Merge branch '82-feature-create-doctest-for-ctpc' into 'dev'

Added doctest for CTPC, some docstrings for F-test and removed some comments in `structure_learning/hypothesis_test.rs`

reCTBN/src/structure_learning/constraint_based_algorithm.rs

@@ -79,6 +79,190 @@ impl<'a, P: ParameterLearning> Cache<'a, P> {
     }
 }
 
+/// Continuous-Time Peter Clark algorithm.
+///
+/// A method to learn the structure of the network.
+///
+/// # Arguments
+///
+/// * [`parameter_learning`](crate::parameter_learning) - is the method used to learn the parameters.
+/// * [`Ftest`](crate::structure_learning::hypothesis_test::F) - is the F-test hyppothesis test.
+/// * [`Chi2test`](crate::structure_learning::hypothesis_test::ChiSquare) - is the chi-squared test (χ2 test) hypothesis test.
+/// # Example
+///
+/// ```rust
+/// # use std::collections::BTreeSet;
+/// # use ndarray::{arr1, arr2, arr3};
+/// # use reCTBN::params;
+/// # use reCTBN::tools::trajectory_generator;
+/// # use reCTBN::process::NetworkProcess;
+/// # use reCTBN::process::ctbn::CtbnNetwork;
+/// use reCTBN::parameter_learning::BayesianApproach;
+/// use reCTBN::structure_learning::StructureLearningAlgorithm;
+/// use reCTBN::structure_learning::hypothesis_test::{F, ChiSquare};
+/// use reCTBN::structure_learning::constraint_based_algorithm::CTPC;
+/// #
+/// # // Create the domain for a discrete node
+/// # let mut domain = BTreeSet::new();
+/// # domain.insert(String::from("A"));
+/// # domain.insert(String::from("B"));
+/// # domain.insert(String::from("C"));
+/// # // Create the parameters for a discrete node using the domain
+/// # let param = params::DiscreteStatesContinousTimeParams::new("n1".to_string(), domain);
+/// # //Create the node n1 using the parameters
+/// # let n1 = params::Params::DiscreteStatesContinousTime(param);
+/// #
+/// # let mut domain = BTreeSet::new();
+/// # domain.insert(String::from("D"));
+/// # domain.insert(String::from("E"));
+/// # domain.insert(String::from("F"));
+/// # let param = params::DiscreteStatesContinousTimeParams::new("n2".to_string(), domain);
+/// # let n2 = params::Params::DiscreteStatesContinousTime(param);
+/// #
+/// # let mut domain = BTreeSet::new();
+/// # domain.insert(String::from("G"));
+/// # domain.insert(String::from("H"));
+/// # domain.insert(String::from("I"));
+/// # domain.insert(String::from("F"));
+/// # let param = params::DiscreteStatesContinousTimeParams::new("n3".to_string(), domain);
+/// # let n3 = params::Params::DiscreteStatesContinousTime(param);
+/// #
+/// # // Initialize a ctbn
+/// # let mut net = CtbnNetwork::new();
+/// #
+/// # // Add the nodes and their edges
+/// # let n1 = net.add_node(n1).unwrap();
+/// # let n2 = net.add_node(n2).unwrap();
+/// # let n3 = net.add_node(n3).unwrap();
+/// # net.add_edge(n1, n2);
+/// # net.add_edge(n1, n3);
+/// # net.add_edge(n2, n3);
+/// #
+/// # match &mut net.get_node_mut(n1) {
+/// # params::Params::DiscreteStatesContinousTime(param) => {
+/// #     assert_eq!(
+/// #         Ok(()),
+/// #         param.set_cim(arr3(&[
+/// #             [
+/// #                 [-3.0, 2.0, 1.0],
+/// #                 [1.5, -2.0, 0.5],
+/// #                 [0.4, 0.6, -1.0]
+/// #             ],
+/// #         ]))
+/// #     );
+/// # }
+/// # }
+/// #
+/// # match &mut net.get_node_mut(n2) {
+/// # params::Params::DiscreteStatesContinousTime(param) => {
+/// #     assert_eq!(
+/// #         Ok(()),
+/// #         param.set_cim(arr3(&[
+/// #             [
+/// #                 [-1.0, 0.5, 0.5],
+/// #                 [3.0, -4.0, 1.0],
+/// #                 [0.9, 0.1, -1.0]
+/// #             ],
+/// #             [
