Several Examined and Concealed States-Dependent Speciation and Extinction


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Documentation for package ‘secsse’ version 2.0.0

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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
example_phy_GeoSSE A phylogeny with traits at the tips
id_paramPos Parameter structure setting
phy A phylogeny with traits at the tips
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