{ "_id": "6a1f2a97b401979e73424a15", "Package": "secsse", "Type": "Package", "Title": "Several Examined and Concealed States-Dependent Speciation and\nExtinction", "Version": "3.7.0", "License": "GPL (>= 3) | file LICENSE", "Authors@R": "c(\nperson(given = \"Leonel\",\nfamily = \"Herrera Alsina\",\nemail = \"leonelhalsina@gmail.com\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-0474-3592\")),\nperson(given = \"Paul\",\nfamily = \"van Els\",\nemail = \"paulvanels@gmail.com\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-9499-8873\")),\nperson(given = \"Thijs\",\nfamily = \"Janzen\",\nemail = \"t.janzen@rug.nl\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-4162-1140\")),\nperson(given = \"Hanno\",\nfamily = \"Hildenbrandt\",\nemail = \"h.hildenbrandt@rug.nl\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-6784-1037\")),\nperson(given = \"Pedro\",\nfamily = \"Santos Neves\",\nemail = \"p.m.santos.neves@rug.nl\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0003-2561-4677\")),\nperson(given = \"Rampal S.\",\nfamily = \"Etienne\",\nemail = \"r.s.etienne@rug.nl\",\nrole = c(\"cre\",\"aut\"),\ncomment = c(ORCID = \"0000-0003-2142-7612\")))", "Description": "Simultaneously infers state-dependent diversification\nacross two or more states of a single or multiple traits while\naccounting for the role of a possible concealed trait. See\nHerrera-Alsina et al. (2019) .", "NeedsCompilation": "yes", "SystemRequirements": "C++17", "Encoding": "UTF-8", "LazyData": "true", "URL": "https://rsetienne.github.io/secsse/,\nhttps://github.com/rsetienne/secsse", "BugReports": "https://github.com/rsetienne/secsse/issues", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Roxygen": "list(markdown = TRUE)", "Config/pak/sysreqs": "cmake libglpk-dev libgmp3-dev make libxml2-dev", "Repository": "https://rsetienne.r-universe.dev", "Date/Publication": "2026-05-15 12:11:50 UTC", "RemoteUrl": "https://github.com/rsetienne/secsse", "RemoteRef": "HEAD", "RemoteSha": "925a70cf59f6013c697ceca07237175716e20bd8", "Packaged": { "Date": "2026-05-15 14:08:20 UTC", "User": "root" }, "Author": "Leonel Herrera Alsina [aut] (ORCID:\n),\nPaul van Els [aut] (ORCID: ),\nThijs Janzen [ctb] (ORCID: ),\nHanno Hildenbrandt [ctb] (ORCID:\n),\nPedro Santos Neves [ctb] (ORCID:\n),\nRampal S. Etienne [cre, aut] (ORCID:\n)", "Maintainer": "Rampal S. 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Etienne" }, "_downloads": { "count": 289, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/secsse" }, "_devurl": "https://github.com/rsetienne/secsse", "_pkgdown": "https://rsetienne.github.io/secsse/", "_searchresults": 34, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/secsse.html", "manual.pdf" ], "_homeurl": "https://github.com/rsetienne/secsse", "_realowner": "rsetienne", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2019-01-30" }, { "version": "1.0.3", "date": "2019-03-13" }, { "version": "2.0.0", "date": "2019-06-25" }, { "version": "2.0.7", "date": "2021-02-12" }, { "version": "2.1.4", "date": "2021-05-23" }, { "version": "2.1.5", "date": "2021-05-25" }, { "version": "2.1.7", "date": "2021-07-16" }, { "version": "2.5.0", "date": "2023-05-03" }, { "version": "2.6.0", "date": "2023-07-06" }, { "version": "3.0.2", "date": "2023-10-22" }, { "version": "3.1.0", "date": "2024-04-30" }, { "version": "3.5.0", "date": "2025-07-24" } ], "_exports": [ "cla_id_paramPos", "cla_secsse_loglik", "cla_secsse_ml", "cla_secsse_ml_func_def_pars", "create_default_lambda_transition_matrix", "create_default_shift_matrix", "create_lambda_list", "create_mu_vector", "create_q_matrix", "default_params_doc", "event_times", "expand_q_matrix", "extract_par_vals", "fill_in", "id_paramPos", "plot_idparslist", "plot_state_exact", "prepare_full_lambdas", "q_doubletrans", "secsse_loglik", "secsse_loglik_eval", "secsse_ml", "secsse_ml_func_def_pars", "secsse_sim", "secsse_single_branch_loglik", "sortingtraits" ], "_datasets": [ { "name": "example_phy_GeoSSE", "title": "A phylogeny with traits at the tips", "object": "example_phy_GeoSSE", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "phylo_vignette", "title": "A phylogenetic reconstuction to run the vignette", "object": "phylo_vignette", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "traits", "title": "A table with trait info to run the vignette", "object": "traits", "class": [ "data.frame" ], "fields": [ "species", "trait" ], "rows": 68, "table": true, "tojson": true } ], "_help": [ { "page": "cla_id_paramPos", "title": "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)", "topics": [ "cla_id_paramPos" ] }, { "page": "cla_secsse_loglik", "title": "Likelihood