CoalescentPhylo
Phylogenetics via Root Distances Method Under the Coalescent
Description
Estimates phylogenetic trees from allele count data using the root distance method under the Coalescent Model. Given a matrix of allele counts across taxa and loci, the package estimates pairwise root distances under the Coalescent Model using maximum likelihood estimation. Then, it estimates a labeled phylogenetic tree from the estimated root distances. See Peng et al. (2021) <doi:10.1016/j.ympev.2021.107142>.
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Last 30 days
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Last 90 days
517
Last year
Trend: +164.1% (30d vs prior 30d)
2
Last 30 days
2
Last 90 days
2
Last year
0
Last 7 days
2
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0
All-time
autoCRAN-only: this name is served only by autoCRAN, so the count is exact.
CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 28, 2026
Code
Structure
Lines of code
1,558
Files
14
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
1
Internal functions
8
Recent export changes
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
100%
\dontrun example ratio
0%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
Yes
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
AGPL-3
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-05-27
Latest release
2026-05-27
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.