R Observatory: Metrics for SAM version 1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SAM

1.3Package record

Sparse Additive Modelling

4packages depend

6Kdownloads / year

72.1%test coverage

13/13flavors OK

Overview

About

Maintained by Tuo ZhaoCRAN page ↗

Computationally efficient tools for high dimensional predictive modeling (regression and classification). SAM is short for sparse additive modeling, and adopts the computationally efficient basis spline technique. We solve the optimization problems by various computational algorithms including the block coordinate descent algorithm, fast iterative soft-thresholding algorithm, and newton method. The computation is further accelerated by warm-start and active-set tricks.

Changes in 1.3

Bug Fixes

Fixed KKT validation: inactive groups are now checked after every Level 1 iteration, not only when not converged.
Fixed grpSVM ya_idx active-set logic that only checked the first element of each group instead of all p coefficients.
Replaced assert() with runtime error checks in grplasso, grpLR, and grpPR (asserts are compiled out under -DNDEBUG).
Added NULL checks for all malloc calls in grpSVM.

New Features

dfmax parameter for early stopping when the number of non-zero groups exceeds a threshold (all four families).
verbose parameter to print per-lambda iteration info.

Show all changes in 1.3Hide the rest of the changes in 1.3

Deviance-ratio and deviance-change early stopping (dev.ratio.thr, dev.change.thr) for samQL, samLL, and samEL.
Unified sam() entry point dispatching by family argument (R and Python).
coef() S3 methods for all four model classes.
solver = "actgd" option for samQL (group active gradient descent with strong-rule screening, L1 only).
type.gaussian option for samQL ("naive" / "covariance" / "auto").
runtime field on fitted objects (R: $runtime, Python: .runtime_seconds).

Python Wrapper

New pysam-sam Python package calling the same C++ core via ctypes.
Pure-Python spline basis (no R dependency at runtime).
Full API parity: samLL, samHL, samEL, samQL + predict functions.

Performance

Cached wXX products and no-op update_auxiliary for linear objective.
C API deduplication via c_api_utils.h.

Code Quality

Removed redundant fit$nkots field from R wrappers.
Removed unused fit$XX (full design matrix) from samQL output.
Removed unused V(d) declarations in grpLR and grpPR.
Extracted shared .sam_print_path() / .sam_plot_path() helpers.
Removed unused scipy dependency from Python package.
Fixed legacy PICASSO_SOLVER_PARAMS_H header guard.
Added root .gitignore.
Added test coverage for samHL and samEL.

From NEWS.md in the release

Install

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

install.packages("SAM", 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-sam

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-SAM

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-SAM

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.7 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
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 1.3

READMEYes · 86 wordsVignettesNoNEWSYes · 100% structured · mentions 1.3Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 18includes a package overview page
Examples that run: 100%5 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 6%

How these are measured

Downloads

6K

CRAN downloads in the past year

Rank #6,889 · ~16/day · ~500/mo

Releases R versions

Daily download trend is not available in this view yet.

47130 days

1.2K90 days

6K1 year

Compare downloads with other packages →

Also on415 r2u8 autocran93 c2d4u

How downloads are counted

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing SAM adds 2 packages (2 with compiled code, 3.5 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppEigen 1.7 MB.

Depends (2)

R >= 2.14splines

Imports (0)

none

LinkingTo (2)

Rcpp RcppEigen

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

0indirect

Imports 4

Depends, Imports or LinkingTo, most downloaded first

DLL GSelection pgraph varEst

How these are counted

Code & Tests

People & History

People (6)

Tuo Zhao

Author, Maintainer since 1.2 (2026)

Haoming Jiang

Author · added in 1.1.0

Xingguo Li

Author

Han Liu

Author

Yukun Ma

Author · added in 1.1.0

Kathryn Roeder

Author

Previously maintained by Haoming Jiang (1.1.0 to 1.1.3) and Tuo Zhao (1.0.2 to 1.0.5).

Listed in earlier versions (2)

Lie Wang

no longer listed · 1.0.2

Xinyu Fei

no longer listed · 1.1.0 to 1.1.1

Releases (11)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.3Latest
record
2026-03-13 · current release · diff ↗ ·
added 1 export
sam
1.2
record
2026-02-19 · diff ↗
R
R 4.5.0 released · 2025-04-11
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
unarchivedReturned to CRAN
2021-07-01
1.1.3
record
2021-07-01 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
orphanedOrphaned by its maintainer
2019-07-02
misuse of package= for PACKAGE= was not corrected despite reminder
1.1.2.1
record
2019-07-02 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.1.2
record
2019-04-07 · diff ↗
1.1.1
record
2019-03-12 · diff ↗

Show 12 earlier eventsHide 12 earlier events

1.1.0
record
2019-02-18 · diff ↗ ·
removed 12 exports
print.samQL, plot.samQL, predict.samQL, print.samHL, plot.samHL, predict.samHL, print.samLL, plot.samLL, predict.samLL, print.samEL, plot.samEL, predict.samEL
R
R 3.5.0 released · 2018-04-23
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
1.0.5
record
2014-02-12 · diff ↗
1.0.4
record
2013-09-18 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.0.3
record
2013-04-02 · diff ↗ ·
removed 9 exports
spam, l1svm, fastscr, print.spam, plot.spam, predict.spam, print.l1svm, plot.l1svm, predict.l1svm

added 16 exports
samQL, print.samQL, plot.samQL, predict.samQL, samHL, print.samHL, plot.samHL, predict.samHL, samLL, print.samLL, plot.samLL, predict.samLL, samEL, print.samEL, plot.samEL, predict.samEL
1.0.2
record
2012-10-15
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-10-15
Total releases: 11 / 14 yrs
License: GPL-2 OSI
Minimum R: ≥ 2.14
Download size: 56 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SAM")

Format

Zhao, T., Jiang, H., Li, X., Liu, H., Ma, Y., & Roeder, K. (2026). SAM: Sparse Additive Modelling (Version 1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.SAM

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 SAM version 1.3 [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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