for SecSSE model, using Rcpp Loglikelihood calculation for the cla_SecSSE model given a set of parameters and data using Rcpp", "topics": [ "cla_secsse_loglik" ] }, { "page": "cla_secsse_ml", "title": "Maximum likehood estimation for (SecSSE)", "topics": [ "cla_secsse_ml" ] }, { "page": "cla_secsse_ml_func_def_pars", "title": "Maximum likehood estimation for (SecSSE) with parameter as complex functions. Cladogenetic version", "topics": [ "cla_secsse_ml_func_def_pars" ] }, { "page": "create_default_lambda_transition_matrix", "title": "Helper function to create a default lambda list", "topics": [ "create_default_lambda_transition_matrix" ] }, { "page": "create_default_shift_matrix", "title": "Helper function to create a default 'shift_matrix' list", "topics": [ "create_default_shift_matrix" ] }, { "page": "create_lambda_list", "title": "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.", "topics": [ "create_lambda_list" ] }, { "page": "create_mu_vector", "title": "Generate mus vector", "topics": [ "create_mu_vector" ] }, { "page": "create_q_matrix", "title": "Helper function to neatly setup a Q matrix, without transitions to concealed states (only observed transitions shown)", "topics": [ "create_q_matrix" ] }, { "page": "event_times", "title": "Event times of a (possibly non-ultrametric) phylogenetic tree", "topics": [ "event_times" ] }, { "page": "example_phy_GeoSSE", "title": "A phylogeny with traits at the tips", "topics": [ "example_phy_GeoSSE" ] }, { "page": "expand_q_matrix", "title": "Function to expand an existing q_matrix to a number of concealed states", "topics": [ "expand_q_matrix" ] }, { "page": "extract_par_vals", "title": "Extract parameter values out of the result of a maximum likelihood inference run", "topics": [ "extract_par_vals" ] }, { "page": "fill_in", "title": "Helper function to enter parameter value on their right place", "topics": [ "fill_in" ] }, { "page": "id_paramPos", "title": "Parameter structure setting Sets the parameters (speciation, extinction and transition) ids. Needed for ML calculation ('secsse_ml()').", "topics": [ "id_paramPos" ] }, { "page": "phylo_vignette", "title": "A phylogenetic reconstuction to run the vignette", "topics": [ "phylo_vignette" ] }, { "page": "plot_idparslist", "title": "function to visualize the structure of the idparslist", "topics": [ "plot_idparslist" ] }, { "page": "plot_state_exact", "title": "Plot the local probability along a tree", "topics": [ "plot_state_exact" ] }, { "page": "prepare_full_lambdas", "title": "Prepares the entire set of lambda matrices for cla_secsse. It provides the set of matrices containing all the speciation rates", "topics": [ "prepare_full_lambdas" ] }, { "page": "q_doubletrans", "title": "Basic Qmatrix Sets a Q matrix where double transitions are not allowed", "topics": [ "q_doubletrans" ] }, { "page": "secsse_loglik", "title": "Likelihood for SecSSE model Loglikelihood calculation for the SecSSE model given a set of parameters and data", "topics": [ "secsse_loglik" ] }, { "page": "secsse_loglik_eval", "title": "Likelihood for SecSSE model Logikelihood calculation for the SecSSE model given a set of parameters and data, returning also the likelihoods along the branches", "topics": [ "secsse_loglik_eval" ] }, { "page": "secsse_ml", "title": "Maximum likehood estimation for (SecSSE)", "topics": [ "secsse_ml" ] }, { "page": "secsse_ml_func_def_pars", "title": "Maximum likehood estimation for (SecSSE) complex functions as parameter", "topics": [ "secsse_ml_func_def_pars" ] }, { "page": "secsse_sim", "title": "Function to simulate a tree, conditional on observing all states.", "topics": [ "secsse_sim" ] }, { "page": "secsse_single_branch_loglik", "title": "Likelihood for SecSSE model Loglikelihood calculation for the SecSSE model given a set of parameters and data, calculated for a single branch", "topics": [ "secsse_single_branch_loglik" ] }, { "page": "sortingtraits", "title": "Data checking and trait sorting In preparation for likelihood calculation, it orders trait data according the tree tips", "topics": [ "sortingtraits" ] }, { "page": "traits", "title": "A table with trait info to run the vignette", "topics": [ "traits" ] } ], "_readme": "https://github.com/rsetienne/secsse/raw/HEAD/README.md", "_rundeps": [ "ape", "BH", "cachem", "cli", "clusterGeneration", "coda", "codetools", "colorspace", "combinat", "cpp11", "DDD", "DEoptim", "deSolve", "digest", "doParallel", "expm", "farver", "fastmap", "fastmatch", "foreach", "geiger", "generics", "ggplot2", "glue", "gmp", "gtable", "igraph", "isoband", 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