From 672de56c3119e700583b9fcb44d3feed76ef81bb Mon Sep 17 00:00:00 2001
From: meliurwen <meliurwen@gmail.com>
Date: Wed, 12 Oct 2022 15:51:52 +0200
Subject: [PATCH 01/12] Added a brief description of the project in form of
 docstrings at the crate level

---
 reCTBN/src/lib.rs | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/reCTBN/src/lib.rs b/reCTBN/src/lib.rs
index 280bd21..da1aa06 100644
--- a/reCTBN/src/lib.rs
+++ b/reCTBN/src/lib.rs
@@ -1,3 +1,9 @@
+//! # reCTBN
+//!
+//! > **Note:** At the moment it's in pre-alpha state. 🧪⚗️💥
+//!
+//! `reCTBN` is a Continuous Time Bayesian Networks Library written in Rust. 🦀
+
 #![allow(non_snake_case)]
 #[cfg(test)]
 extern crate approx;
-- 
2.36.3


From 616d5ec3d551269f184141f48a7a9d638fc49767 Mon Sep 17 00:00:00 2001
From: meliurwen <meliurwen@gmail.com>
Date: Wed, 12 Oct 2022 16:33:47 +0200
Subject: [PATCH 02/12] Fixed and prettified some imprecisions to old
 docstrings and added new ones in `ctbn.rs`

---
 reCTBN/src/ctbn.rs | 24 ++++++++++++++++--------
 1 file changed, 16 insertions(+), 8 deletions(-)

diff --git a/reCTBN/src/ctbn.rs b/reCTBN/src/ctbn.rs
index e2f5dd7..fae7f4d 100644
--- a/reCTBN/src/ctbn.rs
+++ b/reCTBN/src/ctbn.rs
@@ -5,16 +5,18 @@ use ndarray::prelude::*;
 use crate::network;
 use crate::params::{Params, ParamsTrait, StateType};
 
-///CTBN network. It represents both the structure and the parameters of a CTBN. CtbnNetwork is
-///composed by the following elements:
-///- **adj_metrix**: a 2d ndarray representing the adjacency matrix
-///- **nodes**: a vector containing all the nodes and their parameters.
-///The index of a node inside the vector is also used as index for the adj_matrix.
+/// It represents both the structure and the parameters of a CTBN.
 ///
-///# Examples
+/// # Arguments
 ///
-///```
-///    
+/// * `adj_matrix` - A 2D ndarray representing the adjacency matrix
+/// * `nodes` - A vector containing all the nodes and their parameters.
+///
+/// The index of a node inside the vector is also used as index for the `adj_matrix`.
+///
+/// # Example
+///
+/// ```rust
 /// use std::collections::BTreeSet;
 /// use reCTBN::network::Network;
 /// use reCTBN::params;
@@ -66,12 +68,14 @@ impl CtbnNetwork {
 }
 
 impl network::Network for CtbnNetwork {
+    /// Initialize an Adjacency matrix.
     fn initialize_adj_matrix(&mut self) {
         self.adj_matrix = Some(Array2::<u16>::zeros(
             (self.nodes.len(), self.nodes.len()).f(),
         ));
     }
 
+    /// Add a new node.
     fn add_node(&mut self, mut n: Params) -> Result<usize, network::NetworkError> {
         n.reset_params();
         self.adj_matrix = Option::None;
@@ -79,6 +83,7 @@ impl network::Network for CtbnNetwork {
         Ok(self.nodes.len() - 1)
     }
 
+    /// Connect two nodes with a new edge.
     fn add_edge(&mut self, parent: usize, child: usize) {
         if let None = self.adj_matrix {
             self.initialize_adj_matrix();
@@ -94,6 +99,7 @@ impl network::Network for CtbnNetwork {
         0..self.nodes.len()
     }
 
+    /// Get the number of nodes of the network.
     fn get_number_of_nodes(&self) -> usize {
         self.nodes.len()
     }
@@ -138,6 +144,7 @@ impl network::Network for CtbnNetwork {
             .0
     }
 
+    /// Get all the parents of the given node.
     fn get_parent_set(&self, node: usize) -> BTreeSet<usize> {
         self.adj_matrix
             .as_ref()
@@ -149,6 +156,7 @@ impl network::Network for CtbnNetwork {
             .collect()
     }
 
