saemix

3.5

Stochastic Approximation Expectation Maximization (SAEM) Algorithm

4packages depend

11.9Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Emmanuelle CometsFirst published 2011-06-3014 releasesCRAN page ↗

The 'saemix' package implements the Stochastic Approximation EM algorithm for parameter estimation in (non)linear mixed effects models. It (i) computes the maximum likelihood estimator of the population parameters, without any approximation of the model (linearisation, quadrature approximation,...), using the Stochastic Approximation Expectation Maximization (SAEM) algorithm, (ii) provides standard errors for the maximum likelihood estimator (iii) estimates the conditional modes, the conditional means and the conditional standard deviations of the individual parameters, using the Hastings-Metropolis algorithm (see Comets et al. (2017) doi:10.18637/jss.v080.i03). Many applications of SAEM in agronomy, animal breeding and PKPD analysis have been published by members of the Monolix group. The full PDF documentation for the package including references about the algorithm and examples can be downloaded on the github of the IAME research institute for 'saemix': https://github.com/iame-researchCenter/saemix/blob/7638e1b09ccb01cdff173068e01c266e906f76eb/docsaem.pdf.

Install

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

install.packages("saemix", 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-saemix

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-saemix

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-saemix

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

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Slowest check: 4.7 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-11
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 98%
Documented parameters: 96%
Return-value docs: 74%
References docs: 52%

Downloads

11.9K

CRAN downloads in the past year

Rank #4,504 · ~33/day · ~995/mo

Releases R versions

Daily download trend is not available in this view yet.

67130 days

2.1K90 days

11.9K1 year

Compare downloads with other packages →

Also on207 r2u34 autocran62 c2d4u

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

npde

Imports (10)

graphicsstatsmethodsgridExtra ggplot2gridrlang mclust scalesMASS

LinkingTo (0)

none

Suggests (2)

testthatsurvival

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

1indirect

GrowthCurveME mkin nlive varTestnlme

Code & Tests

Code Composition

R 16,664 (74%)Rd 5,972 (26%)

Code characteristics

Object systems

S318S4 class6S4 generic5S4 method38

Cyclomatic complexity: 4.0 median / 66 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

135 41 exported

Complexity

10.8 avg / 66 max

Call network

135 nodes / 184 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Datasets

Bundled datasets · 10

Name	Class	Rows × Cols	Also ships in
PD1.saemix	data.frame	300 × 1	–
PD2.saemix	data.frame	300 × 1	–
cow.saemix	data.frame	5,455 × 1	–
knee.saemix	data.frame	508 × 1	–
lung.saemix	data.frame	450 × 1	–
oxboys.saemix	data.frame	234 × 1	–
rapi.saemix	data.frame	3,616 × 1	–
theo.saemix	data.frame	120 × 1	–
toenail.saemix	data.frame	1,908 × 1	–
yield.saemix	data.frame	224 × 1	–

People & History

People (10)

Maintainer (1)

Emmanuelle Comets

Author, Maintainer

Authors (4)

Emmanuelle Comets

Author, Maintainer

Belhal Karimi

Author · added in 3.0

Audrey Lavenu

Author

Marc Lavielle

Author · added in 2.4

Contributors (6)

Marilou Chanel

Contributor · added in 3.0

Maud Delattre

Contributor · added in 2.4

Lucie Fayette

Contributor · added in 3.0

Sofia Kaisaridi

Contributor · added in 3.0

Alexandra Lavalley-Morelle

Contributor · added in 3.4

Johannes Ranke

Contributor · added in 3.0

Listed in earlier versions (2)

Marc Lavielle.

no longer listed · 0.95 to 1.2

Marc Lavielle (2017)

no longer listed · 2.1 to 2.3

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
3.5Latest
2026-02-25 · current release · diff ↗
3.4
2025-07-31 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
3.3
2024-03-05 · diff ↗
3.2
2023-06-27 · diff ↗
R
R 4.3.0 released · 2023-04-21
3.1
2022-08-05 · diff ↗
R
R 4.2.0 released · 2022-04-22
3.0
2022-02-08 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.4
2021-02-24 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.3
2019-12-06 · diff ↗
R
R 3.6.0 released · 2019-04-26

Show 17 earlier events

2.2
2018-10-10 · diff ↗
unarchivedReturned to CRAN
2018-10-10
archivedRemoved from CRAN
2018-06-01
check problems were not corrected despite reminders
R
R 3.5.0 released · 2018-04-23
2.1
2017-08-24 · diff ↗
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
1.2
2014-02-25 · diff ↗
R
R 3.0.0 released · 2013-04-03
0.96.1
2013-03-01 · diff ↗
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
0.96
2011-07-02 · diff ↗
0.95
2011-06-30
R
R 2.13.0 released · 2011-04-13

Package metadata

First published: 2011-06-30
Total releases: 14 / 15 yrs
License: GPL (>= 2) OSI
Bundled data: 59 KB / 10 files
Download size: 2.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Mixed, Multilevel, and Hierarchical Models in R Analysis of Pharmacokinetic Data

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