treeclimbR
Bioc currentAn algorithm to find optimal signal levels in a tree
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
The arrangement of hypotheses in a hierarchical structure appears in many research fields and often indicates different resolutions at which data can be viewed. This raises the question of which resolution level the signal should best be interpreted on. treeclimbR provides a flexible method to select optimal resolution levels (potentially different levels in different parts of the tree), rather than cutting the tree at an arbitrary level. treeclimbR uses a tuning parameter to generate candidate resolutions and from these selects the optimal one.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
43 26 exported
Complexity
8.1 avg / 40 max
Call network
43 nodes / 82 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
13,427
Files
92
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
26
Internal functions
17
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.92
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
11.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
5
First release
2024-04-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 24 (1 internal)includes a package overview page
- Examples that run
- 100%23 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 95%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- treeclimbR HTML
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/csoneson/treeclimbr on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-04-28 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| da_sim_100_30_18de | – | – | – |
| ds_sim_20_500_8de | – | – | – |
| throat_v35 | – | – | – |
| tinytree_counts | – | – | – |
Topics
People
- Charlotte Soneson author maintainer
- Ruizhu Huang author
Cite
Cite this package
Run in R for the authors' entry:
citation("treeclimbR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s13059-021-02368-1.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.