This package was removed from CRAN on 2022-11-07. Its history is shown below.

Reason: recurring issues were not corrected in time. and policy violation, sending HTML

Details below reflect version 0.4.4, its last release before removal.

chromatographR

0.4.4

Chromatographic Data Analysis Toolset

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Ethan Bass3 releasesCRAN page ↗

Tools for high-throughput analysis of HPLC-DAD/UV chromatograms (or similar data). Includes functions for preprocessing, alignment, peak-finding and fitting, peak-table construction, data-visualization, etc. Preprocessing and peak-table construction follow the rough formula laid out in alsace (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C., 2015. doi:10.1093/bioinformatics/btv299. Alignment of chromatograms is available using parametric time warping (ptw) (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. doi:10.1093/bioinformatics/btv299) or variable penalty dynamic time warping (VPdtw) (Clifford, D., & Stone, G. 2012. doi:10.18637/jss.v047.i08). Peak-finding uses the algorithm by Tom O'Haver http://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm. Peaks are then fitted to a gaussian or exponential-gaussian hybrid peak shape using non-linear least squares (Lan, K. & Jorgenson, J. W. 2001. doi:10.1016/S0021-9673(01)00594-5). See the vignette for more details and suggested workflow.

Install

R (source archive)Ubuntu (r2u)openSUSE (OBS)

url <- "https://cran.r-project.org/src/contrib/Archive/chromatographR/chromatographR_0.4.4.tar.gz"
pkgFile <- "chromatographR_0.4.4.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (0.4.4) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-chromatographr

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

# 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-chromatographR

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.66

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Documentation

READMEYes · 285 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 88%
Documented parameters: 100%
Return-value docs: 95%
References docs: 26%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on123 r2u39 autocran46 c2d4u

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (15)

chromConverter dynamicTreeCut fastclustergraphicsgrDeviceslatticemethodsminpack.lmparallelptw pvclust scales smootherstatsutils

LinkingTo (0)

none

Suggests (6)

knitr rmarkdown spelling testthat vdiffr VPdtw

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Code Composition

R 2,743 (57%)Rd 1,638 (34%)Vignettes 208 (4%)Other 193 (4%)

Code characteristics

Object systems

S37S4 class1

Cyclomatic complexity: 7.0 median / 28 max
Test cases: 24 / 0.66 per code line

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

35 19 exported

Complexity

8 avg / 28 max

Call network

35 nodes / 27 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

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

People & History

People (1)

Maintainer (1)

Ethan Bass

Author, Maintainer

Authors (1)

Ethan Bass

Author, Maintainer

Package Timeline

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

R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2022-11-07
recurring issues were not corrected in time and policy violation, sending HTML
0.4.4
2022-08-24 · diff ↗
0.4.3
2022-08-22 · diff ↗
0.4.1
2022-05-19
R
R 4.2.0 released · 2022-04-22

Package metadata

Total releases: 3
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 2.2 MB / 4 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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