+    /// Get all the children of the given node.
     fn get_children_set(&self, node: usize) -> BTreeSet<usize> {
         self.adj_matrix
             .as_ref()
-- 
2.36.3


From ccced921495558a26703bf351310d5c8429ce7d0 Mon Sep 17 00:00:00 2001
From: meliurwen <meliurwen@gmail.com>
Date: Mon, 17 Oct 2022 11:48:08 +0200
Subject: [PATCH 03/12] Fixed some docstrings in `params.rs`

---
 reCTBN/src/params.rs | 47 ++++++++++++++++++++++----------------------
 1 file changed, 24 insertions(+), 23 deletions(-)

diff --git a/reCTBN/src/params.rs b/reCTBN/src/params.rs
index f994b99..d7bf8f8 100644
--- a/reCTBN/src/params.rs
+++ b/reCTBN/src/params.rs
@@ -23,9 +23,8 @@ pub enum StateType {
     Discrete(usize),
 }
 
-/// Parameters
-/// The Params trait is the core element for building different types of nodes. The goal is to
-/// define the set of method required to describes a generic node.
+/// This is a core element for building different types of nodes; the goal is to define the set of
+/// methods required to describes a generic node.
 #[enum_dispatch(Params)]
 pub trait ParamsTrait {
     fn reset_params(&mut self);
@@ -65,8 +64,8 @@ pub trait ParamsTrait {
     fn get_label(&self) -> &String;
 }
 
-/// The Params enum is the core element for building different types of nodes. The goal is to
-/// define all the supported type of Parameters
+/// Is a core element for building different types of nodes; the goal is to define all the
+/// supported type of Parameters
 #[derive(Clone)]
 #[enum_dispatch]
 pub enum Params {
@@ -76,14 +75,14 @@ pub enum Params {
 /// DiscreteStatesContinousTime.
 /// This represents the parameters of a classical discrete node for ctbn and it's composed by the
 /// following elements:
-/// - **domain**: an ordered and exhaustive set of possible states
-/// - **cim**: Conditional Intensity Matrix
-/// - **Sufficient Statistics**: the sufficient statistics are mainly used during the parameter
-///     learning task and are composed by:
-///     - **transitions**: number of transitions from one state to another given a specific
-///     realization of the parent set
-///     - **residence_time**: permanence time in each possible states given a specific
-///     realization of the parent set
+/// - `label`
+/// - `domain`: an ordered and exhaustive set of possible states.
+/// - `cim`: Conditional Intensity Matrix.
+/// - `transitions`: number of transitions from one state to another given a specific realization
+///   of the parent set; is a sufficient statistics are mainly used during the parameter learning
+///   task.
+/// - `residence_time`: permanence time in each possible state, given a specific realization of the
+///   parent set; is a sufficient statistics are mainly used during the parameter learning task.
 #[derive(Clone)]
 pub struct DiscreteStatesContinousTimeParams {
     label: String,
@@ -104,15 +103,17 @@ impl DiscreteStatesContinousTimeParams {
         }
     }
 
-    ///Getter function for CIM
+    /// Getter function for CIM
     pub fn get_cim(&self) -> &Option<Array3<f64>> {
         &self.cim
     }
 
-    ///Setter function for CIM.\\
-    ///This function check if the cim is valid using the validate_params method.
-    ///- **Valid cim inserted**: it substitute the CIM in self.cim and return Ok(())
-    ///- **Invalid cim inserted**: it replace the self.cim value with None and it retu  ParamsError
+    /// Setter function for CIM.
+    /// 
+    /// This function check if the CIM is valid using the validate_params method:
+    /// - **Valid CIM inserted**: it substitute the CIM in self.cim and return `Ok(())`.
+    /// - **Invalid CIM inserted**: it replace the self.cim value with None and it returns
+    ///   `ParamsError`.
     pub fn set_cim(&mut self, cim: Array3<f64>) -> Result<(), ParamsError> {
         self.cim = Some(cim);
         match self.validate_params() {
@@ -124,27 +125,27 @@ impl DiscreteStatesContinousTimeParams {
         }
     }
 
