numberofalleles

1.0.1

Compute the Probability Distribution of the Number of Alleles in a DNA Mixture

0packages depend

2.2Kdownloads / year

71.8%test coverage

9/13checks pass

Overview

About

Maintained by Maarten KruijverFirst published 2022-04-291 releasesCRAN page ↗

The number of distinct alleles observed in a DNA mixture is informative of the number of contributors to the mixture. The package provides methods for computing the probability distribution of the number of distinct alleles in a mixture for a given set of allele frequencies. The mixture contributors may be related according to a provided pedigree.

Install

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

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

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

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-numberofalleles

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-numberofalleles

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-numberofalleles

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

Health

CRAN checks

4NOTE9OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 2.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.14

71.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-04-22
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
9 OK · 4 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 18%

Downloads

2.2K

CRAN downloads in the past year

Rank #19,859 · ~6/day · ~181/mo

Releases R versions

Daily download trend is not available in this view yet.

20330 days

60790 days

2.2K1 year

Compare downloads with other packages →

Also on420 r2u16 autocran

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (5)

Rcpp pedtools ribd partitionsmethods

LinkingTo (1)

Rcpp

Suggests (4)

rmarkdown knitr testthat ggplot2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 1,149 (49%)Rd 556 (24%)C++ 525 (22%)C 60 (3%)Vignettes 56 (2%)

Code characteristics

Object systems

S33

Cyclomatic complexity: 2.0 median / 20 max
Test cases: 7 / 0.14 per code line

Test coverage

Line coverage

72%

Expression

74.8%

Tests / Examples

71.8% / 66% ex

Functions

44 8 exported

Complexity

3.7 avg / 20 max

Call network

44 nodes / 41 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

44 functions

Function	Cyclo	Coverage
pr_independent_alleles_ped exp	9	0%
read_allele_freqs exp	4	0%
columns	1	0%
get_number_of_unique_alleles	1	0%
plot.pf	4	0%
mean.pf	2	50%

People & History

People (2)

Maintainer (1)

Maarten Kruijver

Author, Maintainer

Authors (2)

Maarten Kruijver

Author, Maintainer

James Curran

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.1Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2022-04-29
Total releases: 1 / 4 yrs
License: GPL (>= 2) OSI
Download size: 44 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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