diff --git a/src/Persistence_matrix/concept/PersistenceMatrixColumn.h b/src/Persistence_matrix/concept/PersistenceMatrixColumn.h
index 221bf4dc7a..a8a00d7a04 100644
--- a/src/Persistence_matrix/concept/PersistenceMatrixColumn.h
+++ b/src/Persistence_matrix/concept/PersistenceMatrixColumn.h
@@ -23,7 +23,7 @@ namespace persistence_matrix {
  * @brief If PersistenceMatrixOptions::has_row_access is true, then @ref Row_access. Otherwise @ref Dummy_row_access.
  * Can eventually be removed if the structure of the column does not allow row access (as for @ref Heap_column), but
  * then it needs to be notified in the documentation of @ref Column_types and as static_assert in
- * @ref Matrix::_assert_options.
+ * Matrix::_assert_options.
  */
 using Row_access_option = Row_access;
 /**
diff --git a/src/Persistence_matrix/doc/Intro_field_elements_and_operators.h b/src/Persistence_matrix/doc/Intro_field_elements_and_operators.h
index 938fccc842..abd6437908 100644
--- a/src/Persistence_matrix/doc/Intro_field_elements_and_operators.h
+++ b/src/Persistence_matrix/doc/Intro_field_elements_and_operators.h
@@ -19,6 +19,8 @@ namespace persistence_fields {
  * @{
  * \author    Hannah Schreiber, Clément Maria
  *
+ * \section fieldintro Persistence Fields
+ *
  * Set of classes allowing addition and multiplication, as well as inverse computation, in \f$ \mathbb{F}_p \f$ fields,
  * with \f$ p \f$ some prime number, or in multi-fields as defined in \cite boissonnat:hal-00922572.
  *
diff --git a/src/Persistence_matrix/doc/Intro_persistence_matrix.h b/src/Persistence_matrix/doc/Intro_persistence_matrix.h
index ce9c2248ee..39cfb2e41d 100644
--- a/src/Persistence_matrix/doc/Intro_persistence_matrix.h
+++ b/src/Persistence_matrix/doc/Intro_persistence_matrix.h
@@ -19,6 +19,8 @@ namespace persistence_matrix {
  * @{
  * \author    Hannah Schreiber
  *
+ * \section matrixintro Persistence Matrix
+ *
  * The module provides a data structure for matrices, in particular thought for matrices representing filtered complexes
  * and used as backend for persistence algorithms, such at persistent homology, @ref persistent_cohomology,
  * or zigzag @cite zigzag.
diff --git a/src/Persistence_matrix/include/gudhi/Fields/Multi_field.h b/src/Persistence_matrix/include/gudhi/Fields/Multi_field.h
index d70647b94f..9b923580f5 100644
--- a/src/Persistence_matrix/include/gudhi/Fields/Multi_field.h
+++ b/src/Persistence_matrix/include/gudhi/Fields/Multi_field.h
@@ -11,7 +11,7 @@
 /**
  * @file Multi_field.h
  * @author Hannah Schreiber, Clément Maria
- * @brief Contains the @ref Multi_field_element class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Multi_field_element class.
  */
 
 #ifndef MATRIX_FIELD_MULTI_H_
diff --git a/src/Persistence_matrix/include/gudhi/Fields/Multi_field_shared.h b/src/Persistence_matrix/include/gudhi/Fields/Multi_field_shared.h
index 233fdebb46..2f44b7a1d7 100644
--- a/src/Persistence_matrix/include/gudhi/Fields/Multi_field_shared.h
+++ b/src/Persistence_matrix/include/gudhi/Fields/Multi_field_shared.h
@@ -11,7 +11,7 @@
 /**
  * @file Multi_field_shared.h
  * @author Hannah Schreiber, Clément Maria
- * @brief Contains the @ref Shared_multi_field_element class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Shared_multi_field_element class.
  */
 
 #ifndef MATRIX_FIELD_MULTI_SHARED_H_
diff --git a/src/Persistence_matrix/include/gudhi/Fields/Multi_field_small.h b/src/Persistence_matrix/include/gudhi/Fields/Multi_field_small.h
index f10a8c7327..7cb6798248 100644
--- a/src/Persistence_matrix/include/gudhi/Fields/Multi_field_small.h
+++ b/src/Persistence_matrix/include/gudhi/Fields/Multi_field_small.h
@@ -11,7 +11,7 @@
 /**
  * @file Multi_field_small.h
  * @author Hannah Schreiber, Clément Maria
- * @brief Contains the @ref Multi_field_element_with_small_characteristics class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Multi_field_element_with_small_characteristics class.
  */
 
