R Observatory: Metrics for DCLEAR version 1.0.13

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DCLEAR

1.0.13Package record

Distance Based Cell Lineage Reconstruction

0packages depend

3.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Il-Youp KwakCRAN page ↗GitHub ↗

R codes for distance based cell lineage reconstruction. Our methods won both sub-challenges 2 and 3 of the Allen Institute Cell Lineage Reconstruction DREAM Challenge in 2020. References: Gong et al. (2021) doi:10.1016/j.cels.2021.05.008, Gong et al. (2022) doi:10.1186/s12859-022-04633-x.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("DCLEAR", 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("ikwak2/DCLEAR")

Development version from ikwak2/DCLEAR. 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-dclear

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 4.2 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.13

READMEYes · 565 wordsVignettesYes · 2 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 57includes a package overview page
Examples that run: 100%4 run in a plain check
Exported functions with examples: 25%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #10,827 · ~9/day · ~275/mo

Releases R versions

Daily download trend is not available in this view yet.

36030 days

96090 days

3.3K1 year

Compare downloads with other packages →

Also on354 r2u

How downloads are counted

Repository

ikwak2/dclear ↗Account: ikwak2

6Stars

2Forks

1Open issues

0Open PRs

0Releases

258Commits

2Commit identities

258 commits · Last activity 2023-09-14

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 10
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2023-04-26 · 62026-07-07 · 6

How these are measured

PracticesBeta

Checks run against github.com/ikwak2/dclear on 2026-10-18.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing DCLEAR adds 53 packages (33 with compiled code, 41 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, igraph 4.8 MB. 2 more not on CRAN are not measured.

Depends (2)

R >= 4.1.0tensorflow

Imports (15)

BiocParallel dplyrMatrixmatrixStats ape phangorn Rcpp igraphmethodspurrr stringr tidyr rBayesianOptimization rlang BiocGenerics

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (3)

knitr rmarkdown markdown

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 (2)

Il-Youp Kwak

Author, Maintainer since 1.0.0 (2021)

Wuming Gong

Author

Releases (5)

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
1.0.13Latest
record
2023-09-14 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.12
record
2023-02-16 · diff ↗
1.0.11
record
2022-11-30 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.8
record
2021-09-03 · diff ↗ ·
added 1 export
positional_mutation_prob
1.0.0
record
2021-07-15
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-07-15
Total releases: 5 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 636 KB / 1 file
Download size: 678 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DCLEAR")

Format

Kwak, I., & Gong, W. (2023). DCLEAR: Distance Based Cell Lineage Reconstruction (Version 1.0.13) [Computer software]. https://doi.org/10.32614/CRAN.package.DCLEAR

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 DCLEAR version 1.0.13 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →