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diff --git a/barraydense-meat-operators_8hpp_source.html b/barraydense-meat-operators_8hpp_source.html index 78de1ac66..030191d14 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 b8bf376f7..fc7d41653 100644 --- a/barraydense-meat_8hpp.html +++ b/barraydense-meat_8hpp.html @@ -252,7 +252,7 @@

  • include
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diff --git a/barraydense-meat_8hpp_source.html b/barraydense-meat_8hpp_source.html index d58b317f6..143dac985 100644 --- a/barraydense-meat_8hpp_source.html +++ b/barraydense-meat_8hpp_source.html @@ -1199,7 +1199,7 @@ diff --git a/barraydensecell-bones_8hpp.html b/barraydensecell-bones_8hpp.html index cd8336c48..597ed67ed 100644 --- a/barraydensecell-bones_8hpp.html +++ b/barraydensecell-bones_8hpp.html @@ -158,7 +158,7 @@

  • include
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diff --git a/barraydensecell-bones_8hpp_source.html b/barraydensecell-bones_8hpp_source.html index e11c95996..d1e19d618 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 557902206..f0ff68200 100644 --- a/barraydensecell-meat_8hpp.html +++ b/barraydensecell-meat_8hpp.html @@ -152,7 +152,7 @@

  • include
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  • barraydensecell-meat.hpp
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  • Generated on Fri Sep 22 2023 22:26:43 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 1ff0c22c0..f96d1be0f 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 0092caf3f..574d7624a 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 a9925e947..e3a1caded 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 02c4a2a29..8c4e8e753 100644 --- a/barraydenserow-bones_8hpp.html +++ b/barraydenserow-bones_8hpp.html @@ -216,7 +216,7 @@

  • include
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  • Generated on Fri Sep 22 2023 22:26:43 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 96370adb0..f83a2704e 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 40533b5b0..7f19c71db 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 1109c64dd..3a1982fb1 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 6b68a920c..dd6ddab25 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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  • Generated on Fri Sep 22 2023 22:26:43 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 7750e9f04..6cd8ff6d5 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 eab170688..ff11e724e 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 2a4a3d314..194c898f9 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 bfae049fd..fa6d112f2 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 b9b4025f4..9bbb102c2 100644 --- a/barrayvector-meat_8hpp_source.html +++ b/barrayvector-meat_8hpp_source.html @@ -446,7 +446,7 @@ diff --git a/barry-configuration_8hpp.html b/barry-configuration_8hpp.html index 272f7c185..ba475a125 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 d4b0fad0d..5cae094c2 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 3749a2264..d75ab9f67 100644 --- a/barry-debug_8hpp.html +++ b/barry-debug_8hpp.html @@ -139,7 +139,7 @@

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diff --git a/barry-debug_8hpp_source.html b/barry-debug_8hpp_source.html index 8d0e8f581..1bb524462 100644 --- a/barry-debug_8hpp_source.html +++ b/barry-debug_8hpp_source.html @@ -146,7 +146,7 @@ diff --git a/barry-macros_8hpp.html b/barry-macros_8hpp.html index bd73f2734..c9deef151 100644 --- a/barry-macros_8hpp.html +++ b/barry-macros_8hpp.html @@ -214,7 +214,7 @@

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diff --git a/barry-macros_8hpp_source.html b/barry-macros_8hpp_source.html index ddd8a1db0..8004616a8 100644 --- a/barry-macros_8hpp_source.html +++ b/barry-macros_8hpp_source.html @@ -114,7 +114,7 @@ diff --git a/barry_8hpp.html b/barry_8hpp.html index e1a6c5244..5118093bb 100644 --- a/barry_8hpp.html +++ b/barry_8hpp.html @@ -402,7 +402,7 @@