 #ifndef MATRIX_FIELD_MULTI_SMALL_H_
diff --git a/src/Persistence_matrix/include/gudhi/Fields/Multi_field_small_operators.h b/src/Persistence_matrix/include/gudhi/Fields/Multi_field_small_operators.h
index f369e98528..2674b18eda 100644
--- a/src/Persistence_matrix/include/gudhi/Fields/Multi_field_small_operators.h
+++ b/src/Persistence_matrix/include/gudhi/Fields/Multi_field_small_operators.h
@@ -11,7 +11,7 @@
 /**
  * @file Multi_field_small_operators.h
  * @author Hannah Schreiber, Clément Maria
- * @brief Contains the @ref Multi_field_operators_with_small_characteristics class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Multi_field_operators_with_small_characteristics class.
  */
 
 #ifndef MATRIX_FIELD_MULTI_SMALL_OPERATORS_H_
diff --git a/src/Persistence_matrix/include/gudhi/Fields/Multi_field_small_shared.h b/src/Persistence_matrix/include/gudhi/Fields/Multi_field_small_shared.h
index 3a024cad7d..19d99d7447 100644
--- a/src/Persistence_matrix/include/gudhi/Fields/Multi_field_small_shared.h
+++ b/src/Persistence_matrix/include/gudhi/Fields/Multi_field_small_shared.h
@@ -11,7 +11,7 @@
 /**
  * @file Multi_field_small_shared.h
  * @author Hannah Schreiber, Clément Maria
- * @brief Contains the @ref Shared_multi_field_element_with_small_characteristics class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Shared_multi_field_element_with_small_characteristics class.
  */
 
 #ifndef MATRIX_FIELD_MULTI_SMALL_SHARED_H_
diff --git a/src/Persistence_matrix/include/gudhi/Fields/Z2_field.h b/src/Persistence_matrix/include/gudhi/Fields/Z2_field.h
index 4877fba31e..7a09508e29 100644
--- a/src/Persistence_matrix/include/gudhi/Fields/Z2_field.h
+++ b/src/Persistence_matrix/include/gudhi/Fields/Z2_field.h
@@ -11,7 +11,7 @@
 /**
  * @file Z2_field.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Z2_field_element class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Z2_field_element class.
  */
 
 #ifndef MATRIX_FIELD_Z2_H_
diff --git a/src/Persistence_matrix/include/gudhi/Fields/Z2_field_operators.h b/src/Persistence_matrix/include/gudhi/Fields/Z2_field_operators.h
index bf6ec53a67..6265db8ef5 100644
--- a/src/Persistence_matrix/include/gudhi/Fields/Z2_field_operators.h
+++ b/src/Persistence_matrix/include/gudhi/Fields/Z2_field_operators.h
@@ -11,7 +11,7 @@
 /**
  * @file Z2_field_operators.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Z2_field_operators class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Z2_field_operators class.
  */
 
 #ifndef MATRIX_FIELD_Z2_OPERATORS_H_
diff --git a/src/Persistence_matrix/include/gudhi/Fields/Zp_field.h b/src/Persistence_matrix/include/gudhi/Fields/Zp_field.h
index 56fb4cf4f3..ac0b067082 100644
--- a/src/Persistence_matrix/include/gudhi/Fields/Zp_field.h
+++ b/src/Persistence_matrix/include/gudhi/Fields/Zp_field.h
@@ -11,7 +11,7 @@
 /**
  * @file Zp_field.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Zp_field_element class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Zp_field_element class.
  */
 
 #ifndef MATRIX_FIELD_ZP_H_
diff --git a/src/Persistence_matrix/include/gudhi/Fields/Zp_field_operators.h b/src/Persistence_matrix/include/gudhi/Fields/Zp_field_operators.h
index eb6b9c4ca9..f5d72a0271 100644
--- a/src/Persistence_matrix/include/gudhi/Fields/Zp_field_operators.h
+++ b/src/Persistence_matrix/include/gudhi/Fields/Zp_field_operators.h
@@ -11,7 +11,7 @@
 /**
  * @file Zp_field_operators.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Zp_field_operators class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Zp_field_operators class.
  */
 
