R Observatory: Metrics for DEploid version 0.5.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DEploid

0.5.7Package record

Deconvolute Mixed Genomes with Unknown Proportions

0packages depend

2.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Joe ZhuCRAN page ↗GitHub ↗Issues ↗

Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haplotype searches in a multiple infection setting. This package is primarily developed as part of the Pf3k project, which is a global collaboration using the latest sequencing technologies to provide a high-resolution view of natural variation in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from patient blood sample, which often contains more than one parasite strain, with unknown proportions. This package is used for deconvoluting mixed haplotypes, and reporting the mixture proportions from each sample.

Install

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

install.packages("DEploid", 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("DEploid-dev/DEploid-r")

Development version from DEploid-dev/DEploid-r. 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-deploid

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-DEploid

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

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 5.9 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25

Show 3 earlier changesHide 3 earlier changes

NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.5.7

READMEYes · 239 wordsVignettesYes · 1 · dynamicNEWS· In the repository, left out of the releaseCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 7 (2 internal)includes a package overview page
Examples that run: 67%4 run in a plain check · 2 never run
Exported functions with examples: 100%
Documented parameters: 95%
Return-value docs: 50%
Help pages citing references: 0%

Vignettes (1)

dEploid-Arguments HTML

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #11,435 · ~8/day · ~235/mo

Releases R versions

Daily download trend is not available in this view yet.

39030 days

92490 days

2.8K1 year

Compare downloads with other packages →

Also on353 r2u

How downloads are counted

Repository

deploid-dev/deploid-r ↗Organization: DEploid-dev

1Stars

3Forks

12Open issues

0Open PRs

10Releases

267Commits

2Commit identities

mcmcdeconvoluting-mixed-genomescranunknown-proportionshmmmalariaparasitesphasing

License file reads as GPL-3.0 · 267 commits · Last activity 2025-01-21 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 6
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2020-05-25 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/deploid-dev/deploid-r on 2026-10-11.

Continuous integration (4)

GitHub ActionsR CMD check workflowTravis CI (config file)AppVeyor

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

Coverage (1)

Coverage reporting (Codecov)

Lint, format, editor (2)

lintrRStudio project

Git structural (2)

.gitattributesSubmodules

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing DEploid adds 66 packages (36 with compiled code, 63 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (2)

R >= 3.1.0DEploid.utils

Imports (6)

Rcpp scales plotly magrittr rmarkdown htmlwidgets

LinkingTo (1)

Rcpp

Suggests (2)

knitr testthat

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 (8)

Joe Zhu

Author, Maintainer since 0.3.2 (2016)

Jacob Almagro-Garcia

Author · added in 0.4.2

Gil McVean

Author · added in 0.4.2

Yinghan Liu

Contributor · added in 0.4.2

University of Oxford

Copyright holder · added in 0.4.2

Deepak Bandyopadhyay

Compiler, Copyright holder · added in 0.4.2

Lutz Kettner

Compiler, Copyright holder · added in 0.4.2

CodeCogs Zyba Ltd

Compiler, Copyright holder · added in 0.4.2

Releases (12)

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
0.5.7Latest
record
2025-01-20 · current release · diff ↗
0.5.6
record
2024-12-23 · diff ↗ ·
removed 1 export
extractVcf
unarchivedReturned to CRAN
2024-10-14
0.5.4
record
2024-10-14 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
archivedRemoved from CRAN
2021-08-01
check problems were not corrected despite multiple reminders
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
unarchivedReturned to CRAN
2020-04-22
0.5.3
record
2020-04-22 · diff ↗ ·
added 1 export
extractVcf
archivedRemoved from CRAN
2020-03-03
check problems were not corrected despite reminders
R
R 3.6.0 released · 2019-04-26

Show 13 earlier eventsHide 13 earlier events

0.5.2
record
2018-10-23 · diff ↗
unarchivedReturned to CRAN
2018-10-21
0.5.1
record
2018-10-21 · diff ↗
archivedRemoved from CRAN
2018-10-10
installation problems were not corrected despite reminders (and suggestions) Two separate compiler warnings, failure under clang trunk for include path conflicts
0.5.0
record
2018-05-18 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.4.4
record
2017-09-01 · diff ↗
0.4.3
record
2017-08-09 · diff ↗
0.4.2
record
2017-08-09 · diff ↗ ·
added 4 exports
plotAltVsRefPlotly, plotHistWSAFPlotly, plotWSAFVsPLAFPlotly, plotObsExpWSAFPlotly
0.4.1
record
2017-07-24 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.3.2
record
2016-11-25
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-11-25
Total releases: 12 / 10 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.1.0
Download size: 928 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("DEploid")

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

It points to 10.1101/099499.

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 DEploid version 0.5.7 [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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