  • include
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  • barry.hpp
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diff --git a/barry_8hpp_source.html b/barry_8hpp_source.html index a34741b84..9efe0123e 100644 --- a/barry_8hpp_source.html +++ b/barry_8hpp_source.html @@ -233,7 +233,7 @@ diff --git a/cell-bones_8hpp.html b/cell-bones_8hpp.html index 79d29711a..69f6f6adb 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 ddc218da6..1175a0e2f 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 76e1b303d..c4c423fa3 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 794d50cc1..789caeabf 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 f1c3066be..46c02a9ea 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 ec935ecf3..4dd7f81d9 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 778d825c3..fd0dc5340 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 7508f32bd..a586e7cdf 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 cd5e7e35e..4aa57accf 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 d0580a18d..dde36c7b2 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 1250f43e5..7924f11ac 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 8170139df..01b1bfbfa 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 26602e21b..ae2ec7ae7 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 888df9a2d..c910b49fe 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 db29fde51..41cbd8b35 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 9602a4e27..04e39d697 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 30dd10d14..dd943492d 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 60d2813f9..873b1b0ef 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 9a7cba1c7..26f7aba4a 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 a95088a4e..fcb6a4426 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 dd6660463..07879b0b0 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 660f153f6..85af466d5 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 c529573ee..6544e4c5e 100644 --- a/class_b_array_dense_row__const.html +++ b/class_b_array_dense_row__const.html @@ -351,7 +351,7 @@

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diff --git a/class_b_array_row-members.html b/class_b_array_row-members.html index efe904efd..a63c76a85 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 85b810107..62826e12f 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 253d9ae90..64039cad3 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 7fb4f0371..5df7176db 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 2248d4f7f..c0ac27263 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 408efe531..eb4ee8c0d 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 d6c6afbbe..c27c978a9 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 660ce7215..576169087 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 c62fd6625..27333c746 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 ccb618649..1c168a5ce 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 efcf4f144..3ccd5ce25 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 4d1ffd3d5..76e517b42 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 e760dd50f..d93053222 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 e9797c037..daaed1be7 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 db20463e1..d087ac6e4 100644 --- a/class_counter.html +++ b/class_counter.html @@ -679,7 +679,7 @@

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diff --git a/class_d_e_f_m-members.html b/class_d_e_f_m-members.html index 69150bf79..ed39a7b0e 100644 --- a/class_d_e_f_m-members.html +++ b/class_d_e_f_m-members.html @@ -114,18 +114,17 @@ get_Y_names() constDEFMinline init()DEFMinline is_motif()DEFMinline - likelihood(std::vector< double > &par, bool as_log=false)DEFM - logodds(const std::vector< double > &par, size_t i, size_t j)DEFMinline - motif_census(std::vector< size_t > idx)DEFMinline - print() constDEFMinline - set_names(std::vector< std::string > Y_names_, std::vector< std::string > X_names_)DEFMinline - simulate(std::vector< double > par, int *y_out)DEFMinline + logodds(const std::vector< double > &par, size_t i, size_t j)DEFMinline + motif_census(std::vector< size_t > idx)DEFMinline + print() constDEFMinline + set_names(std::vector< std::string > Y_names_, std::vector< std::string > X_names_)DEFMinline + simulate(std::vector< double > par, int *y_out)DEFMinline diff --git a/class_d_e_f_m.html b/class_d_e_f_m.html index 4689b1e0a..097ffabd7 100644 --- a/class_d_e_f_m.html +++ b/class_d_e_f_m.html @@ -128,8 +128,6 @@   void init ()   -double likelihood (std::vector< double > &par, bool as_log=false) -  void simulate (std::vector< double > par, int *y_out)   size_t get_n_y () const @@ -626,34 +624,6 @@

Definition at line 438 of file defm-meat.hpp.

