Several Examined and Concealed States-Dependent Speciation and Extinction
Parameter structure setting for cla_secsse It sets the parameters (spe...
Likelihood for SecSSE model, using Rcpp Loglikelihood calculation for ...
Maximum likehood estimation for (SecSSE)
Maximum likehood estimation for (SecSSE) with parameter as complex fun...
Helper function to create a default lambda list
Helper function to create a default shift_matrix list
Helper function to automatically create lambda matrices, based on inpu...
Generate mus vector
Helper function to neatly setup a Q matrix, without transitions to con...
Default parameter documentation
Event times of a (possibly non-ultrametric) phylogenetic tree
Function to expand an existing q_matrix to a number of concealed state...
Extract parameter values out of the result of a maximum likelihood inf...
Helper function to enter parameter value on their right place
Parameter structure setting Sets the parameters (speciation, extinctio...
Plot the local probability along a tree
Prepares the entire set of lambda matrices for cla_secsse. It provides...
Basic Qmatrix Sets a Q matrix where double transitions are not allowed
secsse: Several Examined and Concealed States-Dependent Speciation and...
Likelihood for SecSSE model Loglikelihood calculation for the SecSSE m...
Likelihood for SecSSE model Logikelihood calculation for the SecSSE mo...
Maximum likehood estimation for (SecSSE)
Maximum likehood estimation for (SecSSE) with parameter as complex fun...
Function to simulate a tree, conditional on observing all states.
Data checking and trait sorting In preparation for likelihood calculat...
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) <doi:10.1093/sysbio/syy057>.
Useful links