 #ifndef MATRIX_FIELD_ZP_OPERATOR_H_
diff --git a/src/Persistence_matrix/include/gudhi/Fields/Zp_field_shared.h b/src/Persistence_matrix/include/gudhi/Fields/Zp_field_shared.h
index d553559405..2e9e3121af 100644
--- a/src/Persistence_matrix/include/gudhi/Fields/Zp_field_shared.h
+++ b/src/Persistence_matrix/include/gudhi/Fields/Zp_field_shared.h
@@ -11,7 +11,7 @@
 /**
  * @file Zp_field_shared.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Shared_Zp_field_element class.
+ * @brief Contains the @ref Gudhi::persistence_fields::Shared_Zp_field_element class.
  */
 
 #ifndef MATRIX_FIELD_ZP_VAR_H_
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/allocators/cell_constructors.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/allocators/cell_constructors.h
index 9d3548c932..65588a266c 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/allocators/cell_constructors.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/allocators/cell_constructors.h
@@ -11,7 +11,8 @@
 /**
  * @file cell_constructors.h
  * @author Hannah Schreiber
- * @brief Contains the @ref New_cell_constructor and @ref Pool_cell_constructor structures.
+ * @brief Contains the @ref Gudhi::persistence_matrix::New_cell_constructor and
+ * @ref Gudhi::persistence_matrix::Pool_cell_constructor structures.
  */
 
 #ifndef PM_COLUMN_CELL_CONSTRUCTORS_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_matrix.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_matrix.h
index d930b96403..e862061873 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_matrix.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_matrix.h
@@ -11,7 +11,7 @@
 /**
  * @file base_matrix.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Base_matrix class.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Base_matrix class.
  */
 
 #ifndef PM_BASE_MATRIX_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_matrix_with_column_compression.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_matrix_with_column_compression.h
index c75b57e0e9..ce1424b136 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_matrix_with_column_compression.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_matrix_with_column_compression.h
@@ -11,7 +11,7 @@
 /**
  * @file base_matrix_with_column_compression.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Base_matrix_with_column_compression class.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Base_matrix_with_column_compression class.
  */
 
 #ifndef PM_BASE_MATRIX_COMPRESSION_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_pairing.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_pairing.h
index 8cda78dc62..bdae3f8ceb 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_pairing.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_pairing.h
@@ -11,7 +11,8 @@
 /**
  * @file base_pairing.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Base_pairing class and @ref Dummy_base_pairing structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Base_pairing class and
+ * @ref Gudhi::persistence_matrix::Dummy_base_pairing structure.
  */
 
 #ifndef PM_BASE_PAIRING_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_swap.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_swap.h
index 02d592e722..b1477bcb26 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_swap.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_swap.h
@@ -11,7 +11,8 @@
 /**
  * @file base_swap.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Base_swap class and @ref Dummy_base_swap structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Base_swap class and
+ * @ref Gudhi::persistence_matrix::Dummy_base_swap structure.
  */
 
 #ifndef PM_BASE_SWAP_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/boundary_matrix.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/boundary_matrix.h
index a617c3981e..8556cfe248 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/boundary_matrix.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/boundary_matrix.h
@@ -11,7 +11,7 @@
 /**
  * @file boundary_matrix.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Boundary_matrix class.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Boundary_matrix class.
  */
 
 #ifndef PM_BOUNDARY_MATRIX_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_matrix.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_matrix.h
index e89ce87366..01cb90e4f6 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_matrix.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_matrix.h
@@ -11,7 +11,7 @@
 /**
  * @file chain_matrix.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Chain_matrix class.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Chain_matrix class.
  */
 
 #ifndef PM_CHAIN_MATRIX_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_pairing.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_pairing.h
index 50d0c64867..cc0521a246 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_pairing.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_pairing.h
@@ -11,7 +11,8 @@
 /**
  * @file chain_pairing.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Chain_pairing class and @ref Dummy_chain_pairing structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Chain_pairing class and
+ * @ref Gudhi::persistence_matrix::Dummy_chain_pairing structure.
  */
 
 #ifndef PM_CHAIN_PAIRING_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_rep_cycles.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_rep_cycles.h
index e23c356254..bebc20ec1d 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_rep_cycles.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_rep_cycles.h
@@ -11,7 +11,8 @@
 /**
  * @file chain_rep_cycles.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Chain_representative_cycles class and @ref Dummy_chain_representative_cycles structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Chain_representative_cycles class and
+ * @ref Gudhi::persistence_matrix::Dummy_chain_representative_cycles structure.
  */
 
