makes sense
+
174  if (psets.size() < 1000)
+
175  ncores = 1u;
+
176 
+
177  // Summation over all possible values of X
+
178  const auto & node_offspring = node.offspring;
+
179  std::vector< double > totprob_n(psets.size(), 0.0);
+
180  #if defined(_OPENMP) || defined(__OPENMP)
+
181  if (ncores > 1u)
+
182  {
+
183  #pragma omp parallel for num_threads(ncores) \
+
184  shared(\
+
185  locations, psets, psets_stats, totprob_n, node, states,\
+
186  par0, node_offspring, nfunctions, array_id, norm_const_i, \
+
187  s, node_id) default(none)
+
188  for (size_t n = 0u; n < psets.size(); ++n)
+
189  {
+
190  pset_loop(
+
191  n, s, nfunctions, node_id, norm_const_i, totprob_n,
+
192  par0, states, psets, psets_stats, locations,
+
193  node_offspring
+
194  );
+
195  }
+
196  } else {
+
197  for (size_t n = 0u; n < psets.size(); ++n)
+
198  {
+
199  pset_loop(
+
200  n, s, nfunctions, node_id, norm_const_i, totprob_n,
+
201  par0, states, psets, psets_stats, locations,
+
202  node_offspring
+
203  );
+
204  }
+
205  }
+
206  #else
+
207  for (size_t n = 0u; n < psets.size(); ++n)
+
208  {
+
209  pset_loop(
+
210  n, s, nfunctions, node_id, norm_const_i, totprob_n,
+
211  par0, states, psets, psets_stats, locations,
+
212  node_offspring
+
213  );
+
214  }
+
215  #endif
+
216 
+
217 
+
218  // Setting the probability at the node
+
219  node.subtree_prob[s] = 0.0;
+
220  auto & nsp = node.subtree_prob[s];
+
221  #if defined(_OPENMP) || defined(__OPENMP)
+
222  #pragma omp simd reduction(+:nsp)
+
223  #endif
+
224  for (size_t n = 0u; n < psets.size(); ++n)
+
225  nsp += totprob_n[n];
+
226 
+
227 
+
228  }
+
229 
+
230  // All probabilities should be completed at this point
+
231  if (node.parent == nullptr)
+
232  {
+
233 
+
234  for (size_t s = 0u; s < states.size(); ++s)
+
235  {
+
236 
+
237  double tmpll = 1.0;
+
238 
+
239  for (auto k = 0u; k < nfunctions; ++k)
+
240  {
+
241 
+
242  tmpll *= states[s][k] ? par_root[k] : (1 - par_root[k]);
+
243 
+
244  }
+
245 
+
246  ll += tmpll * node.subtree_prob[s];
+
247 
+
248  }
+
249  }
+
250 
+
251  }
+
252 
+
253  // In the case that the sequence is empty, then it means
+
254  // that we are looking at a completely unnanotated tree,
+
255  // thus the likelihood should be one
+
256  if (preseq.size() == 0u)
+
257  return as_log ? -std::numeric_limits<double>::infinity() : 1.0;
+
258 
259 
-
260 
-
261  return as_log ? std::log(ll) : ll;
-
262 
-
263 }
-
264 #endif
+
260  return as_log ? std::log(ll) : ll;
+
261 
+
262 }
+
263 #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, size_t ncores=1u, bool no_update_normalizing_constant=false)
Definition: geese-meat-likelihood.hpp:115
+
Geese::likelihood
double likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u, bool no_update_normalizing_constant=false)
Definition: geese-meat-likelihood.hpp:109
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
@@ -377,7 +376,7 @@
i
size_t i
Definition: counters-meat.hpp:83
INITIALIZED
#define INITIALIZED()
Definition: geese-bones.hpp:22
-
pset_loop
void pset_loop(size_t n, size_t s, size_t nfunctions, const size_t node_id, double norm_const_i, std::vector< double > &totprob_n, const std::vector< double > &par0, const std::vector< std::vector< bool >> &states, const std::vector< PhyloArray > &psets, const std::vector< double > &psets_stats, std::vector< std::vector< size_t > > &locations, const std::vector< geese::Node * > &node_offspring)
Definition: geese-meat-likelihood.hpp:6
+
pset_loop
void pset_loop(size_t n, size_t s, size_t nfunctions, const size_t node_id, double norm_const_i, std::vector< double > &totprob_n, const std::vector< double > &par0, const std::vector< std::vector< bool >> &states, const std::vector< PhyloArray > &psets, const std::vector< double > &psets_stats, const std::vector< std::vector< size_t > > &locations, const std::vector< geese::Node * > &node_offspring)
Definition: geese-meat-likelihood.hpp:6
likelihood_
double likelihood_(const double *stats_target, const std::vector< double > &params, const double normalizing_constant, size_t n_params, bool log_=false)
Definition: model-meat.hpp:90
@@ -385,7 +384,7 @@ diff --git a/geese-meat-likelihood__exhaust_8hpp.html b/geese-meat-likelihood__exhaust_8hpp.html index 0c43e79bb..81eaab450 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 b2451acf1..33ec71e5c 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 7eaee121e..0def2e05f 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 0417a12bf..e4fa4313d 100644 --- a/geese-meat-predict_8hpp_source.html +++ b/geese-meat-predict_8hpp_source.html @@ -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, size_t ncores=1u, bool no_update_normalizing_constant=false)
Definition: geese-meat-likelihood.hpp:115
+
Geese::likelihood
double likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u, bool no_update_normalizing_constant=false)
Definition: geese-meat-likelihood.hpp:109
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 014dd5c51..63b68e415 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 f586238d4..f9246a14c 100644 --- a/geese-meat-predict__exhaust_8hpp_source.html +++ b/geese-meat-predict__exhaust_8hpp_source.html @@ -268,7 +268,7 @@
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::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::likelihood
double likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u, bool no_update_normalizing_constant=false)
Definition: geese-meat-likelihood.hpp:115
+
Geese::likelihood
double likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u, bool no_update_normalizing_constant=false)
Definition: geese-meat-likelihood.hpp:109
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
Geese::predict_exhaust
std::vector< std::vector< double > > predict_exhaust(const std::vector< double > &par)
Definition: geese-meat-predict_exhaust.hpp:5
@@ -294,7 +294,7 @@ diff --git a/geese-meat-predict__sim_8hpp.html b/geese-meat-predict__sim_8hpp.html index 77934cd56..313a793d8 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 073b94173..66af3504c 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 ec38ce803..c77172de0 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 341d4fd22..b7faa06ec 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 5f2ba623d..080cd07ef 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 cca801745..8b7e683ec 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 173d116e9..56a2cca43 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 0e16a4c87..470a954d6 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 d2420f2f5..a6c804093 100644 --- a/geese-types_8hpp.html +++ b/geese-types_8hpp.html @@ -384,7 +384,7 @@