-    ///Unchecked version of the setter function for CIM.
+    /// Unchecked version of the setter function for CIM.
     pub fn set_cim_unchecked(&mut self, cim: Array3<f64>) {
         self.cim = Some(cim);
     }
 
-    ///Getter function for transitions
+    /// Getter function for transitions.
     pub fn get_transitions(&self) -> &Option<Array3<usize>> {
         &self.transitions
     }
 
-    ///Setter function for transitions
+    /// Setter function for transitions.
     pub fn set_transitions(&mut self, transitions: Array3<usize>) {
         self.transitions = Some(transitions);
     }
 
-    ///Getter function for residence_time
+    /// Getter function for residence_time.
     pub fn get_residence_time(&self) -> &Option<Array2<f64>> {
         &self.residence_time
     }
 
-    ///Setter function for residence_time
+    ///Setter function for residence_time.
     pub fn set_residence_time(&mut self, residence_time: Array2<f64>) {
         self.residence_time = Some(residence_time);
     }
-- 
2.36.3


From 2153f46758b367f9803bc520fcf0d9ee7be2abbb Mon Sep 17 00:00:00 2001
From: meliurwen <meliurwen@gmail.com>
Date: Mon, 17 Oct 2022 12:03:14 +0200
Subject: [PATCH 04/12] Fixed small lint problem and added a paragraph to the
 README

---
 README.md            | 8 ++++++++
 reCTBN/src/params.rs | 3 +--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index f928955..6a60dff 100644
--- a/README.md
+++ b/README.md
@@ -56,3 +56,11 @@ To check the **formatting**:
 ```sh
 cargo fmt --all -- --check
 ```
+
+## Documentation
+
+To generate the **documentation**:
+
+```sh
+cargo rustdoc --package reCTBN --open -- --default-theme=ayu
+```
diff --git a/reCTBN/src/params.rs b/reCTBN/src/params.rs
index d7bf8f8..65db06c 100644
--- a/reCTBN/src/params.rs
+++ b/reCTBN/src/params.rs
@@ -72,7 +72,6 @@ pub enum Params {
     DiscreteStatesContinousTime(DiscreteStatesContinousTimeParams),
 }
 
-/// DiscreteStatesContinousTime.
 /// This represents the parameters of a classical discrete node for ctbn and it's composed by the
 /// following elements:
 /// - `label`
@@ -109,7 +108,7 @@ impl DiscreteStatesContinousTimeParams {
     }
 
     /// Setter function for CIM.
-    /// 
+    ///
     /// This function check if the CIM is valid using the validate_params method:
     /// - **Valid CIM inserted**: it substitute the CIM in self.cim and return `Ok(())`.
     /// - **Invalid CIM inserted**: it replace the self.cim value with None and it returns
-- 
2.36.3


From 064b582833e25b903ebee32bc062967870272c78 Mon Sep 17 00:00:00 2001
From: meliurwen <meliurwen@gmail.com>
Date: Mon, 17 Oct 2022 12:59:39 +0200
Subject: [PATCH 05/12] Added docstrings for the chi-squared test

---
 .../src/structure_learning/hypothesis_test.rs | 28 +++++++++++++++++--
 1 file changed, 26 insertions(+), 2 deletions(-)

diff --git a/reCTBN/src/structure_learning/hypothesis_test.rs b/reCTBN/src/structure_learning/hypothesis_test.rs
index 4f2ce18..7083d38 100644
--- a/reCTBN/src/structure_learning/hypothesis_test.rs
+++ b/reCTBN/src/structure_learning/hypothesis_test.rs
@@ -20,6 +20,17 @@ pub trait HypothesisTest {
         P: parameter_learning::ParameterLearning;
 }
 
