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:
secsse_3.1.0.tar.gz
secsse_3.1.0.zip(r-4.5)secsse_3.1.0.zip(r-4.4)secsse_3.1.0.zip(r-4.3)
secsse_3.1.0.tgz(r-4.4-x86_64)secsse_3.1.0.tgz(r-4.4-arm64)secsse_3.1.0.tgz(r-4.3-x86_64)secsse_3.1.0.tgz(r-4.3-arm64)
secsse_3.1.0.tar.gz(r-4.5-noble)secsse_3.1.0.tar.gz(r-4.4-noble)
secsse.pdf |secsse.html✨
secsse/json (API)
NEWS
# Install 'secsse' in R: |
install.packages('secsse', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rsetienne/secsse/issues
- example_phy_GeoSSE - A phylogeny with traits at the tips
- phylo_vignette - A phylogenetic reconstuction to run the vignette
- traits - A table with trait info to run the vignette
Last updated 4 months agofrom:814dca97b4. Checks:OK: 7 NOTE: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 28 2024 |
R-4.5-win-x86_64 | NOTE | Aug 28 2024 |
R-4.5-linux-x86_64 | NOTE | Aug 28 2024 |
R-4.4-win-x86_64 | OK | Aug 28 2024 |
R-4.4-mac-x86_64 | OK | Aug 28 2024 |
R-4.4-mac-aarch64 | OK | Aug 28 2024 |
R-4.3-win-x86_64 | OK | Aug 28 2024 |
R-4.3-mac-x86_64 | OK | Aug 28 2024 |
R-4.3-mac-aarch64 | OK | Aug 28 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:apeBHcliclusterGenerationcodacodetoolscolorspacecombinatcpp11DDDDEoptimdeSolvedigestdoParallelexpmfansifarverfastmatchforeachgeigergenericsggplot2ggseqlogogluegtableigraphisobanditeratorslabelinglatticelifecyclemagrittrmapsMASSMatrixmgcvmnormtmunsellmvtnormncbitnlmenloptrnumDerivoptimParallelphangornphytoolspillarpkgconfigquadprogR6RColorBrewerRcppRcppEigenRcppParallelrlangscalesscatterplot3dSparseMsubplextibbletreestatsutf8vctrsviridisLitewithr
Plotting probabilities
Rendered fromplotting_states.Rmd
usingknitr::rmarkdown
on Aug 28 2024.Last update: 2023-07-27
Started: 2023-04-26
Simulating with secsse
Rendered fromsim_with_secsse.Rmd
usingknitr::rmarkdown
on Aug 28 2024.Last update: 2023-07-27
Started: 2023-07-27
Starting secsse
Rendered fromstarting_secsse.Rmd
usingknitr::rmarkdown
on Aug 28 2024.Last update: 2023-10-03
Started: 2023-07-27
Using secsse with complete phylogenies (with extinction)
Rendered fromcomplete_tree.Rmd
usingknitr::rmarkdown
on Aug 28 2024.Last update: 2023-10-03
Started: 2023-07-27