  • include
  • barry
  • models
  • geese
  • geese-types.hpp
    • -
  • Generated on Mon Oct 2 2023 21:11:12 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:58 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/geese-types_8hpp_source.html b/geese-types_8hpp_source.html index 8c3d2019a..7a3a86c40 100644 --- a/geese-types_8hpp_source.html +++ b/geese-types_8hpp_source.html @@ -283,7 +283,7 @@ diff --git a/geese_2counters_8hpp.html b/geese_2counters_8hpp.html index 8fcac93bf..dfa25ed4f 100644 --- a/geese_2counters_8hpp.html +++ b/geese_2counters_8hpp.html @@ -215,7 +215,7 @@ diff --git a/geese_2counters_8hpp_source.html b/geese_2counters_8hpp_source.html index 11c468f75..ef0092ee8 100644 --- a/geese_2counters_8hpp_source.html +++ b/geese_2counters_8hpp_source.html @@ -2148,7 +2148,7 @@ diff --git a/geese_8hpp.html b/geese_8hpp.html index 0f74678c8..c65a967a9 100644 --- a/geese_8hpp.html +++ b/geese_8hpp.html @@ -148,7 +148,7 @@ diff --git a/geese_8hpp_source.html b/geese_8hpp_source.html index dc1e9c85c..3b2111f73 100644 --- a/geese_8hpp_source.html +++ b/geese_8hpp_source.html @@ -146,7 +146,7 @@ diff --git a/globals.html b/globals.html index a2cc794bb..08cc45dde 100644 --- a/globals.html +++ b/globals.html @@ -104,7 +104,7 @@