- - - -

◆ likelihood()

- -
-
- - - - - - - - - - - - - - - - - - -
double DEFM::likelihood (std::vector< double > & par,
bool as_log = false 
)
-
-
@@ -841,7 +811,7 @@

  • DEFM
    • -
  • Generated on Tue Sep 19 2023 19:46:43 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Sep 22 2023 22:26:43 for barry: Your go-to motif accountant by doxygen 1.9.1
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  • Entries
    • -
  • Generated on Tue Sep 19 2023 19:46:43 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
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  • Flock
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diff --git a/class_model-members.html b/class_model-members.html index 0227db835..8050cf57a 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 6942a5dc9..eaa870ca5 100644 --- a/class_model.html +++ b/class_model.html @@ -2476,7 +2476,7 @@

  • Model
    • -
  • Generated on Tue Sep 19 2023 19:46:43 for barry: Your go-to motif accountant by doxygen 1.9.1
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  • Node
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  • NodeData
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  • PowerSet
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  • Progress
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diff --git a/class_rule-members.html b/class_rule-members.html index a70fd7e81..2ae7cc063 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 26c947472..bcc42df69 100644 --- a/class_rule.html +++ b/class_rule.html @@ -452,7 +452,7 @@

  • Rule
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diff --git a/class_rules-members.html b/class_rules-members.html index d78e51d58..8384451e7 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 28d444b18..94ae6c376 100644 --- a/class_rules.html +++ b/class_rules.html @@ -617,7 +617,7 @@

  • Rules
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  • Generated on Tue Sep 19 2023 19:46:43 for barry: Your go-to motif accountant by doxygen 1.9.1
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diff --git a/class_stats_counter-members.html b/class_stats_counter-members.html index 5ae4ec0d2..0320ad38c 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 fc8759360..ad995cb07 100644 --- a/class_stats_counter.html +++ b/class_stats_counter.html @@ -519,7 +519,7 @@

  • StatsCounter
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  • Support
    • -
  • Generated on Tue Sep 19 2023 19:46:43 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Sep 22 2023 22:26:43 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/classes.html b/classes.html index 3f919413e..4571d69a6 100644 --- a/classes.html +++ b/classes.html @@ -140,7 +140,7 @@ diff --git a/col-bones_8hpp.html b/col-bones_8hpp.html index 6a0475d62..f4ba32d52 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 1ce5a350c..afd92ed28 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 239f8c3a3..66fb95ac8 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 adc3dc5f0..b59e59d8c 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 2194da846..f12797316 100644 --- a/counters-meat_8hpp.html +++ b/counters-meat_8hpp.html @@ -1568,7 +1568,7 @@

