mixsqp

0.3-54

Sequential Quadratic Programming for Fast Maximum-Likelihood Estimation of Mixture Proportions

3packages depend

136.9Kdownloads / year

91.7%test coverage

12/13checks pass

Overview

About

Maintained by Peter CarbonettoFirst published 2018-11-147 releasesCRAN page ↗GitHub ↗

Provides an optimization method based on sequential quadratic programming (SQP) for maximum likelihood estimation of the mixture proportions in a finite mixture model where the component densities are known. The algorithm is expected to obtain solutions that are at least as accurate as the state-of-the-art MOSEK interior-point solver (called by function "KWDual" in the 'REBayes' package), and they are expected to arrive at solutions more quickly when the number of samples is large and the number of mixture components is not too large. This implements the "mix-SQP" algorithm, with some improvements, described in Y. Kim, P. Carbonetto, M. Stephens & M. Anitescu (2020) DOI:10.1080/10618600.2019.1689985.

Install

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

install.packages("mixsqp", 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("stephenslab/mixsqp")

Development version from stephenslab/mixsqp. 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-mixsqp

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-mixsqp

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-mixsqp

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

Health

CRAN checks

1NOTE12OK

Failing flavors

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

Slowest check: 3.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.40

91.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 82%
Return-value docs: 100%
References docs: 20%

Downloads

136.9K

CRAN downloads in the past year

Rank #1,116 · ~375/day · ~11.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

13K30 days

35K90 days

136.9K1 year

Compare downloads with other packages →

Also on2.2K r2u3 autocran56.2K conda_forge63 c2d4u

Repository

GitHub ↗ stephenslab/mixsqp

11Stars

6Forks

8Open issues

0Open PRs

6Releases

467Commits

5Contributors

467 commits · Last activity 2023-12-21

Stars over time

2024-09-30 · 112026-07-07 · 11

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/stephenslab/mixsqp on 2026-07-30.

Continuous integration (2)

Travis CIAppVeyor

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.3.0

Imports (4)

utilsstatsirlba Rcpp

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (3)

testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

13indirect

ashr ebnm susieR

Code & Tests

People & History

People (6)

Maintainer (1)

Peter Carbonetto

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Contributors (2)

Jean Morrison

Contributor · added in 0.1-97

Jason Willwerscheid

Contributor · added in 0.1-97

Package Timeline

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

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
0.3-54Latest
2023-12-20 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
0.3-48
2022-11-16 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.3-43
2020-05-14 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.3-17
2020-01-29 · diff ↗
unarchivedReturned to CRAN
2020-01-29
archivedRemoved from CRAN
2020-01-16
check issues were not corrected in time
0.2-2
2019-10-16 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.1-97
2019-02-18 · diff ↗

Show 4 earlier events

unarchivedReturned to CRAN
2019-02-18
archivedRemoved from CRAN
2019-02-05
check errors were not corrected despite reminders
0.1-79
2018-11-14
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-11-14
Total releases: 7 / 8 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.3.0
Bundled data: 17 KB / 1 file
Download size: 216 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Optimization and Mathematical Programming

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