- a -

  • include
  • barry
  • models
    • -
  • Generated on Mon Oct 2 2023 21:11:13 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 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 67cccfd61..17099da1d 100644 --- a/dir_000003_000005.html +++ b/dir_000003_000005.html @@ -98,7 +98,7 @@

models → geese Relation

  • include
  • barry
  • models
    • -
  • Generated on Mon Oct 2 2023 21:11:13 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Mon Oct 2 2023 23:04:59 for barry: Your go-to motif accountant by doxygen 1.9.1
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Transition effects

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                                                                                          diff --git a/geese-bones_8hpp.html b/geese-bones_8hpp.html index 76e4eba09..b79139677 100644 --- a/geese-bones_8hpp.html +++ b/geese-bones_8hpp.html @@ -291,7 +291,7 @@

                                                                                          • include
                                                                                          • barry
                                                                                          • models
                                                                                          • geese
                                                                                          • geese-bones.hpp
                                                                                            • -
                                                                                          • Generated on Mon Oct 2 2023 21:11:12 for barry: Your go-to motif accountant by doxygen 1.9.1
                                                                                            • +
                                                                                          • Generated on Mon Oct 2 2023 23:04:58 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 c0dcb3307..e106a6fb0 100644 --- a/geese-bones_8hpp_source.html +++ b/geese-bones_8hpp_source.html @@ -367,7 +367,7 @@
                                                                                          Geese::initialized
                                                                                          bool initialized
                                                                                          Definition: geese-bones.hpp:141
                                                                                          Geese::calc_sequence
                                                                                          void calc_sequence(Node *n=nullptr)
                                                                                          Definition: geese-meat.hpp:314
                                                                                          Geese::inherit_support
                                                                                          void inherit_support(const Geese &model_, bool delete_support_=false)
                                                                                          Definition: geese-meat.hpp:257
                                                                                          -
                                                                                          Geese::likelihood
                                                                                          double likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u, bool no_update_normalizing_constant=false)
                                                                                          Definition: geese-meat-likelihood.hpp:115
                                                                                          +
                                                                                          Geese::likelihood
                                                                                          double likelihood(const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u, bool no_update_normalizing_constant=false)
                                                                                          Definition: geese-meat-likelihood.hpp:109
                                                                                          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::simulate
                                                                                          std::vector< std::vector< size_t > > simulate(const std::vector< double > &par)
                                                                                          Definition: geese-meat-simulate.hpp:8
                                                                                          Geese::nannotations
                                                                                          std::vector< size_t > nannotations() const noexcept
                                                                                          Number of annotations.
                                                                                          Definition: geese-meat.hpp:471
                                                                                          @@ -404,7 +404,7 @@ diff --git a/geese-meat-constructors_8hpp.html b/geese-meat-constructors_8hpp.html index 064211375..08cd6b8db 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 9b39a0401..436991c5b 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 a704484e3..723000933 100644 --- a/geese-meat-likelihood_8hpp.html +++ b/geese-meat-likelihood_8hpp.html @@ -122,12 +122,12 @@

- - + +

Functions

void pset_loop (size_t n, size_t s, size_t nfunctions, const size_t node_id, double norm_const_i, std::vector< double > &totprob_n, const std::vector< double > &par0, const std::vector< std::vector< bool >> &states, const std::vector< PhyloArray > &psets, const std::vector< double > &psets_stats, std::vector< std::vector< size_t > > &locations, const std::vector< geese::Node * > &node_offspring)
 
void pset_loop (size_t n, size_t s, size_t nfunctions, const size_t node_id, double norm_const_i, std::vector< double > &totprob_n, const std::vector< double > &par0, const std::vector< std::vector< bool >> &states, const std::vector< PhyloArray > &psets, const std::vector< double > &psets_stats, const std::vector< std::vector< size_t > > &locations, const std::vector< geese::Node * > &node_offspring)
 

Function Documentation

- -

◆ pset_loop()

+ +

◆ pset_loop()

@@ -198,7 +198,7 @@

std::vector< std::vector< size_t > > & const std::vector< std::vector< size_t > > &  locations,