+/// Does the chi-squared test (χ2 test).
+///
+/// Used to determine if a difference between two sets of data is due to chance, or if it is due to
+/// a relationship (dependence) between the variables.
+///
+/// # Arguments
+///
+/// * `alpha` - is the significance level, the probability to reject a true null hypothesis;
+///   in other words is the risk of concluding that an association between the variables exists
+///   when there is no actual association.
+
 pub struct ChiSquare {
     alpha: f64,
 }
@@ -30,8 +41,21 @@ impl ChiSquare {
     pub fn new(alpha: f64) -> ChiSquare {
         ChiSquare { alpha }
     }
-    // Restituisce true quando le matrici sono molto simili, quindi indipendenti
-    // false quando sono diverse, quindi dipendenti
+
+    /// Compare two matrices extracted from two 3rd-orer tensors.
+    ///
+    /// # Arguments
+    ///
+    /// * `i` - Position of the matrix of `M1` to compare with `M2`.
+    /// * `M1` - 3rd-order tensor 1.
+    /// * `j` - Position of the matrix of `M2` to compare with `M1`.
+    /// * `M2` - 3rd-order tensor 2.
+    ///
+    /// # Returns
+    ///
+    /// * `true` - when the matrices `M1` and `M2` are very similar, then **dependendent**.
+    /// * `false` - when the matrices `M1` and `M2` are too different, then **independent**.
+
     pub fn compare_matrices(
         &self,
         i: usize,
-- 
2.36.3


From 9ca8973550010a503b0c74cb6b1672886401ee22 Mon Sep 17 00:00:00 2001
From: meliurwen <meliurwen@gmail.com>
Date: Mon, 17 Oct 2022 13:17:34 +0200
Subject: [PATCH 06/12] Harmonized some docstrings in `params.rs`

---
 reCTBN/src/params.rs | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/reCTBN/src/params.rs b/reCTBN/src/params.rs
index 65db06c..e533f21 100644
--- a/reCTBN/src/params.rs
+++ b/reCTBN/src/params.rs
@@ -73,14 +73,17 @@ pub enum Params {
 }
 
 /// This represents the parameters of a classical discrete node for ctbn and it's composed by the
-/// following elements:
-/// - `label`
-/// - `domain`: an ordered and exhaustive set of possible states.
-/// - `cim`: Conditional Intensity Matrix.
-/// - `transitions`: number of transitions from one state to another given a specific realization
+/// following elements.
+///
+/// # Arguments
+///
+/// * `label` - node's variable name.
+/// * `domain` - an ordered and exhaustive set of possible states.
+/// * `cim` - Conditional Intensity Matrix.
+/// * `transitions` - number of transitions from one state to another given a specific realization
 ///   of the parent set; is a sufficient statistics are mainly used during the parameter learning
 ///   task.
-/// - `residence_time`: permanence time in each possible state, given a specific realization of the
+/// * `residence_time` - residence time in each possible state, given a specific realization of the
 ///   parent set; is a sufficient statistics are mainly used during the parameter learning task.
 #[derive(Clone)]
 pub struct DiscreteStatesContinousTimeParams {
@@ -109,9 +112,9 @@ impl DiscreteStatesContinousTimeParams {
 
     /// Setter function for CIM.
     ///
-    /// This function check if the CIM is valid using the validate_params method:
-    /// - **Valid CIM inserted**: it substitute the CIM in self.cim and return `Ok(())`.
-    /// - **Invalid CIM inserted**: it replace the self.cim value with None and it returns
+    /// This function checks if the CIM is valid using the [`validate_params`](self::ParamsTrait::validate_params) method:
+    /// * **Valid CIM inserted** - it substitutes the CIM in `self.cim` and returns `Ok(())`.
+    /// * **Invalid CIM inserted** - it replaces the `self.cim` value with `None` and it returns
     ///   `ParamsError`.
     pub fn set_cim(&mut self, cim: Array3<f64>) -> Result<(), ParamsError> {
         self.cim = Some(cim);
@@ -144,7 +147,7 @@ impl DiscreteStatesContinousTimeParams {
         &self.residence_time
     }
 
-    ///Setter function for residence_time.
+    /// Setter function for residence_time.
     pub fn set_residence_time(&mut self, residence_time: Array2<f64>) {
         self.residence_time = Some(residence_time);
     }
-- 
2.36.3


From f7165d034598a14cc3f0460ee09ddbd31a831e95 Mon Sep 17 00:00:00 2001
From: meliurwen <meliurwen@gmail.com>
Date: Mon, 17 Oct 2022 14:19:26 +0200
Subject: [PATCH 07/12] Added docstrings to `networks.rs`

