R Observatory: Metrics for tidydr version 0.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

tidydr

0.0.7Package record

Unify Dimensionality Reduction Results

0packages depend

246.2Kdownloads / year

86.3%test coverage

13/13flavors OK

Overview

About

Maintained by Guangchuang YuCRAN page ↗GitHub ↗Issues ↗

Dimensionality reduction is widely used in many domains for analyzing and visualizing high-dimensional data. 'tidydr' provides uniform output and is compatible with multiple methods, including 'prcomp', 'cmdscale', 'Rtsne', 'umap' and 'metaMDS'. Any function returning a numeric matrix can also be used. The unified result can be visualized directly with 'ggplot2', and several methods can be run and compared in a single call.

Changes in 0.0.7

nk() can now use any clustering method through fun (2026-10-08, Thu)
fun defaults to cluster::pam, so the default result is bit-for-bit unchanged
stats::kmeans works out of the box; stats::hclust is cut with cutree()
a function returning a plain vector of cluster labels is also accepted
for non-pam clusterers the silhouette width is computed with cluster::silhouette() and assembled into the same shape pam() produces
silinfo_widths() exports the fine-grained silhouette widths of one k (2026-10-08, Thu)
returns a data.frame with sample, cluster, neighbor and sil_width
the per-cluster averages are attached as the "clus.avg.widths" attribute
autoplot() for a silinfo object gained a silhouette bar plot (2026-10-08, Thu)
type = "silhouette" draws the classic per-cluster bar plot
type is inferred from k when it is not given, so autoplot(x) is unchanged and autoplot(x, k = 3) still draws the same plot — except that the sample labels are now correct (see the fix below)

Show all changes in 0.0.7Hide the rest of the changes in 0.0.7

fixed: autoplot(x, k = ) aligned pam()'s silhouette table to the samples by position, but pam() returns that table sorted by cluster; the labels are now matched by sample name (agreement with the true clustering on iris, k = 3, goes from 84% to 100%)
added dr_compare() to run several dimensionality reduction methods at once (2026-10-08, Thu)
every method is evaluated independently: a method that fails is reported in $summary with its error message instead of aborting the whole call
$summary gives method, status, n, k, has_eigenvalue, has_stress and error, so it is visible which methods ran and which did not
autoplot() facets the methods that produced plottable coordinates
DrResult gained a sample_info slot for method-specific, per-sample information (2026-10-08, Thu)
a dr_extract() method may return sample_info; fortify() merges its length-n elements into the returned data.frame as columns
print() output is unchanged
the methods advertised by available_methods() are now backed by tests (2026-10-08, Thu)
all 14 advertised methods are exercised end-to-end through dr()
vegan, smacof, ecodist, ade4, labdsv added to Suggests, together with ape, MASS, Rtsne and uwot, which the tests already used
available_methods("all") prints its closing note once instead of twice (2026-10-08, Thu)
the note is shared by the data and the distance listing but was printed from both branches, so it appeared twice; it is now printed once, after both listings
the "data" and "distance" branches are unchanged, and the returned value is unaffected
dr() now validates its data input and fails early with a tidydr-specific message instead of forwarding an obscure error from the underlying method (2026-10-08, Thu)
rejects NULL, bare vectors (hint: use as.dist() for distance vectors), non-numeric data, data.frames with non-numeric columns, and NA/NaN/Inf
dist objects remain supported
nk() now validates data and k (2026-10-08, Thu)
k = 1 is rejected: the silhouette width is undefined for a single cluster (previously produced an object that could not be printed)
k >= n, non-integer and non-numeric k are rejected with clear messages
data may still be a numeric matrix, a numeric data.frame, or a 'dist' object
fortify() no longer mishandles metadata (2026-10-08, Thu)
matrix metadata is no longer silently dropped (converted to a data.frame)
a list of length n no longer creates n junk .group.* columns
atomic vectors (including classed ones such as Date) are used as .group
unsupported types raise a warning listing the supported types
added a dr_extract() fallback for plain numeric matrices (2026-10-08, Thu)
makes stats::cmdscale() (and any wrapped method returning a bare matrix) work
any function returning a numeric matrix with at least two columns is accepted
non-numeric or single-column matrices are rejected
a hand-written dr_extract() method may return the coordinates as a numeric matrix (2026-10-08, Thu)
previously rejected with "length of 'dimnames' [2] not equal to array extent": the Dim1, Dim2, ... names were assigned with seq_along(), which counts *elements* rather than columns on a matrix
the matrix is now converted to a data.frame, so fortify() -- a 'ggplot2' generic -- always returns a data.frame
a drdata that is neither a data.frame nor a numeric matrix is now rejected with a message pointing at ?dr_extract, instead of a cryptic error
added a GitHub Actions workflow that runs R CMD check on push and PR (2026-10-08, Thu)

From NEWS.md in the release

Install

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

install.packages("tidydr", 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/tidydr")

Development version from YuLab-SMU/tidydr. 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-tidydr

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-tidydr

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-tidydr

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

13OK

CRAN check page ↗

Slowest check: 12.7 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
NOTE12 OK, 1 NOTE2026-06-07
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.7

READMEYes · 167 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.0.7Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 11 (2 internal)includes a package overview page
Examples that run: 100%5 run in a plain check
Exported functions with examples: 50%
Documented parameters: 93%
Return-value docs: 90%
Help pages citing references: 0%

Vignettes (1)

tidydr

How these are measured

Downloads

246.2K

CRAN downloads in the past year

Rank #705 · ~675/day · ~20.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

24.8K30 days

75.2K90 days

246.2K1 year

Compare downloads with other packages →

Also on8K r2u8 autocran47.9K conda_forge

How downloads are counted

Repository

yulab-smu/tidydr ↗Organization: YuLab-SMU

15Stars

7Forks

0Open issues

0Open PRs

0Releases

42Commits

4Commit identities

42 commits · Last activity 2026-10-13 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 1,493
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-06-22 · 152026-07-07 · 15

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

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

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Reproducibility and dev environment (1)

Makefile

CRAN release process (1)

CRAN-SUBMISSION

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing tidydr adds 30 packages (15 with compiled code, 18 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, fs 1.4 MB.

Depends (0)

none

Imports (7)

clusterggfun ggplot2gridrlangstatsutils

LinkingTo (0)

none

Suggests (15)

knitr rmarkdown prettydoc SingleCellExperiment SummarizedExperiment apeMASSRtsne uwot vegan smacof ecodist ade4 labdsv testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Guangchuang Yu

Shuangbin Xu

Author

Listed in earlier versions (1)

Erqiang Hu

no longer listed · 0.0.3 to 0.0.6

Releases (5)

Pick two releases to compare their code metrics.

0.0.7Latest
record
2026-10-09 · current release · diff ↗ ·
added 2 exports
dr_compare, silinfo_widths
R
R 4.6.0 released · 2026-04-24
0.0.6
record
2025-07-25 · diff ↗ ·
added 1 export
nk
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
0.0.5
record
2023-03-08 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.0.4
record
2022-03-16 · diff ↗ ·
added 1 export
available_methods
0.0.3
record
2021-12-08
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-12-08
Total releases: 5 / 5 yrs
License: Artistic-2.0 OSI
Download size: 334 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("tidydr")

Format

Yu, G., & Xu, S. (2026). tidydr: Unify Dimensionality Reduction Results (Version 0.0.7) [Computer software]. https://doi.org/10.32614/CRAN.package.tidydr

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 tidydr version 0.0.7 [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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