  • include
  • barry
  • counters-meat.hpp
    • -
  • Generated on Tue Sep 19 2023 19:46:42 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Sep 22 2023 22:26:43 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 43e43dbec..c085b3783 100644 --- a/counters-meat_8hpp_source.html +++ b/counters-meat_8hpp_source.html @@ -415,7 +415,7 @@ diff --git a/defm-bones_8hpp.html b/defm-bones_8hpp.html index f976a5f89..a5ea79da6 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 3cb6662ce..ffbdf10da 100644 --- a/defm-bones_8hpp_source.html +++ b/defm-bones_8hpp_source.html @@ -145,47 +145,46 @@
52 
53  void init();
54 
-
55  double likelihood(std::vector< double > & par, bool as_log = false);
-
56  void simulate(std::vector< double > par, int * y_out);
-
57 
-
58  size_t get_n_y() const;
-
59  size_t get_n_obs() const;
-
60  size_t get_n_covars() const;
-
61  size_t get_m_order() const;
-
62  size_t get_n_rows() const;
-
63 
-
64  const int * get_Y() const;
-
65  const int * get_ID() const;
-
66  const double * get_X() const;
-
67 
-
68  barry::FreqTable<int> motif_census(
-
69  std::vector< size_t > idx
-
70  );
-
71 
-
72  std::vector< double > logodds(
-
73  const std::vector< double > & par,
-
74  size_t i,
-
75  size_t j
-
76  );
-
77 
-
78  void set_names(
-
79  std::vector< std::string > Y_names_,
-
80  std::vector< std::string > X_names_
-
81  );
-
82 
-
83  const std::vector< std::string > & get_Y_names() const;
-
84  const std::vector< std::string > & get_X_names() const;
-
85 
-
86  void print() const;
-
87 
-
88  std::vector< bool > is_motif();
-
89 
-
90  bool get_column_major() const noexcept;
-
91 
-
92 };
-
93 
-
94 #endif
-
95 
+
55  void simulate(std::vector< double > par, int * y_out);
+
56 
+
57  size_t get_n_y() const;
+
58  size_t get_n_obs() const;
+
59  size_t get_n_covars() const;
+
60  size_t get_m_order() const;
+
61  size_t get_n_rows() const;
+
62 
+
63  const int * get_Y() const;
+
64  const int * get_ID() const;
+
65  const double * get_X() const;
+
66 
+
67  barry::FreqTable<int> motif_census(
+
68  std::vector< size_t > idx
+
69  );
+
70 
+
71  std::vector< double > logodds(
+
72  const std::vector< double > & par,
+
73  size_t i,
+
74  size_t j
+
75  );
+
76 
+
77  void set_names(
+
78  std::vector< std::string > Y_names_,
+
79  std::vector< std::string > X_names_
+
80  );
+
81 
+
82  const std::vector< std::string > & get_Y_names() const;
+
83  const std::vector< std::string > & get_X_names() const;
+
84 
+
85  void print() const;
+
86 
+
87  std::vector< bool > is_motif();
+
88 
+
89  bool get_column_major() const noexcept;
+
90 
+
91 };
+
92 
+
93 #endif
+
94 
DEFM::is_motif
std::vector< bool > is_motif()
Definition: defm-meat.hpp:438
DEFM::get_n_covars
size_t get_n_covars() const
Definition: defm-meat.hpp:289
@@ -194,7 +193,6 @@
DEFM::init
void init()
Definition: defm-meat.hpp:214
DEFM::get_m_order
size_t get_m_order() const
Definition: defm-meat.hpp:294
DEFM::set_names
void set_names(std::vector< std::string > Y_names_, std::vector< std::string > X_names_)
Definition: defm-meat.hpp:400
-
DEFM::likelihood
double likelihood(std::vector< double > &par, bool as_log=false)
DEFM::get_n_rows
size_t get_n_rows() const
Definition: defm-meat.hpp:299
DEFM::get_ID
const int * get_ID() const
Definition: defm-meat.hpp:309
DEFM::get_model
DEFMModel & get_model()
Definition: defm-bones.hpp:49
@@ -218,7 +216,7 @@ diff --git a/defm-meat_8hpp.html b/defm-meat_8hpp.html index b0d394360..af3433361 100644 --- a/defm-meat_8hpp.html +++ b/defm-meat_8hpp.html @@ -213,7 +213,7 @@

  • include
  • barry
  • models
  • defm
  • defm-meat.hpp
    • -
  • Generated on Tue Sep 19 2023 19:46:42 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Sep 22 2023 22:26:43 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 740ba0cf8..c68bf3883 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 4a0d29d94..5ba3ae3a2 100644 --- a/defm-types_8hpp.html +++ b/defm-types_8hpp.html @@ -171,7 +171,7 @@

  • include
  • barry
  • models
  • defm
  • defm-types.hpp
    • -
  • Generated on Tue Sep 19 2023 19:46:42 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Sep 22 2023 22:26:43 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 c3325ee38..b6f3e21d0 100644 --- a/defm-types_8hpp_source.html +++ b/defm-types_8hpp_source.html @@ -306,7 +306,7 @@ diff --git a/defm_2counters_8hpp.html b/defm_2counters_8hpp.html index 6fbdc0261..98ca5f7c0 100644 --- a/defm_2counters_8hpp.html +++ b/defm_2counters_8hpp.html @@ -307,16 +307,16 @@