---
 reCTBN/src/network.rs | 87 ++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 78 insertions(+), 9 deletions(-)

diff --git a/reCTBN/src/network.rs b/reCTBN/src/network.rs
index cbae339..8fc8271 100644
--- a/reCTBN/src/network.rs
+++ b/reCTBN/src/network.rs
@@ -11,33 +11,102 @@ pub enum NetworkError {
     NodeInsertionError(String),
 }
 
-///Network
-///The Network trait define the required methods for a structure used as pgm (such as ctbn).
+/// It defines the required methods for a structure used as a PGM (such as a CTBN).
 pub trait Network {
     fn initialize_adj_matrix(&mut self);
     fn add_node(&mut self, n: params::Params) -> Result<usize, NetworkError>;
+    /// Add an **directed edge** between a two nodes of the network.
+    ///
+    /// # Arguments
+    ///
+    /// * `parent` - parent node.
+    /// * `child` - child node.
     fn add_edge(&mut self, parent: usize, child: usize);
 
-    ///Get all the indices of the nodes contained inside the network
+    /// Get all the indices of the nodes contained inside the network.
     fn get_node_indices(&self) -> std::ops::Range<usize>;
+
+    /// Get the numbers of nodes contained in the network.
     fn get_number_of_nodes(&self) -> usize;
+
+    /// Get the **node param**.
+    ///
+    /// # Arguments
+    ///
+    /// * `node_idx` - node index value.
+    ///
+    /// # Return
+    ///
+    /// * The selected **node param**.
     fn get_node(&self, node_idx: usize) -> &params::Params;
+
+    /// Get the **node param**.
+    ///
+    /// # Arguments
+    ///
+    /// * `node_idx` - node index value.
+    ///
+    /// # Return
+    ///
+    /// * The selected **node mutable param**.
     fn get_node_mut(&mut self, node_idx: usize) -> &mut params::Params;
 
-    ///Compute the index that must be used to access the parameters of a node given a specific
-    ///configuration of the network. Usually, the only values really used in *current_state* are
-    ///the ones in the parent set of the *node*.
+    /// Compute the index that must be used to access the parameters of a `node`, given a specific
+    /// configuration of the network.
+    ///
+    /// Usually, the only values really used in `current_state` are the ones in the parent set of
+    /// the `node`.
+    ///
+    /// # Arguments
+    ///
+    /// * `node` - selected node.
+    /// * `current_state` - current configuration of the network.
+    ///
+    /// # Return
+    ///
+    /// * Index of the `node` relative to the network.
     fn get_param_index_network(&self, node: usize, current_state: &Vec<params::StateType>)
         -> usize;
 
-    ///Compute the index that must be used to access the parameters of a node given a specific
-    ///configuration of the network and a generic parent_set. Usually, the only values really used
-    ///in *current_state* are the ones in the parent set of the *node*.
+    /// Compute the index that must be used to access the parameters of a `node`, given a specific
+    /// configuration of the network and a generic `parent_set`.
+    ///
+    /// Usually, the only values really used in `current_state` are the ones in the parent set of
+    /// the `node`.
+    ///
+    /// # Arguments
+    ///
+    /// * `current_state` - current configuration of the network.
+    /// * `parent_set` - parent set of the selected `node`.
+    ///
+    /// # Return
+    ///
+    /// * Index of the `node` relative to the network.
     fn get_param_index_from_custom_parent_set(
         &self,
         current_state: &Vec<params::StateType>,
         parent_set: &BTreeSet<usize>,
     ) -> usize;
+
+    /// Get the **parent set** of a given **node**.
+    ///
+    /// # Arguments
+    ///
+    /// * `node` - node index value.
+    ///
+    /// # Return
+    ///
+    /// * The **parent set** of the selected node.
     fn get_parent_set(&self, node: usize) -> BTreeSet<usize>;
+
+    /// Get the **children set** of a given **node**.
+    ///
+    /// # Arguments
+    ///
+    /// * `node` - node index value.
+    ///
+    /// # Return
+    ///
+    /// * The **children set** of the selected node.
     fn get_children_set(&self, node: usize) -> BTreeSet<usize>;
 }
-- 
2.36.3


From 08623e28d4f479cfcacc3746c19e1ff903a0e5ef Mon Sep 17 00:00:00 2001
From: meliurwen <meliurwen@gmail.com>
Date: Tue, 18 Oct 2022 15:11:15 +0200
Subject: [PATCH 08/12] Added various docstrings notes to all rust modules

