cla_id_paramPos         Parameter structure setting for cla_secsse
cla_secsse_loglik       Likelihood for SecSSE model
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
event_times             Event times of a (possibly non-ultrametric)
                        phylogenetic tree
example_phy_GeoSSE      A phylogeny with traits at the tips
id_paramPos             Parameter structure setting
phylo_Vign              A phylogenetic reconstuction to run the
                        vignette
prepare_full_lambdas    Prepares the entire set of lambda matrices for
                        cla_secsse.
q_doubletrans           Basic Qmatrix
secsse_loglik           Likelihood for SecSSE model
secsse_ml               Maximum likehood estimation for (SecSSE)
secsse_ml_func_def_pars
                        Maximum likehood estimation for (SecSSE) with
                        parameter as complex functions.
sortingtraits           Data checking and trait sorting
traitinfo               A table with trait info to run the vignette
