This package was removed from CRAN on 2023-09-28. Its history is shown below.

Reason: requires archived package 'apTreeshape'

Details below reflect version 1.1.0, its last release before removal.

treeducken

1.1.0

Nested Phylogenetic Tree Simulator

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Wade Dismukes2 releasesCRAN page ↗

Simulates nested phylogenetic trees (gene trees in species tree, symbiont trees in host trees) using birth-death processes and transfers between lineages. Simulations of gene trees within species trees are performed using a three-tree model with species trees, locus trees, and gene trees. The cophylogenetic birth-death process is used to simulate sets of host and symbiont trees with extant associations between tips. For more information about the three-tree model see: Mallo et al. (2015) doi:10.1093/sysbio/syv082, Rasmussen and Kellis (2012) doi:10.1101/gr.123901.111.

Install

R (source archive)Ubuntu (r2u)openSUSE (OBS)

url <- "https://cran.r-project.org/src/contrib/Archive/treeducken/treeducken_1.1.0.tar.gz"
pkgFile <- "treeducken_1.1.0.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.1.0) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-treeducken

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

# 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-treeducken

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.09

not tracked

Coverage

Dependencies · direct

Documentation

READMEYes · 237 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 42%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on342 r2u13 autocran36 c2d4u

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

ape

Imports (4)

Rcpp apTreeshapegraphicsmethods

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Code Composition

C++ 5,199 (46%)R 3,198 (28%)Rd 1,978 (18%)C 666 (6%)Vignettes 217 (2%)Shell 7 (0%)

Code characteristics

Object systems

S322

Cyclomatic complexity: 1.0 median / 23 max
Test cases: 11 / 0.09 per code line
System requirements: 1 external

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

283 0 exported

Complexity

3.1 avg / 23 max

Call network

283 nodes / 66 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (10)

Maintainer (1)

Wade Dismukes

Author, Maintainer

Authors (2)

Wade Dismukes

Author, Maintainer

Tracy A.

Author

Contributors (8)

Contributor

Contributor

Contributor

Contributor

Contributor

Contributor

Contributor

Contributor

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2023-09-28
requires archived package 'apTreeshape'
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.1.0
2021-03-02 · diff ↗
1.0.0
2020-10-06
R
R 4.0.0 released · 2020-04-24

Package metadata

Total releases: 2
License: GPL-3 OSI
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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