---
 reCTBN/src/ctbn.rs                                          | 2 ++
 reCTBN/src/network.rs                                       | 5 ++++-
 reCTBN/src/parameter_learning.rs                            | 2 ++
 reCTBN/src/params.rs                                        | 2 ++
 reCTBN/src/sampling.rs                                      | 2 ++
 reCTBN/src/structure_learning.rs                            | 2 ++
 reCTBN/src/structure_learning/constraint_based_algorithm.rs | 2 ++
 reCTBN/src/structure_learning/hypothesis_test.rs            | 2 ++
 reCTBN/src/structure_learning/score_based_algorithm.rs      | 2 ++
 reCTBN/src/structure_learning/score_function.rs             | 2 ++
 reCTBN/src/tools.rs                                         | 2 ++
 11 files changed, 24 insertions(+), 1 deletion(-)

diff --git a/reCTBN/src/ctbn.rs b/reCTBN/src/ctbn.rs
index fae7f4d..2b01d14 100644
--- a/reCTBN/src/ctbn.rs
+++ b/reCTBN/src/ctbn.rs
@@ -1,3 +1,5 @@
+//! Continuous Time Bayesian Network
+
 use std::collections::BTreeSet;
 
 use ndarray::prelude::*;
diff --git a/reCTBN/src/network.rs b/reCTBN/src/network.rs
index 8fc8271..fbdd2e6 100644
--- a/reCTBN/src/network.rs
+++ b/reCTBN/src/network.rs
@@ -1,3 +1,5 @@
+//! Defines methods for dealing with Probabilistic Graphical Models like the CTBNs
+
 use std::collections::BTreeSet;
 
 use thiserror::Error;
@@ -11,7 +13,8 @@ pub enum NetworkError {
     NodeInsertionError(String),
 }
 
-/// It defines the required methods for a structure used as a PGM (such as a CTBN).
+/// It defines the required methods for a structure used as a Probabilistic Graphical Models (such
+/// as a CTBN).
 pub trait Network {
     fn initialize_adj_matrix(&mut self);
     fn add_node(&mut self, n: params::Params) -> Result<usize, NetworkError>;
diff --git a/reCTBN/src/parameter_learning.rs b/reCTBN/src/parameter_learning.rs
index bdb5d4a..61d4dca 100644
--- a/reCTBN/src/parameter_learning.rs
+++ b/reCTBN/src/parameter_learning.rs
@@ -1,3 +1,5 @@
+//! Module containing methods used to learn the parameters.
+
 use std::collections::BTreeSet;
 
 use ndarray::prelude::*;
diff --git a/reCTBN/src/params.rs b/reCTBN/src/params.rs
index e533f21..070c997 100644
--- a/reCTBN/src/params.rs
+++ b/reCTBN/src/params.rs
@@ -1,3 +1,5 @@
+//! Module containing methods to define different types of nodes.
+
 use std::collections::BTreeSet;
 
 use enum_dispatch::enum_dispatch;
diff --git a/reCTBN/src/sampling.rs b/reCTBN/src/sampling.rs
index 0660939..d435634 100644
--- a/reCTBN/src/sampling.rs
+++ b/reCTBN/src/sampling.rs
@@ -1,3 +1,5 @@
+//! Module containing methods for the sampling.
+
 use crate::{
     network::Network,
     params::{self, ParamsTrait},
diff --git a/reCTBN/src/structure_learning.rs b/reCTBN/src/structure_learning.rs
index 8b90cdf..57fed1e 100644
--- a/reCTBN/src/structure_learning.rs
+++ b/reCTBN/src/structure_learning.rs
@@ -1,3 +1,5 @@
+//! Learn the structure of the network.
+
 pub mod constraint_based_algorithm;
 pub mod hypothesis_test;
 pub mod score_based_algorithm;
diff --git a/reCTBN/src/structure_learning/constraint_based_algorithm.rs b/reCTBN/src/structure_learning/constraint_based_algorithm.rs
index b3fc3e1..670c8ed 100644
--- a/reCTBN/src/structure_learning/constraint_based_algorithm.rs
+++ b/reCTBN/src/structure_learning/constraint_based_algorithm.rs
@@ -1,3 +1,5 @@
+//! Module containing constraint based algorithms like CTPC and Hiton.
+
 //pub struct CTPC {
 //
 //}
diff --git a/reCTBN/src/structure_learning/hypothesis_test.rs b/reCTBN/src/structure_learning/hypothesis_test.rs
index 7083d38..1404b8e 100644
--- a/reCTBN/src/structure_learning/hypothesis_test.rs
+++ b/reCTBN/src/structure_learning/hypothesis_test.rs
@@ -1,3 +1,5 @@
+//! Module containing an hypothesis test for constraint based algorithms like chi-squared test, F test, etc...
+
 use std::collections::BTreeSet;
 