Value:
(\
-
((a) == 0) ? "\u2080" : (\
-
((a) == 1) ? "\u2081" : (\
-
((a) == 2) ? "\u2082" : (\
-
((a) == 3) ? "\u2083" : (\
-
((a) == 4) ? "\u2084" : (\
-
((a) == 5) ? "\u2085" : (\
-
((a) == 6) ? "\u2086" : (\
-
((a) == 7) ? "\u2087" : (\
-
((a) == 8) ? "\u2088" : \
-
"\u2089"))))))))\
+
((a) == 0) ? u8"\u2080" : (\
+
((a) == 1) ? u8"\u2081" : (\
+
((a) == 2) ? u8"\u2082" : (\
+
((a) == 3) ? u8"\u2083" : (\
+
((a) == 4) ? u8"\u2084" : (\
+
((a) == 5) ? u8"\u2085" : (\
+
((a) == 6) ? u8"\u2086" : (\
+
((a) == 7) ? u8"\u2087" : (\
+
((a) == 8) ? u8"\u2088" : \
+
u8"\u2089"))))))))\
)
@@ -327,7 +327,7 @@

  • include
  • barry
  • models
  • defm
  • counters.hpp
    • -
  • Generated on Tue Sep 19 2023 19:46:42 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Sep 22 2023 22:26:43 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 06eeba98f..fe77e00f1 100644 --- a/defm_2counters_8hpp_source.html +++ b/defm_2counters_8hpp_source.html @@ -499,16 +499,16 @@
439  #else
440  #define UNI_SUB(a) \
441  (\
-
442  ((a) == 0) ? "\u2080" : (\
-
443  ((a) == 1) ? "\u2081" : (\
-
444  ((a) == 2) ? "\u2082" : (\
-
445  ((a) == 3) ? "\u2083" : (\
-
446  ((a) == 4) ? "\u2084" : (\
-
447  ((a) == 5) ? "\u2085" : (\
-
448  ((a) == 6) ? "\u2086" : (\
-
449  ((a) == 7) ? "\u2087" : (\
-
450  ((a) == 8) ? "\u2088" : \
-
451  "\u2089"))))))))\
+
442  ((a) == 0) ? u8"\u2080" : (\
+
443  ((a) == 1) ? u8"\u2081" : (\
+
444  ((a) == 2) ? u8"\u2082" : (\
+
445  ((a) == 3) ? u8"\u2083" : (\
+
446  ((a) == 4) ? u8"\u2084" : (\
+
447  ((a) == 5) ? u8"\u2085" : (\
+
448  ((a) == 6) ? u8"\u2086" : (\
+
449  ((a) == 7) ? u8"\u2087" : (\
+
450  ((a) == 8) ? u8"\u2088" : \
+
451  u8"\u2089"))))))))\
452  )
453  #endif
454 
@@ -538,7 +538,7 @@
478  #ifdef BARRY_WITH_LATEX
479  name += (motif(i,j) < 0 ? "^-" : "^+");
480  #else
-
481  name += (motif(i,j) < 0 ? "\u207B" : "\u207A");
+
481  name += (motif(i,j) < 0 ? u8"\u207B" : u8"\u207A");
482  #endif
483 
484  }
@@ -580,7 +580,7 @@
520  #ifdef BARRY_WITH_LATEX
521  name += (motif(m_order, j) < 0 ? "^-" : "^+" );
522  #else
-
523  name += (motif(m_order, j) < 0 ? "\u207B" : "\u207A" );
+
523  name += (motif(m_order, j) < 0 ? u8"\u207B" : u8"\u207A" );
524  #endif
525 
526 
@@ -797,7 +797,7 @@ diff --git a/defm_8hpp.html b/defm_8hpp.html index 16afc4544..0bd83bc36 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 1067801c3..dbd5385c8 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 db72d33ff..3babde9bb 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 7034061b2..956054701 100644 --- a/dir_000003_000004.html +++ b/dir_000003_000004.html @@ -98,7 +98,7 @@

models → defm Relation

  • include
  • barry
  • models
    • -
  • Generated on Tue Sep 19 2023 19:46:43 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Sep 22 2023 22:26:43 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 c8f5bb6f4..93bc9d413 100644 --- a/dir_000003_000005.html +++ b/dir_000003_000005.html @@ -98,7 +98,7 @@