 #ifndef PM_CHAIN_REP_CYCLES_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_vine_swap.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_vine_swap.h
index f2f3c4bc13..65ceaa3864 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_vine_swap.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_vine_swap.h
@@ -11,8 +11,10 @@
 /**
  * @file chain_vine_swap.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Chain_barcode_swap and @ref Chain_vine_swap classes, as well as the
- * @ref Dummy_chain_vine_swap and @ref Dummy_chain_vine_pairing structures.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Chain_barcode_swap and
+ * @ref Gudhi::persistence_matrix::Chain_vine_swap classes, as well as the
+ * @ref Gudhi::persistence_matrix::Dummy_chain_vine_swap and
+ * @ref Gudhi::persistence_matrix::Dummy_chain_vine_pairing structures.
  */
 
 #ifndef PM_CHAIN_VINE_SWAP_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/cell_types.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/cell_types.h
index e7fd3c43d7..77ecee572a 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/cell_types.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/cell_types.h
@@ -11,9 +11,11 @@
 /**
  * @file cell_types.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Cell, @ref Cell_column_index and @ref Cell_field_element classes, as well as the
- * @ref Dummy_cell_column_index_mixin and @ref Dummy_cell_field_element_mixin structures. Also defines the
- * std::hash method for @ref Cell.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Cell, @ref Gudhi::persistence_matrix::Cell_column_index and
+ * @ref Gudhi::persistence_matrix::Cell_field_element classes, as well as the
+ * @ref Gudhi::persistence_matrix::Dummy_cell_column_index_mixin and
+ * @ref Gudhi::persistence_matrix::Dummy_cell_field_element_mixin structures.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::Cell.
  */
 
 #ifndef PM_MATRIX_CELL_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/chain_column_extra_properties.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/chain_column_extra_properties.h
index 5ae038d997..6187f67a0f 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/chain_column_extra_properties.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/chain_column_extra_properties.h
@@ -11,7 +11,8 @@
 /**
  * @file chain_column_extra_properties.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Chain_column_extra_properties class and @ref Dummy_chain_properties structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Chain_column_extra_properties class and
+ * @ref Gudhi::persistence_matrix::Dummy_chain_properties structure.
  */
 
 #ifndef PM_CHAIN_COLUMN_PROP_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/column_dimension_holder.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/column_dimension_holder.h
index 9775f9d24c..d32af86c1b 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/column_dimension_holder.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/column_dimension_holder.h
@@ -11,7 +11,8 @@
 /**
  * @file column_dimension_holder.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Column_dimension_holder class and @ref Dummy_dimension_holder structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Column_dimension_holder class and
+ * @ref Gudhi::persistence_matrix::Dummy_dimension_holder structure.
  */
 
 #ifndef PM_COLUMN_DIM_HOLDER_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/heap_column.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/heap_column.h
index 8e05b06d0a..947bedacb0 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/heap_column.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/heap_column.h
@@ -11,7 +11,8 @@
 /**
  * @file heap_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Heap_column class. Also defines the std::hash method for @ref Heap_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Heap_column class. Also defines the std::hash method
+ * for @ref Gudhi::persistence_matrix::Heap_column.
  */
 
 #ifndef PM_HEAP_COLUMN_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/intrusive_list_column.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/intrusive_list_column.h
index 4d67e8d2e2..a6381ec3f2 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/intrusive_list_column.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/intrusive_list_column.h
@@ -11,8 +11,8 @@
 /**
  * @file intrusive_list_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Intrusive_list_column class.
- * Also defines the std::hash method for @ref Intrusive_list_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Intrusive_list_column class.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::Intrusive_list_column.
  */
 
 #ifndef PM_INTRUSIVE_LIST_COLUMN_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/intrusive_set_column.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/intrusive_set_column.h
index 9c8b418954..822bfa3be5 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/intrusive_set_column.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/intrusive_set_column.h
@@ -11,8 +11,8 @@
 /**
  * @file intrusive_set_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Intrusive_set_column class.
- * Also defines the std::hash method for @ref Intrusive_set_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Intrusive_set_column class.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::Intrusive_set_column.
  */
 
 #ifndef PM_INTRUSIVE_SET_COLUMN_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/list_column.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/list_column.h
index 7dcbb3b2ee..0beae05f00 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/list_column.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/list_column.h
@@ -11,8 +11,8 @@
 /**
  * @file list_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref List_column class.
- * Also defines the std::hash method for @ref List_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::List_column class.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::List_column.
  */
 
