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]

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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

6.70 score 23 stars 18 scripts 313 downloads 3 exports 6 dependencies

Last updated from:d5453e58ee. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK153
linux-devel-x86_64OK150
source / vignettesOK227
linux-release-arm64OK157
linux-release-x86_64OK157
macos-release-arm64OK81
macos-release-x86_64OK294
macos-oldrel-arm64OK82
macos-oldrel-x86_64OK218
windows-develOK167
windows-releaseOK158
windows-oldrelOK134
wasm-releaseOK157

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