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>.

Version: 3.5.0
Depends: R (≥ 4.2.0)
Imports: utils, DDD (≥ 5.0), ape, geiger, Rcpp (≥ 1.0.10), RcppParallel, ggplot2, tibble, rlang, treestats
LinkingTo: Rcpp, RcppParallel, BH (≥ 1.81.0-1)
Suggests: diversitree, phytools, testthat, subplex, knitr, rmarkdown
Published: 2025-07-24
DOI: 10.32614/CRAN.package.secsse
Author: Leonel Herrera Alsina ORCID iD [aut], Paul van Els ORCID iD [aut], Thijs Janzen ORCID iD [ctb], Hanno Hildenbrandt ORCID iD [ctb], Pedro Santos Neves ORCID iD [ctb], Rampal S. Etienne ORCID iD [cre, aut]
Maintainer: Rampal S. Etienne <r.s.etienne at rug.nl>
BugReports: https://github.com/rsetienne/secsse/issues
License: GPL (≥ 3) | file LICENSE
Copyright: see file COPYRIGHTS
URL: https://rsetienne.github.io/secsse/, https://github.com/rsetienne/secsse
NeedsCompilation: yes
SystemRequirements: C++17
Citation: secsse citation info
Materials: NEWS
In views: Phylogenetics
CRAN checks: secsse results

Documentation:

Reference manual: secsse.html , secsse.pdf
Vignettes: Using secsse with complete phylogenies (with extinction) (source, R code)
Plotting probabilities (source, R code)
Simulating with secsse (source, R code)
Starting secsse (source, R code)

Downloads:

Package source: secsse_3.5.0.tar.gz
Windows binaries: r-devel: secsse_3.5.0.zip, r-release: secsse_3.5.0.zip, r-oldrel: secsse_3.5.0.zip
macOS binaries: r-release (arm64): secsse_3.5.0.tgz, r-oldrel (arm64): secsse_3.5.0.tgz, r-release (x86_64): secsse_3.5.0.tgz, r-oldrel (x86_64): secsse_3.5.0.tgz
Old sources: secsse archive

Linking:

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