 use ndarray::{Array3, Axis};
diff --git a/reCTBN/src/structure_learning/score_based_algorithm.rs b/reCTBN/src/structure_learning/score_based_algorithm.rs
index cc8541a..9e329eb 100644
--- a/reCTBN/src/structure_learning/score_based_algorithm.rs
+++ b/reCTBN/src/structure_learning/score_based_algorithm.rs
@@ -1,3 +1,5 @@
+//! Module containing score based algorithms like Hill Climbing and Tabu Search.
+
 use std::collections::BTreeSet;
 
 use crate::structure_learning::score_function::ScoreFunction;
diff --git a/reCTBN/src/structure_learning/score_function.rs b/reCTBN/src/structure_learning/score_function.rs
index b3b1597..cb6ad7b 100644
--- a/reCTBN/src/structure_learning/score_function.rs
+++ b/reCTBN/src/structure_learning/score_function.rs
@@ -1,3 +1,5 @@
+//! Module for score based algorithms containing score functions algorithms like Log Likelihood, BIC, etc...
+
 use std::collections::BTreeSet;
 
 use ndarray::prelude::*;
diff --git a/reCTBN/src/tools.rs b/reCTBN/src/tools.rs
index 70bbf76..aa48883 100644
--- a/reCTBN/src/tools.rs
+++ b/reCTBN/src/tools.rs
@@ -1,3 +1,5 @@
+//! Contains commonly used methods used across the crate.
+
 use ndarray::prelude::*;
 
 use crate::sampling::{ForwardSampler, Sampler};
-- 
2.36.3


From 245b3b5d4598b8fa14c44ce85a830c336966d888 Mon Sep 17 00:00:00 2001
From: meliurwen <meliurwen@gmail.com>
Date: Tue, 18 Oct 2022 15:34:37 +0200
Subject: [PATCH 09/12] Replaced the static docstrings at the crate level in
 `lib.rs` withthe external file `README.md`

---
 reCTBN/src/lib.rs | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/reCTBN/src/lib.rs b/reCTBN/src/lib.rs
index da1aa06..b1cf773 100644
--- a/reCTBN/src/lib.rs
+++ b/reCTBN/src/lib.rs
@@ -1,8 +1,4 @@
-//! # reCTBN
-//!
-//! > **Note:** At the moment it's in pre-alpha state. 🧪⚗️💥
-//!
-//! `reCTBN` is a Continuous Time Bayesian Networks Library written in Rust. 🦀
+#![doc = include_str!("../../README.md")]
 
 #![allow(non_snake_case)]
 #[cfg(test)]
-- 
2.36.3


From 3522e1b6f633fd4ed0c9bee167ef604d869502ea Mon Sep 17 00:00:00 2001
From: meliurwen <meliurwen@gmail.com>
Date: Tue, 18 Oct 2022 15:40:59 +0200
Subject: [PATCH 10/12] Small formatting fix and rewording of a docstring

---
 reCTBN/src/lib.rs                                | 1 -
 reCTBN/src/structure_learning/hypothesis_test.rs | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/reCTBN/src/lib.rs b/reCTBN/src/lib.rs
index b1cf773..db33ae4 100644
--- a/reCTBN/src/lib.rs
+++ b/reCTBN/src/lib.rs
@@ -1,5 +1,4 @@
 #![doc = include_str!("../../README.md")]
-
 #![allow(non_snake_case)]
 #[cfg(test)]
 extern crate approx;
diff --git a/reCTBN/src/structure_learning/hypothesis_test.rs b/reCTBN/src/structure_learning/hypothesis_test.rs
index 1404b8e..f931e77 100644
--- a/reCTBN/src/structure_learning/hypothesis_test.rs
+++ b/reCTBN/src/structure_learning/hypothesis_test.rs
@@ -1,4 +1,4 @@
-//! Module containing an hypothesis test for constraint based algorithms like chi-squared test, F test, etc...
+//! Module for constraint based algorithms containing hypothesis test algorithms like chi-squared test, F test, etc...
 
