calc_expected_hidden_nodes
                        Calculate the number of expected hidden nodes
                        in a phylogenetic tree
calc_fraction           Calculate the expected fraction of
                        substitutions at the nodes, relative to the
                        fraction at the branches
calc_required_node_time
                        Calculate the required node time to obtain a
                        desired fraction of substitutions at the node
calc_sum_stats          calculate summary statistics of a phylogenetic
                        tree, compared with a reference tree. The
                        following statistics are calculated: the beta
                        statistic, gamma statistic, crown age, mean
                        branch length, number of tips, the nLTT
                        statistic and the laplacian difference, given
                        by RPANDA's JSDtree. Because JSDtree can
                        sometimes cause issues, some additional checks
                        are performed to ensure that is possible to run
                        this function.
count_hidden            Function to calculate the number of hidden
                        speciation events, e.g. speciation events that
                        have lead to an extinct species. Thus, these
                        hidden speciation events can only be detected
                        in complete trees (as opposed to reconstructed
                        trees).
create_balanced_tree    create a balanced tree out of branching times
create_equal_alignment
                        function create an alignment with identical
                        information content
create_equal_alignment_explicit
                        function create an alignment with identical
                        information content, using the explicit method
                        to simulate substitutions
create_unbalanced_tree
                        create an unbalanced tree out of branching
                        times
estimate_marginal_models
                        estimate the marginal likelihood of the relaxed
                        and strict clock model for a provided alignment
get_p_matrix            calculate p matrix
infer_phylogeny         infer the time calibrated phylogeny associated
                        with the provided alignment. This function uses
                        the R package babette to infer the phylogeny
                        using BEAST2.
nodeSub-package         Package providing functions to simulate
                        sequences under different DNA evolution models
reduce_tree             Function to remove speciation events occuring
                        after an extinction event. Extinct species are
                        pruned randomly, such that only a single
                        extinct species per branching event (if any
                        extinct species) remains.
sim_linked              simulate a sequence assuming conditional
                        substitutions on the node.
sim_normal              Simulate sequences for a given evolutionary
                        tree, using a standard model of sequence
                        evolution along the branches. Code for this
                        function was heavily inspired by the function
                        'simSeq' from the phangorn package.
sim_normal_explicit     simulate a sequence assuming substitutions are
                        only accumulated along the branches, using the
                        explicit simulation method (e.g. reverse
                        substitutions are modeled explicitly)
sim_unlinked            Simulate a sequence assuming node substitutions
                        are not shared amongst offspring, given two
                        substitution matrices: one for substitutions
                        occuring on the nodes, and one for
                        substitutions occuring along the branches.
sim_unlinked_explicit   Simulate a sequence assuming node substitutions
                        are not shared amongst offspring, using the
                        explicit simulation method (e.g. reverse
                        substitutions are modeled explicitly)
slow_matrix             this function calculates the p matrix within R
                        this is slower than the C++ implementation in
                        'get_p_matrix' but provides a way to debug and
                        verify
