cla_id_paramPos         Parameter structure setting for cla_secsse It
                        sets the parameters (speciation, extinction and
                        transition) IDs. Needed for ML calculation with
                        cladogenetic options (cla_secsse_ml)
cla_secsse_loglik       Likelihood for SecSSE model, using Rcpp
                        Loglikelihood calculation for the cla_SecSSE
                        model given a set of parameters and data using
                        Rcpp
cla_secsse_ml           Maximum likehood estimation for (SecSSE)
cla_secsse_ml_func_def_pars
                        Maximum likehood estimation for (SecSSE) with
                        parameter as complex functions. Cladogenetic
                        version
create_default_lambda_transition_matrix
                        Helper function to create a default lambda list
create_default_shift_matrix
                        Helper function to create a default
                        'shift_matrix' list
create_lambda_list      Helper function to automatically create lambda
                        matrices, based on input. When choosing the CTD
                        model, rates associated with observed states
                        are now re-distributed to concealed states.
                        This implicitly assumes that the number of
                        observed and concealed states is identical.
create_mu_vector        Generate mus vector
create_q_matrix         Helper function to neatly setup a Q matrix,
                        without transitions to concealed states (only
                        observed transitions shown)
event_times             Event times of a (possibly non-ultrametric)
                        phylogenetic tree
example_phy_GeoSSE      A phylogeny with traits at the tips
expand_q_matrix         Function to expand an existing q_matrix to a
                        number of concealed states
extract_par_vals        Extract parameter values out of the result of a
                        maximum likelihood inference run
fill_in                 Helper function to enter parameter value on
                        their right place
id_paramPos             Parameter structure setting Sets the parameters
                        (speciation, extinction and transition) ids.
                        Needed for ML calculation ('secsse_ml()').
phylo_vignette          A phylogenetic reconstuction to run the
                        vignette
plot_idparslist         function to visualize the structure of the
                        idparslist
plot_state_exact        Plot the local probability along a tree
prepare_full_lambdas    Prepares the entire set of lambda matrices for
                        cla_secsse. It provides the set of matrices
                        containing all the speciation rates
q_doubletrans           Basic Qmatrix Sets a Q matrix where double
                        transitions are not allowed
secsse_loglik           Likelihood for SecSSE model Loglikelihood
                        calculation for the SecSSE model given a set of
                        parameters and data
secsse_loglik_eval      Likelihood for SecSSE model Logikelihood
                        calculation for the SecSSE model given a set of
                        parameters and data, returning also the
                        likelihoods along the branches
secsse_ml               Maximum likehood estimation for (SecSSE)
secsse_ml_func_def_pars
                        Maximum likehood estimation for (SecSSE)
                        complex functions as parameter
secsse_sim              Function to simulate a tree, conditional on
                        observing all states.
secsse_single_branch_loglik
                        Likelihood for SecSSE model Loglikelihood
                        calculation for the SecSSE model given a set of
                        parameters and data, calculated for a single
                        branch
sortingtraits           Data checking and trait sorting In preparation
                        for likelihood calculation, it orders trait
                        data according the tree tips
traits                  A table with trait info to run the vignette