+/// #                 [-6.0, 2.0, 4.0],
+/// #                 [1.5, -2.0, 0.5],
+/// #                 [3.0, 1.0, -4.0]
+/// #             ],
+/// #             [
+/// #                 [-1.0, 0.1, 0.9],
+/// #                 [2.0, -2.5, 0.5],
+/// #                 [0.9, 0.1, -1.0]
+/// #             ],
+/// #         ]))
+/// #     );
+/// # }
+/// # }
+/// #
+/// # match &mut net.get_node_mut(n3) {
+/// # params::Params::DiscreteStatesContinousTime(param) => {
+/// #     assert_eq!(
+/// #         Ok(()),
+/// #         param.set_cim(arr3(&[
+/// #             [
+/// #                 [-1.0, 0.5, 0.3, 0.2],
+/// #                 [0.5, -4.0, 2.5, 1.0],
+/// #                 [2.5, 0.5, -4.0, 1.0],
+/// #                 [0.7, 0.2, 0.1, -1.0]
+/// #             ],
+/// #             [
+/// #                 [-6.0, 2.0, 3.0, 1.0],
+/// #                 [1.5, -3.0, 0.5, 1.0],
+/// #                 [2.0, 1.3, -5.0, 1.7],
+/// #                 [2.5, 0.5, 1.0, -4.0]
+/// #             ],
+/// #             [
+/// #                 [-1.3, 0.3, 0.1, 0.9],
+/// #                 [1.4, -4.0, 0.5, 2.1],
+/// #                 [1.0, 1.5, -3.0, 0.5],
+/// #                 [0.4, 0.3, 0.1, -0.8]
+/// #             ],
+/// #             [
+/// #                 [-2.0, 1.0, 0.7, 0.3],
+/// #                 [1.3, -5.9, 2.7, 1.9],
+/// #                 [2.0, 1.5, -4.0, 0.5],
+/// #                 [0.2, 0.7, 0.1, -1.0]
+/// #             ],
+/// #             [
+/// #                 [-6.0, 1.0, 2.0, 3.0],
+/// #                 [0.5, -3.0, 1.0, 1.5],
+/// #                 [1.4, 2.1, -4.3, 0.8],
+/// #                 [0.5, 1.0, 2.5, -4.0]
+/// #             ],
+/// #             [
+/// #                 [-1.3, 0.9, 0.3, 0.1],
+/// #                 [0.1, -1.3, 0.2, 1.0],
+/// #                 [0.5, 1.0, -3.0, 1.5],
+/// #                 [0.1, 0.4, 0.3, -0.8]
+/// #             ],
+/// #             [
+/// #                 [-2.0, 1.0, 0.6, 0.4],
+/// #                 [2.6, -7.1, 1.4, 3.1],
+/// #                 [5.0, 1.0, -8.0, 2.0],
+/// #                 [1.4, 0.4, 0.2, -2.0]
+/// #             ],
+/// #             [
+/// #                 [-3.0, 1.0, 1.5, 0.5],
+/// #                 [3.0, -6.0, 1.0, 2.0],
+/// #                 [0.3, 0.5, -1.9, 1.1],
+/// #                 [5.0, 1.0, 2.0, -8.0]
+/// #             ],
+/// #             [
+/// #                 [-2.6, 0.6, 0.2, 1.8],
+/// #                 [2.0, -6.0, 3.0, 1.0],
+/// #                 [0.1, 0.5, -1.3, 0.7],
+/// #                 [0.8, 0.6, 0.2, -1.6]
+/// #             ],
+/// #         ]))
+/// #     );
+/// # }
+/// # }
+/// #
+/// # // Generate the trajectory
+/// # let data = trajectory_generator(&net, 300, 30.0, Some(4164901764658873));
+///
+/// // Initialize the hypothesis tests to pass to the CTPC with their
+/// // respective significance level `alpha`
+/// let f = F::new(1e-6);
+/// let chi_sq = ChiSquare::new(1e-4);
+/// // Use the bayesian approach to learn the parameters
+/// let parameter_learning = BayesianApproach { alpha: 1, tau:1.0 };
+///
+/// //Initialize CTPC
+/// let ctpc = CTPC::new(parameter_learning, f, chi_sq);
+///
+/// // Learn the structure of the network from the generated trajectory
+/// let net = ctpc.fit_transform(net, &data);
+/// #
+/// # // Compare the generated network with the original one
+/// # assert_eq!(BTreeSet::new(), net.get_parent_set(0));
+/// # assert_eq!(BTreeSet::from_iter(vec![0]), net.get_parent_set(1));
+/// # assert_eq!(BTreeSet::from_iter(vec![0, 1]), net.get_parent_set(2));
+/// ```
 pub struct CTPC<P: ParameterLearning> {
     parameter_learning: P,
     Ftest: F,

