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secsse (version 3.5.0)

Several Examined and Concealed States-Dependent Speciation and Extinction

Description

Simultaneously infers state-dependent diversification across two or more states of a single or multiple traits while accounting for the role of a possible concealed trait. See Herrera-Alsina et al. (2019) .

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Install

install.packages('secsse')

Monthly Downloads

278

Version

3.5.0

License

GPL (>= 3) | file LICENSE

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Repository

https://github.com/rsetienne/secsse

Homepage

https://rsetienne.github.io/secsse/

Maintainer

Rampal Etienne

Last Published

July 24th, 2025

Functions in secsse (3.5.0)

Event times of a (possibly non-ultrametric) phylogenetic tree

Helper function to enter parameter value on their right place

expand_q_matrix

Function to expand an existing q_matrix to a number of concealed states

plot_idparslist

function to visualize the structure of the idparslist

extract_par_vals

Extract parameter values out of the result of a maximum likelihood inference run

prepare_full_lambdas

Prepares the entire set of lambda matrices for cla_secsse. It provides the set of matrices containing all the speciation rates

Likelihood for SecSSE model Loglikelihood calculation for the SecSSE model given a set of parameters and data

secsse: Several Examined and Concealed States-Dependent Speciation and Extinction

Basic Qmatrix Sets a Q matrix where double transitions are not allowed

secsse_ml_func_def_pars

Maximum likehood estimation for (SecSSE) complex functions as parameter

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

Maximum likehood estimation for (SecSSE)

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

A table with trait info to run the vignette

create_default_lambda_transition_matrix

Helper function to create a default lambda list

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)

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

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

create_q_matrix

Helper function to neatly setup a Q matrix, without transitions to concealed states (only observed transitions shown)

Maximum likehood estimation for (SecSSE)

default_params_doc

Default parameter documentation

cla_secsse_ml_func_def_pars

Maximum likehood estimation for (SecSSE) with parameter as complex functions. Cladogenetic version

A phylogenetic reconstuction to run the vignette

Parameter structure setting Sets the parameters (speciation, extinction and transition) ids. Needed for ML calculation (secsse_ml()).

plot_state_exact

Plot the local probability along a tree

example_phy_GeoSSE

A phylogeny with traits at the tips

Data checking and trait sorting In preparation for likelihood calculation, it orders trait data according the tree tips

Function to simulate a tree, conditional on observing all states.