 #ifndef PM_LIST_COLUMN_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/naive_vector_column.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/naive_vector_column.h
index 439b1b4efc..b3e4cbff7b 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/naive_vector_column.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/naive_vector_column.h
@@ -11,8 +11,8 @@
 /**
  * @file naive_vector_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Naive_vector_column class.
- * Also defines the std::hash method for @ref Naive_vector_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Naive_vector_column class.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::Naive_vector_column.
  */
 
 #ifndef PM_NAIVE_VECTOR_COLUMN_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/row_access.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/row_access.h
index 241926f371..56f36e2f34 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/row_access.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/row_access.h
@@ -11,7 +11,8 @@
 /**
  * @file row_access.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Row_access class and @ref Dummy_row_access structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Row_access class and
+ * @ref Gudhi::persistence_matrix::Dummy_row_access structure.
  */
 
 #ifndef PM_ROW_ACCESS_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/set_column.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/set_column.h
index b87eb841f4..f5bb0bdb38 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/set_column.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/set_column.h
@@ -11,8 +11,8 @@
 /**
  * @file set_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Set_column class.
- * Also defines the std::hash method for @ref Set_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Set_column class.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::Set_column.
  */
 
 #ifndef PM_SET_COLUMN_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/unordered_set_column.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/unordered_set_column.h
index 87cd1e5ae8..e67082503d 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/unordered_set_column.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/unordered_set_column.h
@@ -11,8 +11,8 @@
 /**
  * @file unordered_set_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Unordered_set_column class.
- * Also defines the std::hash method for @ref Unordered_set_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Unordered_set_column class.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::Unordered_set_column.
  */
 
 #ifndef PM_UNORDERED_SET_COLUMN_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/vector_column.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/vector_column.h
index c0a11ad3e8..b200437ee4 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/vector_column.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/columns/vector_column.h
@@ -11,8 +11,8 @@
 /**
  * @file vector_column.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Vector_column class.
- * Also defines the std::hash method for @ref Vector_column.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Vector_column class.
+ * Also defines the std::hash method for @ref Gudhi::persistence_matrix::Vector_column.
  */
 
 #ifndef PM_VECTOR_COLUMN_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/matrix_dimension_holders.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/matrix_dimension_holders.h
index 113c7cc755..dfc195c57f 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/matrix_dimension_holders.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/matrix_dimension_holders.h
@@ -11,8 +11,9 @@
 /**
  * @file matrix_dimension_holders.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Matrix_max_dimension_holder @ref Matrix_all_dimension_holder classes
- * and the @ref Dummy_matrix_dimension_holder structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Matrix_max_dimension_holder
+ * @ref Gudhi::persistence_matrix::Matrix_all_dimension_holder classes
+ * and the @ref Gudhi::persistence_matrix::Dummy_matrix_dimension_holder structure.
  */
 
 #ifndef PM_MATRIX_DIM_HOLDER_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/matrix_row_access.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/matrix_row_access.h
index 1bdf868ed0..836302ef15 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/matrix_row_access.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/matrix_row_access.h
@@ -11,7 +11,8 @@
 /**
  * @file matrix_row_access.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Matrix_row_access class and @ref Dummy_matrix_row_access structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Matrix_row_access class and
+ * @ref Gudhi::persistence_matrix::Dummy_matrix_row_access structure.
  */
 
 #ifndef PM_BASE_MATRIX_RA_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/overlay_ididx_to_matidx.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/overlay_ididx_to_matidx.h
index 83197b434c..f2037318c1 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/overlay_ididx_to_matidx.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/overlay_ididx_to_matidx.h
@@ -11,7 +11,7 @@
 /**
  * @file overlay_ididx_to_matidx.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Id_to_index_overlay class.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Id_to_index_overlay class.
  */
 