reCTBN/src/structure_learning/hypothesis_test.rs

@@ -39,6 +39,17 @@ pub struct ChiSquare {
     alpha: f64,
 }
 
+/// Does the F-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 F {
     alpha: f64,
 }
@@ -48,6 +59,20 @@ impl F {
         F { alpha }
     }
 
+    /// 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 **independendent**.
+    /// * `false` - when the matrices `M1` and `M2` are too different, then **dependent**.
+
     pub fn compare_matrices(
         &self,
         i: usize,
@@ -164,26 +189,8 @@ impl ChiSquare {
         // continuous-time Bayesian networks.
         // International Journal of Approximate Reasoning, 138, pp.105-122.
         // Also: https://www.itl.nist.gov/div898/software/dataplot/refman1/auxillar/chi2samp.htm
-        //
-        // M  = M            M  = M
-        //  1    xx'|s        2    xx'|y,s
         let M1 = M1.index_axis(Axis(0), i).mapv(|x| x as f64);
         let M2 = M2.index_axis(Axis(0), j).mapv(|x| x as f64);
-        //                   __________________
-        //                  /    ===
-        //                 /     \       M
-        //                /      /        xx'|s
-        //               /       ===
-        //              /    x'ϵVal /X \
-        //             /            \ i/                  1
-        //K =         /      ------------------       L = -
-        //           /           ===                      K
-        //          /            \       M
-        //         /             /        xx'|y,s
-        //        /              ===
-        //       /           x'ϵVal /X \
-        //   \  /                   \ i/
-        //    \/
         let K = M1.sum_axis(Axis(1)) / M2.sum_axis(Axis(1));
         let K = K.mapv(f64::sqrt);
         // Reshape to column vector.
@@ -191,34 +198,16 @@ impl ChiSquare {
             let n = K.len();
             K.into_shape((n, 1)).unwrap()
         };
-        //println!("K: {:?}", K);
         let L = 1.0 / &K;
-        //        =====                   2
-        //         \      (K . M  - L . M)
-        //          \           2        1
-        //          /      ---------------
-        //         /           M  + M
-        //        =====         2    1
-        //     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);
         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)));
         let ret = X_2.into_iter().all(|x| n.cdf(x) < (1.0 - self.alpha));
-        //println!("test: {:?}", ret);
         ret
     }
 }
 
-// ritorna false quando sono dipendenti e false quando sono indipendenti
 impl HypothesisTest for ChiSquare {
     fn call<T, P>(
         &self,
@@ -233,13 +222,9 @@ impl HypothesisTest for ChiSquare {
         T: process::NetworkProcess,
         P: parameter_learning::ParameterLearning,
     {
-        // Prendo dalla cache l'apprendimento dei parametri, che sarebbe una CIM
-        // di dimensione nxn
-        //  (CIM, M, T)
         let P_small = match cache.fit(net, &dataset, child_node, Some(separation_set.clone())) {
             Params::DiscreteStatesContinousTime(node) => node,
         };
-        //
         let mut extended_separation_set = separation_set.clone();
         extended_separation_set.insert(parent_node);
 
@@ -251,7 +236,6 @@ impl HypothesisTest for ChiSquare {
         ) {
             Params::DiscreteStatesContinousTime(node) => node,
         };
-        // Commentare qui
         let partial_cardinality_product: usize = extended_separation_set
             .iter()
             .take_while(|x| **x != parent_node)