Package: treestructure 1.0.1

Erik Volz

treestructure: Detect Population Structure Within Phylogenetic Trees

Algorithms for detecting population structure from the history of coalescent events recorded in phylogenetic trees. This method classifies each tip and internal node of a tree into disjoint sets characterized by similar coalescent patterns.

Authors:Erik Volz [aut, cre], Fabricia F. Nascimento [ctb], Vinicius B. Franceschi [ctb]

treestructure_1.0.1.tar.gz
treestructure_1.0.1.zip(r-4.7-x86_64)treestructure_1.0.1.zip(r-4.7-arm64)treestructure_1.0.1.zip(r-4.6-x86_64)treestructure_1.0.1.zip(r-4.6-arm64)treestructure_1.0.1.zip(r-4.5-x86_64)
treestructure_1.0.1.tgz(r-4.6-x86_64)treestructure_1.0.1.tgz(r-4.6-arm64)treestructure_1.0.1.tgz(r-4.5-x86_64)treestructure_1.0.1.tgz(r-4.5-arm64)
treestructure_1.0.1.tar.gz(r-4.7-arm64)treestructure_1.0.1.tar.gz(r-4.7-x86_64)treestructure_1.0.1.tar.gz(r-4.6-arm64)treestructure_1.0.1.tar.gz(r-4.6-x86_64)
treestructure_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
treestructure/json (API)

# Install 'treestructure' in R:
install.packages('treestructure', repos = c('https://emvolz-phylodynamics.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/emvolz-phylodynamics/treestructure/issues

Pkgdown/docs site:https://emvolz-phylodynamics.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

6.52 score 23 stars 18 scripts 336 downloads 3 exports 6 dependencies

Last updated from:d5453e58ee. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK106
linux-devel-x86_64OK191
source / vignettesOK205
linux-release-arm64OK150
linux-release-x86_64OK143
macos-release-arm64OK134
macos-release-x86_64OK376
macos-oldrel-arm64OK118
macos-oldrel-x86_64OK458
windows-devel-arm64OK338
windows-devel-x86_64OK175
windows-release-arm64OK382
windows-release-x86_64OK135
windows-oldrel-x86_64OK122
wasm-releaseOK109

Exports:addtipstreestructure.testtrestruct

Dependencies:apedigestlatticenlmeRcpprlang

Calibrating cluster detection to a false discovery rate
Why a false discovery rate? | What fdr controls | A test for any structure at all | The false discovery rate is controlled | Serially sampled (heterochronous) trees | Large trees: Bonferroni vs Benjamini-Hochberg | Combining with node support
Rendered fromfalse_discovery_rate.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2026-07-02

Node support values using treestructure (v2)
Introduction | Assign clusters without using node support | Sensitivity to the minimum clade size | Assign clusters using branch support | Using the CH-index
Rendered fromsupportValues.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2025-09-23

treestructure applied to structured coalescent simulation
Structured coalescent simulation | Plotting results | Parameter choice and number of clusters | False discovery rate (default) | Subjective significance level | CH index
Rendered fromtreestructure.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2025-03-28

Update of a treestructure object with new sequences
Introduction | Assign clusters using node support | Update a previous treestrucuture object with new sequences
Rendered fromupdating_treestructure.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2025-09-23