R Observatory: Metrics for serrsBayes version 0.6-1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

serrsBayes

0.6-1Package record

Bayesian Modelling of Raman Spectroscopy

0packages depend

3.3Kdownloads / year

69.2%test coverage

13/13flavors OK

Overview

About

Maintained by Matt MooresCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: Engineering and Physical Sciences Research Council

Sequential Monte Carlo (SMC) algorithms for fitting a generalised additive mixed model (GAMM) to surface-enhanced resonance Raman spectroscopy (SERRS), using the method of Moores et al. (2026) doi:10.48550/arXiv.1604.07299. Multivariate observations of SERRS are highly collinear and lend themselves to a reduced-rank representation. The GAMM separates the SERRS signal into three components: a sequence of Lorentzian, Gaussian, or pseudo-Voigt peaks; a smoothly-varying baseline; and additive white noise. The parameters of each component of the model are estimated iteratively using SMC. The posterior distributions of the parameters given the observed spectra are represented as a population of weighted particles.

Changes in 0.6-1

New Features

Added unit tests for residualResampling and resampleParticles
Migrated pkgdown website from

Bug Fixes

Fixed residual resampling in fitSpectraSMC: parents were not kept in place, so the in-place (OpenMP-parallel) copy could overwrite particles that were still being copied from. This caused biased resampling and, with multiple threads, a data race (CRAN check failure on r-devel-linux-x86_64-fedora-gcc)
resampleParticles now copies the full spectral signature of each particle, not only the first npeaks wavenumbers
residualResampling no longer modifies the caller's log-weights

From NEWS.md in the release

Install

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

install.packages("serrsBayes", 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("mooresm/serrsBayes")

Development version from mooresm/serrsBayes. 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-serrsbayes

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-serrsBayes

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-serrsBayes

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: 10.2 min · r-patched-linux-x86_64

Status changes

OK13 OK2026-10-23
ERROR12 OK, 1 ERROR2026-10-20
OK13 OK2026-10-07
NOTE11 OK, 2 NOTE2026-05-12
WARNING11 OK, 1 NOTE, 1 WARNING2026-05-11

Show 3 earlier changesHide 3 earlier changes

NOTE10 OK, 4 NOTE2026-04-22
ERROR9 OK, 4 NOTE, 1 ERROR2026-04-18
NOTE10 OK, 4 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.6-1

READMEYes · 145 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.6-1Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 27includes a package overview page
Examples that run: 100%10 run in a plain check
Exported functions with examples: 41%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 44%

Vignettes (2)

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #10,198 · ~9/day · ~274/mo

Releases R versions

Daily download trend is not available in this view yet.

44230 days

1K90 days

3.3K1 year

Compare downloads with other packages →

Also on360 r2u4 autocran56 c2d4u

How downloads are counted

Repository

mooresm/serrsbayes ↗Account: mooresm

8Stars

3Forks

0Open issues

0Open PRs

7Releases

106Commits

2Commit identities

bayesiansequential-monte-carlospectroscopyramanchemometrics

License file reads as GPL-2.0 · 106 commits · Last activity 2026-10-21 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 1,146
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2024-09-17 · 82026-07-07 · 8

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/mooresm/serrsbayes on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-21

pkgdown site last built 2026-10-21

Coverage (1)

Coverage reporting (Codecov)

CRAN release process (1)

cran-comments.md

Show all practicesHide 2 practices

Research and citation (1)

Zenodo

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing serrsBayes adds 3 packages (3 with compiled code, 3.5 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppEigen 1.7 MB, truncnorm 11 KB.

Depends (4)

R >= 3.5.0Matrixtruncnormsplines

Imports (2)

Rcppmethods

LinkingTo (2)

Rcpp RcppEigen

Suggests (4)

testthat knitr rmarkdown Hmisc

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (10)

Matt Moores

Author, Maintainer since 0.3-10 (2018)

Jake Carson

Author

Mark Girolami

Author

Dirk Eddelbuettel

Contributor · added in 0.6-0

Benjamin Moskowitz

Contributor · added in 0.4-0

University of Warwick

Copyright holder

Engineering and Physical Sciences Research Council

Funder

EPSRC programme grant ref: EP/L014165/1

Karen Faulds

Data contributor · added in 0.4-0

Kirsten Gracie

Data contributor · added in 0.4-0

Duncan Graham

Data contributor · added in 0.6-0

Releases (10)

Pick two releases to compare their code metrics.

0.6-1Latest
record
2026-10-21 · current release · diff ↗ ·
listed once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-21 10:55 UTC, so it stayed less than the time between readings.
0.6-0
record
2026-10-03 · diff ↗
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
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.5-0
record
2021-06-28 · diff ↗
0.4-2
record
2021-06-07 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.4-1
record
2020-02-05 · diff ↗
0.4-0
record
2019-04-29 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.3-13
record
2018-06-05 · diff ↗
R
R 3.5.0 released · 2018-04-23

Show 4 earlier eventsHide 4 earlier events

0.3-12
record
2018-02-18 · diff ↗
0.3-11
record
2018-02-16 · diff ↗
0.3-10
record
2018-02-14
R
R 3.4.0 released · 2017-04-21

Across CRAN, the median accepted release of the past year spent 26 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2018-02-14
Total releases: 10 / 8 yrs
License: GPL (>= 2) | file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 267 KB / 4 files
Download size: 891 KB

Appears in task views

Chemometrics and Computational Physics

Cite

Cite this package

Run in R for the authors' entry:

citation("serrsBayes")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.5281/zenodo.3861862, 10.48550/arxiv.1604.07299, 10.1021/acs.analchem.5b02776, 10.15129/2c186689-2334-4746-955e-f9579ca15909, 10.1021/acs.jpcb.0c04378.

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 serrsBayes version 0.6-1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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