 use std::collections::BTreeSet;
 
-- 
2.36.3


From 832922922ade46f91904842c75841ceebd67e429 Mon Sep 17 00:00:00 2001
From: meliurwen <meliurwen@gmail.com>
Date: Thu, 20 Oct 2022 08:58:02 +0200
Subject: [PATCH 11/12] Fixed error in chi2 compare matrices docstring

---
 reCTBN/src/structure_learning/hypothesis_test.rs | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/reCTBN/src/structure_learning/hypothesis_test.rs b/reCTBN/src/structure_learning/hypothesis_test.rs
index f931e77..4e1cb24 100644
--- a/reCTBN/src/structure_learning/hypothesis_test.rs
+++ b/reCTBN/src/structure_learning/hypothesis_test.rs
@@ -55,8 +55,8 @@ impl ChiSquare {
     ///
     /// # Returns
     ///
-    /// * `true` - when the matrices `M1` and `M2` are very similar, then **dependendent**.
-    /// * `false` - when the matrices `M1` and `M2` are too different, then **independent**.
+    /// * `true` - when the matrices `M1` and `M2` are very similar, then **independendent**.
+    /// * `false` - when the matrices `M1` and `M2` are too different, then **dependent**.
 
     pub fn compare_matrices(
         &self,
-- 
2.36.3


From 0ae2168a9439635b91ffaa680db79569b3604c29 Mon Sep 17 00:00:00 2001
From: meliurwen <meliurwen@gmail.com>
Date: Thu, 20 Oct 2022 09:36:02 +0200
Subject: [PATCH 12/12] Commented out some prints in chi2 compare matrices

---
 .../src/structure_learning/hypothesis_test.rs  | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/reCTBN/src/structure_learning/hypothesis_test.rs b/reCTBN/src/structure_learning/hypothesis_test.rs
index 4e1cb24..6474155 100644
--- a/reCTBN/src/structure_learning/hypothesis_test.rs
+++ b/reCTBN/src/structure_learning/hypothesis_test.rs
@@ -97,7 +97,7 @@ impl ChiSquare {
             let n = K.len();
             K.into_shape((n, 1)).unwrap()
         };
-        println!("K: {:?}", K);
+        //println!("K: {:?}", K);
         let L = 1.0 / &K;
         //        =====                   2
         //         \      (K . M  - L . M)
@@ -108,18 +108,18 @@ impl ChiSquare {
         //     x'ϵVal /X \
         //            \ i/
         let mut X_2 = (&K * &M2 - &L * &M1).mapv(|a| a.powi(2)) / (&M2 + &M1);
-        println!("M1: {:?}", M1);
-        println!("M2: {:?}", M2);
-        println!("L*M1: {:?}", (L * &M1));
-        println!("K*M2: {:?}", (K * &M2));
-        println!("X_2: {:?}", X_2);
+        //println!("M1: {:?}", M1);
+        //println!("M2: {:?}", M2);
+        //println!("L*M1: {:?}", (L * &M1));
+        //println!("K*M2: {:?}", (K * &M2));
+        //println!("X_2: {:?}", X_2);
         X_2.diag_mut().fill(0.0);
         let X_2 = X_2.sum_axis(Axis(1));
         let n = ChiSquared::new((X_2.dim() - 1) as f64).unwrap();
-        println!("CHI^2: {:?}", n);
-        println!("CHI^2 CDF: {:?}", X_2.mapv(|x| n.cdf(x)));
+        //println!("CHI^2: {:?}", n);
+        //println!("CHI^2 CDF: {:?}", X_2.mapv(|x| n.cdf(x)));
         let ret = X_2.into_iter().all(|x| n.cdf(x) < (1.0 - self.alpha));
-        println!("test: {:?}", ret);
+        //println!("test: {:?}", ret);
         ret
     }
 }
-- 
2.36.3