Package: secsse 3.1.0

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

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>.

Authors:Leonel Herrera Alsina [aut], Paul van Els [aut], Thijs Janzen [ctb], Hanno Hildenbrandt [ctb], Pedro Santos Neves [ctb], Rampal S. Etienne [cre, aut]

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secsse.pdf |secsse.html✨
secsse/json (API)
NEWS

# Install 'secsse' in R:
install.packages('secsse', repos = c('https://rsetienne.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/rsetienne/secsse/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

5.79 score 1 stars 31 scripts 675 downloads 24 exports 64 dependencies

Last updated 7 months agofrom:814dca97b4. Checks:OK: 7 NOTE: 1 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-win-x86_64ERROROct 27 2024
R-4.5-linux-x86_64NOTEOct 27 2024
R-4.4-win-x86_64OKOct 27 2024
R-4.4-mac-x86_64OKOct 27 2024
R-4.4-mac-aarch64OKOct 27 2024
R-4.3-win-x86_64OKOct 27 2024
R-4.3-mac-x86_64OKOct 27 2024
R-4.3-mac-aarch64OKOct 27 2024

Exports:cla_id_paramPoscla_secsse_loglikcla_secsse_mlcla_secsse_ml_func_def_parscreate_default_lambda_transition_matrixcreate_default_shift_matrixcreate_lambda_listcreate_mu_vectorcreate_q_matrixdefault_params_docevent_timesexpand_q_matrixextract_par_valsfill_inid_paramPosplot_state_exactprepare_full_lambdasq_doubletranssecsse_logliksecsse_loglik_evalsecsse_mlsecsse_ml_func_def_parssecsse_simsortingtraits

Dependencies:apeBHcliclusterGenerationcodacodetoolscolorspacecombinatcpp11DDDDEoptimdeSolvedigestdoParallelexpmfansifarverfastmatchforeachgeigergenericsggplot2gluegtableigraphisobanditeratorslabelinglatticelifecyclemagrittrmapsMASSMatrixmgcvmnormtmunsellmvtnormncbitnlmenloptrnumDerivoptimParallelphangornphytoolspillarpkgconfigquadprogR6RColorBrewerRcppRcppEigenRcppParallelrlangscalesscatterplot3dSparseMsubplextibbletreestatsutf8vctrsviridisLitewithr

Plotting probabilities

Thijs Janzen

Rendered fromplotting_states.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2023-07-27
Started: 2023-04-26

Simulating with secsse

Thijs Janzen

Rendered fromsim_with_secsse.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2023-07-27
Started: 2023-07-27

Starting secsse

Thijs Janzen

Rendered fromstarting_secsse.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2023-10-03
Started: 2023-07-27

Using secsse with complete phylogenies (with extinction)

Pedro Santos Neves

Rendered fromcomplete_tree.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2023-10-03
Started: 2023-07-27

Readme and manuals

Help Manual

Help pageTopics
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_id_paramPos
Likelihood for SecSSE model, using Rcpp Loglikelihood calculation for the cla_SecSSE model given a set of parameters and data using Rcppcla_secsse_loglik
Maximum likehood estimation for (SecSSE)cla_secsse_ml
Maximum likehood estimation for (SecSSE) with parameter as complex functions. Cladogenetic versioncla_secsse_ml_func_def_pars
Helper function to create a default lambda listcreate_default_lambda_transition_matrix
Helper function to create a default 'shift_matrix' listcreate_default_shift_matrix
Helper function to automatically create lambda matrices, based on inputcreate_lambda_list
Generate mus vectorcreate_mu_vector
Helper function to neatly setup a Q matrix, without transitions to concealed states (only observed transitions shown)create_q_matrix
Event times of a (possibly non-ultrametric) phylogenetic treeevent_times
A phylogeny with traits at the tipsexample_phy_GeoSSE
Function to expand an existing q_matrix to a number of concealed statesexpand_q_matrix
Extract parameter values out of the result of a maximum likelihood inference runextract_par_vals
Helper function to enter parameter value on their right placefill_in
Parameter structure setting Sets the parameters (speciation, extinction and transition) ids. Needed for ML calculation ('secsse_ml()').id_paramPos
A phylogenetic reconstuction to run the vignettephylo_vignette
Plot the local probability along a treeplot_state_exact
Prepares the entire set of lambda matrices for cla_secsse. It provides the set of matrices containing all the speciation ratesprepare_full_lambdas
Basic Qmatrix Sets a Q matrix where double transitions are not allowedq_doubletrans
Likelihood for SecSSE model Loglikelihood calculation for the SecSSE model given a set of parameters and datasecsse_loglik
Likelihood for SecSSE model Logikelihood calculation for the SecSSE model given a set of parameters and data, returning also the likelihoods along the branchessecsse_loglik_eval
Maximum likehood estimation for (SecSSE)secsse_ml
Maximum likehood estimation for (SecSSE) with parameter as complex functions.secsse_ml_func_def_pars
Function to simulate a tree, conditional on observing all states.secsse_sim
Data checking and trait sorting In preparation for likelihood calculation, it orders trait data according the tree tipssortingtraits
A table with trait info to run the vignettetraits