Rtropical

1.2.1

Data Analysis Tools over Space of Phylogenetic Trees Using Tropical Geometry

0packages depend

2.5Kdownloads / year

17.6%test coverage

11/13checks pass

Overview

About

Maintained by Houjie WangFirst published 2021-11-091 releasesCRAN page ↗GitHub ↗

Process phylogenetic trees with tropical support vector machine and principal component analysis defined with tropical geometry. Details about tropical support vector machine are available in : Tang, X., Wang, H. & Yoshida, R. (2020) arXiv:2003.00677. Details about tropical principle component analysis are available in : Page, R., Yoshida, R. & Zhang L. (2020) doi:10.1093/bioinformatics/btaa564 and Yoshida, R., Zhang, L. & Zhang, X. (2019) doi:10.1007/s11538-018-0493-4.

Install

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

install.packages("Rtropical", 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("HoujieWang/Rtropical")

Development version from HoujieWang/Rtropical. 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-rtropical

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-Rtropical

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-Rtropical

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 10.7 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.01

17.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-05
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-04
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-07-03
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-01
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-06-15
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 10 earlier snapshots

ERROR2026-06-13
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-05-10
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-09
11 OK · 1 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-05-02
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
9 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-13
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-12
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 118 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 79%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.5K

CRAN downloads in the past year

Rank #17,418 · ~7/day · ~211/mo

Releases R versions

Daily download trend is not available in this view yet.

20430 days

67090 days

2.5K1 year

Compare downloads with other packages →

Also on93 r2u12 autocran

Repository

GitHub ↗ houjiewang/rtropical

0Stars

2Forks

0Open issues

0Open PRs

0Releases

124Commits

3Contributors

License GPL-3.0 · 124 commits · Last activity 2022-05-14

Forks over time

2021-06-24 · 22026-07-07 · 2

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/houjiewang/rtropical on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (7)

ape lpSolve lpSolveAPIparallelRfast RcppAlgos caret

LinkingTo (0)

none

Suggests (4)

rmarkdown knitr e1071 testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 1,720 (61%)Rd 995 (35%)Vignettes 95 (3%)

Code characteristics

Object systems

S38

Cyclomatic complexity: 2.0 median / 11 max
Test cases: 3 / 0.01 per code line

Test coverage

Line coverage

18%

Expression

19.5%

Tests / Examples

17.6% / 59% ex

Functions

30 20 exported

Complexity

2.9 avg / 11 max

Call network

30 nodes / 21 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

30 functions

Function	Cyclo	Coverage
coef.cv.tropsvm exp	1	0%
coef.tropsvm exp	1	0%
cv.tropsvm exp	11	0%
linsp_to_poly exp	1	0%
plot.troppca exp	10	0%
predict.cv.tropsvm exp	1	0%

People & History

People (5)

Maintainer (1)

Houjie Wang

Author, Maintainer

Authors (5)

Author, Maintainer

Author

Author

Author

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.2.1Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2021-11-09
Total releases: 1 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 329 KB / 4 files
Download size: 386 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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