hisse

2.1.11

Hidden State Speciation and Extinction

1packages depend

11.4Kdownloads / year

38.0%test coverage

0/13checks pass

Overview

About

Maintained by Jeremy BeaulieuFirst published 2015-02-2034 releasesCRAN page ↗

Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) doi:10.1093/sysbio/syw022.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)

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

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

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-hisse

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-hisse

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

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

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 12.5 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.10

38.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-06-09
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-25
0 OK · 12 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-30
0 OK · 13 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 99%
Return-value docs: 77%
References docs: 77%

Downloads

11.4K

CRAN downloads in the past year

Rank #7,158 · ~31/day · ~951/mo

Releases R versions

Daily download trend is not available in this view yet.

38930 days

1.5K90 days

11.4K1 year

Compare downloads with other packages →

Also on404 r2u106 c2d4u

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Depends (5)

ape deSolve GenSA subplex nloptr

Imports (12)

parallelphytools data.table igraphmethodsdiversitree paleotree plotrix geiger phangorn TreeSim corHMM

LinkingTo (0)

none

Suggests (4)

testthat knitr rmarkdown markdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

fishtree

Code & Tests

Code Composition

R 18,868 (65%)C 5,357 (18%)Rd 2,845 (10%)Vignettes 2,058 (7%)Other 53 (0%)

Code characteristics

Object systems

S318

Cyclomatic complexity: 5.0 median / 51 max
Test cases: 43 / 0.10 per code line

Test coverage

Line coverage

38%

Expression

38.3%

Tests / Examples

38.0% / 0% ex

Functions

253 50 exported

Complexity

10.4 avg / 51 max

Call network

253 nodes / 280 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

253 functions

Function	Cyclo	Coverage
AddFossilPoints exp	2	0%
AddStratIntervals exp	2	0%
GeoHiSSE exp	37	0%
GeoHiSSE.old exp	49	0%
GetAICWeights exp	2	0%
GetModelAveRates exp	33	0%

People & History

People (5)

Maintainer (1)

Jeremy Beaulieu

Author, Maintainer · added in 1.8.4

Authors (5)

Jeremy Beaulieu

Author, Maintainer · added in 1.8.4

James Boyko

Author · added in 1.9.6

Daniel Caetano

Author · added in 1.8.6

Brian O'Meara

Author

Thais Vasconcelos

Author · added in 2.1.5

Listed in earlier versions (1)

Jeremy M. Beaulieu

no longer listed · 1.0 to 1.8.2

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
2.1.11Latest
2023-02-11 · current release · diff ↗
unarchivedReturned to CRAN
2023-02-11
archivedRemoved from CRAN
2023-02-04
issues were not corrected in time
2.1.10
2023-01-19 · diff ↗
2.1.9
2022-06-15 · diff ↗
unarchivedReturned to CRAN
2022-06-15
archivedRemoved from CRAN
2022-06-11
requires archived package 'corHMM'
2.1.8
2022-06-09 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.1.6
2021-11-16 · diff ↗
2.1.5
2021-11-11 · diff ↗
R
R 4.1.0 released · 2021-05-18

Show 37 earlier events

1.9.19
2021-05-15 · diff ↗
1.9.18
2021-02-20 · diff ↗
1.9.13
2021-01-19 · diff ↗
1.9.10
2020-10-28 · diff ↗
1.9.9
2020-10-20 · diff ↗
1.9.8
2020-06-15 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.9.6
2019-12-06 · diff ↗
1.9.5
2019-07-11 · diff ↗
1.9.4
2019-05-10 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.9.1
2019-02-20 · diff ↗
1.9.0
2019-01-28 · diff ↗
unarchivedReturned to CRAN
2019-01-28
archivedRemoved from CRAN
2019-01-25
issues were not corrected in time Has 'src/Makevars.in' without configure
1.8.9
2018-11-06 · diff ↗
1.8.8
2018-10-20 · diff ↗
1.8.7
2018-10-19 · diff ↗
1.8.6
2018-09-25 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.8.5
2017-10-10 · diff ↗
1.8.4
2017-07-23 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.8.2
2017-04-05 · diff ↗
1.8.1
2017-02-21 · diff ↗
1.8
2016-08-25 · diff ↗
1.7
2016-06-14 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.6
2016-03-30 · diff ↗
1.5
2016-03-19 · diff ↗
1.4
2016-01-07 · diff ↗
1.3
2015-10-03 · diff ↗
1.2
2015-09-25 · diff ↗
1.1
2015-06-17 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.0
2015-02-20
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2015-02-20
Total releases: 34 / 11 yrs
License: GPL (>= 2) OSI
Download size: 2.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

Report a problem with this page →