 #ifndef PM_ID_TO_POS_TRANSLATION_H
@@ -277,8 +277,9 @@ class Id_to_index_overlay
    * For @ref boundarymatrix "RU matrices", the returned row is from \f$ R \f$.
    * The type of the row depends on the choosen options, see @ref PersistenceMatrixOptions::has_intrusive_rows.
    *
-   * @warning The @ref get_column_index method of the row cells returns the original @ref PosIdx indices (before any
-   * swaps) for @ref boundarymatrix "boundary matrices" and @ref MatIdx indices for @ref chainmatrix "chain matrices".
+   * @warning The @ref Cell_column_index::get_column_index "get_column_index" method of the row cells returns the
+   * original @ref PosIdx indices (before any swaps) for @ref boundarymatrix "boundary matrices" and
+   * @ref MatIdx indices for @ref chainmatrix "chain matrices".
    * 
    * @param rowIndex @ref rowindex "Row index" of the row to return: @ref IDIdx for @ref chainmatrix "chain matrices"
    * or updated @ref IDIdx for @ref boundarymatrix "boundary matrices" if swaps occured.
@@ -322,7 +323,8 @@ class Id_to_index_overlay
    * Also updates the barcode if it was computed.
    *
    * For @ref chainmatrix "chain matrices", using the other version of the method could perform better depending on
-   * how the data is maintained on the side of the user. Then, @ref has_column_pairings also do not need to be true.
+   * how the data is maintained on the side of the user. Then, @ref PersistenceMatrixOptions::has_column_pairings also
+   * do not need to be true.
    *
    * See also @ref remove_last.
    * 
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/overlay_posidx_to_matidx.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/overlay_posidx_to_matidx.h
index e5a99dc814..81776e6de8 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/overlay_posidx_to_matidx.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/overlay_posidx_to_matidx.h
@@ -11,7 +11,7 @@
 /**
  * @file overlay_posidx_to_matidx.h
  * @author Hannah Schreiber
- * @brief Contains the @ref Position_to_index_overlay class.
+ * @brief Contains the @ref Gudhi::persistence_matrix::Position_to_index_overlay class.
  */
 
 #ifndef PM_POS_TO_ID_TRANSLATION_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_matrix.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_matrix.h
index 8bfa76a253..8397c48c82 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_matrix.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_matrix.h
@@ -11,7 +11,7 @@
 /**
  * @file ru_matrix.h
  * @author Hannah Schreiber
- * @brief Contains the @ref RU_matrix class.
+ * @brief Contains the @ref Gudhi::persistence_matrix::RU_matrix class.
  */
 
 #ifndef PM_RU_MATRIX_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_pairing.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_pairing.h
index 8a89576b9d..dc22999ed0 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_pairing.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_pairing.h
@@ -11,7 +11,8 @@
 /**
  * @file ru_pairing.h
  * @author Hannah Schreiber
- * @brief Contains the @ref RU_pairing class and @ref Dummy_ru_pairing structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::RU_pairing class and
+ * @ref Gudhi::persistence_matrix::Dummy_ru_pairing structure.
  */
 
 #ifndef PM_RU_PAIRING_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_rep_cycles.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_rep_cycles.h
index c8d6a6abbe..fa4b314b83 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_rep_cycles.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_rep_cycles.h
@@ -11,7 +11,8 @@
 /**
  * @file ru_rep_cycles.h
  * @author Hannah Schreiber
- * @brief Contains the @ref RU_representative_cycles class and @ref Dummy_ru_representative_cycles structure.
+ * @brief Contains the @ref Gudhi::persistence_matrix::RU_representative_cycles class and
+ * @ref Gudhi::persistence_matrix::Dummy_ru_representative_cycles structure.
  */
 
 #ifndef PM_RU_REP_CYCLES_H
diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_vine_swap.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_vine_swap.h
index cfe9666c0b..84f1953486 100644
--- a/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_vine_swap.h
+++ b/src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_vine_swap.h
@@ -11,8 +11,9 @@
 /**
  * @file ru_vine_swap.h
  * @author Hannah Schreiber
- * @brief Contains the @ref RU_vine_swap class, as well as the
- * @ref Dummy_ru_vine_swap and @ref Dummy_ru_vine_pairing structures.
+ * @brief Contains the @ref Gudhi::persistence_matrix::RU_vine_swap class, as well as the
+ * @ref Gudhi::persistence_matrix::Dummy_ru_vine_swap and
+ * @ref Gudhi::persistence_matrix::Dummy_ru_vine_pairing structures.
  */
 
 #ifndef PM_RU_VINE_SWAP_H
diff --git a/src/Persistence_matrix/include/gudhi/matrix.h b/src/Persistence_matrix/include/gudhi/matrix.h
index 811c25c7fe..5fa8b2bf42 100644
--- a/src/Persistence_matrix/include/gudhi/matrix.h
+++ b/src/Persistence_matrix/include/gudhi/matrix.h
@@ -269,7 +269,7 @@ class Matrix {
   /**
    * @brief Type of the rows stored in the matrix. Is either an intrusive list of @ref Cell_type (not ordered) if
    * @ref PersistenceMatrixOptions::has_intrusive_rows is true, or a set of @ref Cell_type (ordered by
-   * @ref get_column_index) otherwise.
+   * column index) otherwise.
    */
   using Row_type =
       typename std::conditional<PersistenceMatrixOptions::has_intrusive_rows,