Several Examined and Concealed States-Dependent Speciation and Extinction


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Documentation for package ‘secsse’ version 2.6.0

Help Pages

cla_id_paramPos Parameter structure setting for cla_secsse
cla_secsse_eval Likelihood for SecSSE model, using Rcpp
cla_secsse_loglik Likelihood for SecSSE model, 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_list helper function to create a default lambda list
create_default_q_list helper function to create a default q_matrix list
create_lambda_matrices helper function to automatically create lambda matrices, based on input
create_mus function to generate generic mus vector
create_transition_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 function to 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
phy A phylogeny with traits at the tips
phylo_Vign A phylogenetic reconstuction to run the vignette
plot_state_exact function to plot the local probability along the tree, including the branches
plot_state_exact_cla function to plot the local probability along the tree, including the branches, for the CLA model.
prepare_full_lambdas Prepares the entire set of lambda matrices for cla_secsse.
q_doubletrans Basic Qmatrix
secsse_loglik Likelihood for SecSSE model
secsse_loglik_eval 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.
secsse_sim Function to simulate a tree, conditional on observing all states.
sortingtraits Data checking and trait sorting
traitinfo A table with trait info to run the vignette