models → geese Relation

  • include
  • barry
  • models
    • -
  • Generated on Tue Sep 19 2023 19:46:43 for barry: Your go-to motif accountant by doxygen 1.9.1
    • +
  • Generated on Fri Sep 22 2023 22:26:43 for barry: Your go-to motif accountant by doxygen 1.9.1
diff --git a/dir_488ec4010567cc6d95c62bdcb57a6d3e.html b/dir_488ec4010567cc6d95c62bdcb57a6d3e.html index 16ff4da40..72a3a9a9f 100644 --- a/dir_488ec4010567cc6d95c62bdcb57a6d3e.html +++ b/dir_488ec4010567cc6d95c62bdcb57a6d3e.html @@ -130,7 +130,7 @@ diff --git a/dir_6e63e3665115632dc5d61b2d6d6c3354.html b/dir_6e63e3665115632dc5d61b2d6d6c3354.html index 91a94a3d1..41bfc1764 100644 --- a/dir_6e63e3665115632dc5d61b2d6d6c3354.html +++ b/dir_6e63e3665115632dc5d61b2d6d6c3354.html @@ -203,7 +203,7 @@ diff --git a/dir_b3150c389b0f5b078392750f1ae70361.html b/dir_b3150c389b0f5b078392750f1ae70361.html index 925b1f14b..d38255796 100644 --- a/dir_b3150c389b0f5b078392750f1ae70361.html +++ b/dir_b3150c389b0f5b078392750f1ae70361.html @@ -110,7 +110,7 @@ diff --git a/dir_c5954a04c87570f0664da134464d5428.html b/dir_c5954a04c87570f0664da134464d5428.html index 13d584347..8fedc6bca 100644 --- a/dir_c5954a04c87570f0664da134464d5428.html +++ b/dir_c5954a04c87570f0664da134464d5428.html @@ -134,7 +134,7 @@ diff --git a/dir_d44c64559bbebec7f509842c48db8b23.html b/dir_d44c64559bbebec7f509842c48db8b23.html index 7b49ffdb1..d3fe4cb43 100644 --- a/dir_d44c64559bbebec7f509842c48db8b23.html +++ b/dir_d44c64559bbebec7f509842c48db8b23.html @@ -117,7 +117,7 @@ diff --git a/dir_d7a554d3e09ed8456d56450fe8436947.html b/dir_d7a554d3e09ed8456d56450fe8436947.html index 8f5e4bb96..04304db7e 100644 --- a/dir_d7a554d3e09ed8456d56450fe8436947.html +++ b/dir_d7a554d3e09ed8456d56450fe8436947.html @@ -116,7 +116,7 @@ diff --git a/files.html b/files.html index b0f492a3e..73c1e74cc 100644 --- a/files.html +++ b/files.html @@ -173,7 +173,7 @@ diff --git a/flock-bones_8hpp.html b/flock-bones_8hpp.html index 3889c523a..f17e75081 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 0d0e0850e..bb879bce0 100644 --- a/flock-bones_8hpp_source.html +++ b/flock-bones_8hpp_source.html @@ -196,7 +196,7 @@ diff --git a/flock-meat_8hpp.html b/flock-meat_8hpp.html index a7bf232b1..1036b763b 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 ffbff3acb..1d2e4341c 100644 --- a/flock-meat_8hpp_source.html +++ b/flock-meat_8hpp_source.html @@ -450,7 +450,7 @@ diff --git a/formula_8hpp.html b/formula_8hpp.html index 225bfb017..97a109167 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 b0121ecd2..b52fb26d3 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 16e11ba77..61adce6db 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 38ff50840..d9cdbbaee 100644 --- a/freqtable_8hpp_source.html +++ b/freqtable_8hpp_source.html @@ -357,7 +357,7 @@ diff --git a/functions.html b/functions.html index a38cc5fbb..68a8cc586 100644 --- a/functions.html +++ b/functions.html @@ -159,7 +159,7 @@

- a -