# Several Examined and Concealed States-Dependent Speciation and Extinction

## Documentation for package ‘secsse’ version 3.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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