secsse

3.7.0

Several Examined and Concealed States-Dependent Speciation and Extinction

0packages depend

4.4Kdownloads / year

91.0%test coverage

13/13checks pass

Overview

About

Maintained by Rampal S. EtienneFirst published 2019-01-3013 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("secsse", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("rsetienne/secsse")

Development version from rsetienne/secsse. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-secsse

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-secsse

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-secsse

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 5.2 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.70

91.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-06-07
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 88%
References docs: 0%

Downloads

4.4K

CRAN downloads in the past year

Rank #6,927 · ~12/day · ~371/mo

Releases R versions

Daily download trend is not available in this view yet.

38230 days

1.4K90 days

4.4K1 year

Compare downloads with other packages →

Also on417 r2u42 autocran58 c2d4u

Repository

GitHub ↗ rsetienne/secsse

1Stars

2Forks

0Open issues

1Open PRs

2Releases

880Commits

8Contributors

License GPL-3.0 · 880 commits · Last activity 2026-06-10

Stars over time

2023-04-11 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/rsetienne/secsse on 2026-07-26.

Continuous integration (1)

GitHub Actions

Research and citation (1)

Zenodo

Lint, format, editor (2)

VS CodeRStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (11)

utilsDDD ape geiger Rcpp RcppParallel ggplot2 tibble rlang treestats pracma

LinkingTo (3)

Rcpp RcppParallel BH

Suggests (6)

diversitree phytools testthat subplex knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Rampal S. Etienne

Maintainer, Author · added in 2.0.7

Authors (3)

Rampal S. Etienne

Maintainer, Author · added in 2.0.7

Leonel Herrera Alsina

Author

Paul van Els

Author

Contributors (3)

Hanno Hildenbrandt

Contributor · added in 2.5.0

Thijs Janzen

Contributor · added in 2.5.0

Pedro Santos Neves

Contributor · added in 2.6.0

Listed in earlier versions (1)

Rampal Etienne

no longer listed · 1.0.0 to 2.0.0

Package Timeline

13 releases. Pick two to compare their code metrics. R releases are shown for context.

3.7.0Latest
2026-05-15 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
3.5.0
2025-07-24 · diff ↗
R
R 4.5.0 released · 2025-04-11
3.1.0
2024-04-30 · diff ↗
R
R 4.4.0 released · 2024-04-24
3.0.2
2023-10-22 · diff ↗
2.6.0
2023-07-06 · diff ↗
unarchivedReturned to CRAN
2023-07-06
archivedRemoved from CRAN
2023-05-17
issues were not corrected in time
2.5.0
2023-05-03 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
2.1.7
2021-07-16 · diff ↗
2.1.5
2021-05-25 · diff ↗
2.1.4
2021-05-23 · diff ↗

Show 13 earlier events

R
R 4.1.0 released · 2021-05-18
2.0.7
2021-02-12 · diff ↗
unarchivedReturned to CRAN
2021-02-12
archivedRemoved from CRAN
2021-01-28
check problems were not corrected in time Misuse of Fortran REAL(16)
R
R 4.0.0 released · 2020-04-24
2.0.0
2019-06-25 · diff ↗
unarchivedReturned to CRAN
2019-06-25
R
R 3.6.0 released · 2019-04-26
1.0.3
2019-03-13 · diff ↗
unarchivedReturned to CRAN
2019-03-13
, but previous problem remained so archived again
archivedRemoved from CRAN
2019-02-07
installation errors were not corrected despite reminder cleans in parallel with making SHLIB
1.0.0
2019-01-30
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-01-30
Total releases: 13 / 7 yrs
License: GPL (>= 3) | file LICENSE OSI
Minimum R: ≥ 4.2.0
Bundled data: 14 KB / 3 files
Download size: 372 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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Phylogenetics

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