R Observatory: Metrics for gcxgclab version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

gcxgclab

1.1.0Package record

GCxGC Preprocessing and Analysis

0packages depend

2.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Stephanie GambleCRAN page ↗Declared funder: NNSA, US DOE

Provides complete detailed preprocessing of two-dimensional gas chromatogram (GCxGC) samples. Baseline correction, smoothing, peak detection, and peak alignment. Also provided are some analysis functions, such as finding extracted ion chromatograms, finding mass spectral data, targeted analysis, and nontargeted analysis with either the 'National Institute of Standards and Technology Mass Spectral Library' or with the mass data. There are also several visualization methods provided for each step of the preprocessing and analysis.

Changes in 1.1.0

This is a minor release adding new additional capabilities and providing some improvements and bug fixes.

Bug fixes

Fixes erros in 'align()' caused if all peaks found are above the given threshold, THR.
Inconsequencial warnings are suppressed in 'align()'.
Modification to the color scale ledgend for data of various scales.

Improvements

'align()' has two additional optional inputs: use_ref_peak and ref_peak. Previously, 'align()' assumed the presense of toluene (present with themal desorption tubes using Tenax TA sorbent material). For users that do not have toluene present, a different initial reference m/z value can be input for ref_peak to provide an initial shift to the data for alignment. Alternatively, the boolean use_ref_peak can be set to FALSE to skip the initial shift to a reference peak completely.
'plot_chr()' has two additional option inputs: xlab and ylab. This allows modification of the axes labeling on the hoizontal (x) and vertical (x) axis.
'plot_peak()' has two additional option inputs: xlab and ylab. This allows modification of the axes labeling on the hoizontal (x) and vertical (x) axis.
'batch_preprocess()' now has three addtional optional inputs: do_align, use_ref_peak, and ref_peak. do_align allows the user to change a boolean to skip alignment of the given list of files to preprocess if alignment is not necessary. It also includes the two new inputs use_ref_peak and ref_peak for 'align()'.
'extract_data()' has been modified to address irregularly shaped data. If the last column of data is incomplete (not a full modulation period), this data is now removed to allow plotting and analysis.
Addtional commenting added to 'align()' for code organiziation and understandablility.

Show all changes in 1.1.0Hide the rest of the changes in 1.1.0

New capabilities

New function 'batch_extract()' which extracts data from all CFD files in a given folder path, using the methods of 'extract_data()'. Resulting data frames are returned in a list.
New function 'TIC_integrate()' allows the user to integrate the area under the entire TIC curve. Previously area could only be calculated for a given peak. The user may also indicate starting and ending times for the region of integration.

From NEWS.md in the release

Install

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

install.packages("gcxgclab", 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-gcxgclab

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-gcxgclab

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-gcxgclab

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: 2.5 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMENoVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.1.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 34
Examples that run: 100%28 run in a plain check
Exported functions with examples: 82%
Documented parameters: 95%
Return-value docs: 100%
Help pages citing references: 38% with a bibliography file

Vignettes (1)

gcxgclab: GCxGC Preprocessing and Analysis HTML

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #16,784 · ~7/day · ~219/mo

Releases R versions

Daily download trend is not available in this view yet.

30030 days

75790 days

2.6K1 year

Compare downloads with other packages →

Also on102 r2u4 autocran

How downloads are counted

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing gcxgclab adds 41 packages (24 with compiled code, 38 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, ptw 4.0 MB.

Depends (1)

R >= 4.2.0

Imports (10)

ncdf4 dplyr ggplot2 ptwstatsutilsnilde (>= 1.1.6)zoo nls.multstart Rdpack (>= 2.4.0)

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (5)

Stephanie Gamble

Author, Maintainer since 1.0.0 (2024)

Granger Caroline

Contributor · added in 1.0.1

Mannion Joseph

Contributor

Battelle Savannah River Alliance

Copyright holder

NNSA, US DOE

Funder

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
record
2025-11-25 · current release · diff ↗ ·
added 2 exports
TIC_integrate, batch_extract
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.1
record
2024-01-22 · diff ↗
1.0.0
record
2024-01-17
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-01-17
Total releases: 3 / 2 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.2.0
Download size: 2.3 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("gcxgclab")

Format

Gamble, S., Battelle Savannah River Alliance, NNSA, US DOE, Caroline, G., & Joseph, M. (2025). gcxgclab: GCxGC Preprocessing and Analysis (Version 1.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.gcxgclab

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 gcxgclab version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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