R Observatory: Metrics for TDbook version 0.0.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TDbook

Companion Package for the Book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574)

0packages depend

8.4Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Guangchuang YuCRAN page ↗GitHub ↗Website ↗Issues ↗

The companion package that provides all the datasets used in the book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574).

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("TDbook", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("YuLab-SMU/TDbook")

Development version from YuLab-SMU/TDbook. Installs pak first if it is not already available.

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-tdbook

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-TDbook

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# 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-TDbook

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Guangchuang Yu <guangchuangyu@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 59 s · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-07-16
WARNING11 OK, 1 NOTE, 1 WARNING2026-07-15
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.6

README· In the repository, left out of the releaseVignettesNoNEWSNoCitation fileYes · cites a publicationWebsiteYes

Help pages: 28 (1 internal)includes a package overview page
Examples that run: 100%27 run in a plain check
Exported functions with examples: not tracked
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 46%

How these are measured

Downloads

8.4K

CRAN downloads in the past year

Rank #8,327 · ~23/day · ~696/mo

Releases R versions

Daily download trend is not available in this view yet.

41130 days

1.1K90 days

8.4K1 year

Compare downloads with other packages →

Also on116 r2u12 autocran

How downloads are counted

Repository

yulab-smu/tdbook ↗Organization: YuLab-SMU

13Stars

3Forks

0Open issues

0Open PRs

0Releases

42Commits

3Commit identities

42 commits · Last activity 2022-09-15 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 86%
Median days to close, 50 most recently updated closed issues: 20
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2023-04-08 · 132026-07-07 · 13

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/yulab-smu/tdbook on 2026-10-11.

Reproducibility and dev environment (1)

Makefile

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Installing TDbook adds no packages beyond those that come with R.

Depends (1)

R >= 3.5

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Guangchuang Yu

Lin Li

Author

Shuangbin Xu

Author

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.0.6Latest
record
2022-08-13 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
0.0.5
record
2022-03-03 · diff ↗
0.0.4
record
2021-11-03 · diff ↗
0.0.3
record
2021-10-28
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-10-28
Total releases: 4 / 5 yrs
License: Artistic-2.0 OSI
Minimum R: ≥ 3.5
Bundled data: 122 KB / 28 files
Download size: 3.0 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("TDbook")

The package provides a citation file, so citation() returns the authors' own entry.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for TDbook version 0.0.6 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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