dcifer

1.5.2

Genetic Relatedness Between Polyclonal Infections

0packages depend

3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Inna GerlovinaFirst published 2022-07-157 releasesCRAN page ↗GitHub ↗

An implementation of Dcifer (Distance for complex infections: fast estimation of relatedness), an identity by descent (IBD) based method to calculate genetic relatedness between polyclonal infections from biallelic and multiallelic data. The package includes functions that format and preprocess the data, implement the method, and visualize the results. Gerlovina et al. (2022) doi:10.1093/genetics/iyac126.

Install

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

install.packages("dcifer", 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("EPPIcenter/dcifer")

Development version from EPPIcenter/dcifer. 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-dcifer

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

# 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-dcifer

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-dcifer

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

Health

CRAN checks

13OK

Slowest check: 2.6 min · r-release-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

README

Dependencies · direct

Check history

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-30
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

CRAN downloads in the past year

Rank #13,708 · ~8/day · ~249/mo

dcifer By source Releases R versions

Daily download trend is not available in this view yet.

27430 days

79090 days

3K1 year

Compare downloads with other packages →

Also on480 r2u17 autocran

Repository

GitHub ↗ eppicenter/dcifer

8Stars

5Forks

2Open issues

0Open PRs

8Releases

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.4.0

Imports (3)

statsutilsgraphics

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

C 1,656 (35%)R 1,330 (28%)Rd 1,047 (22%)Other 391 (8%)Vignettes 285 (6%)

Code characteristics

Cyclomatic complexity: 4.0 median / 56 max
Documented parameters: 83%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

36 16 exported

Complexity

8.5 avg / 56 max

Call network

36 nodes / 41 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 (1)

Maintainer (1)

Inna Gerlovina

Author, Maintainer

Authors (1)

Inna Gerlovina

Author, Maintainer

Release timeline

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

1.5.2Latest
2026-05-07 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.5.0
2025-11-11 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.2.1
2023-12-12 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.0
2022-10-31 · diff ↗
1.1.1
2022-08-10 · diff ↗
1.1.0
2022-08-06 · diff ↗
1.0.1
2022-07-15
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-07-15
Total releases: 7 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.4.0
Bundled data: 101 KB / 3 files
Download size: 524 KB
Installed size: not tracked yet
With dependencies: not tracked yet