OpenSpecy

Analyze, Process, Identify, and Share, Raman and (FT)IR Spectra

https://github.com/wincowgerdev/openspecy-package

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 12 DOI reference(s) in README
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Academic publication links
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Committers with academic emails
1 of 7 committers (14.3%) from academic institutions
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (13.9%) to scientific vocabulary

Last synced: 7 months ago · JSON representation

Repository

Analyze, Process, Identify, and Share, Raman and (FT)IR Spectra

Basic Info

Host: GitHub
Owner: wincowgerDEV
License: cc-by-4.0
Language: R
Default Branch: main
Homepage: https://raw.githack.com/wincowgerDEV/OpenSpecy-package/main/docs/index.html
Size: 183 MB

Statistics

Stars: 31
Watchers: 3
Forks: 11
Open Issues: 21
Releases: 21

Created about 5 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog Funding License

Open Specy 1.0

Analyze, Process, Identify, and Share Raman and (FT)IR Spectra

Raman and (FT)IR spectral analysis tool for plastic particles and other environmental samples (Cowger et al. 2021, doi: 10.1021/acs.analchem.1c00123). With read_any(), Open Specy provides a single function for reading individual, batch, or map spectral data files like .asp, .csv, .jdx, .spc, .spa, .0, and .zip. process_spec() simplifies processing spectra, including smoothing, baseline correction, range restriction and flattening, intensity conversions, wavenumber alignment, and min-max normalization. Spectra can be identified in batch using an onboard reference library (Cowger et al. 2020, doi: 10.1177/0003702820929064) using match_spec(). A Shiny app is available via run_app() or online at https://www.openanalysis.org/openspecy/.

Installation

OpenSpecy is available from CRAN and GitHub.

Install from CRAN (stable version)

You can install the latest release of OpenSpecy from CRAN with:

r install.packages("OpenSpecy")

Install from GitHub (development version)

To install the development version of this package, paste the following code into your R console (requires devtools):

r if (!require(devtools)) install.packages("devtools") devtools::install_github("wincowgerDEV/OpenSpecy-package")

Install on Web Assemply through webr (experimental), you can test here: https://webr.r-wasm.org/latest/

```r library(caTools) library(data.table) library(jsonlite) library(yaml) library(hyperSpec) library(mmand) library(plotly) library(digest) library(signal) library(glmnet) library(jpeg) library(shiny) webr::install("OpenSpecy", repos = "https://wincowger.com/OpenSpecy-package/") library(OpenSpecy)

```

Getting started

r library(OpenSpecy) run_app()

Simple workflow for single spectral identification

See package vignette for a detailed standard operating procedure.

```r

Fetch current spectral library from https://osf.io/x7dpz/

get_lib("derivative")

Load library into global environment

speclib <- loadlib("derivative")

Read sample spectrum

ramanhdpe <- readextdata("ramanhdpe.csv") |> readany()

Look at the spectrum

plotlyspec(ramanhdpe)

Process the spectra and conform it to the library format

ramanproc <- ramanhdpe |> processspec(conformspecargs = list(range = speclib$wavenumbers), smoothintens = T, makerel = T)

Compare raw and processed spectra

plotlyspec(ramanhdpe, raman_proc)

topmatches <- matchspec(ramanproc, library = speclib, na.rm = T, topn = 5, addlibrarymetadata = "samplename", addobjectmetadata = "col_id")

Print the top 5 results with relevant metadata

topmatches[, c("objectid", "libraryid", "matchval", "SpectrumType", "SpectrumIdentity")]

Get all metadata for the matches

getmetadata(speclib, logic = topmatches$libraryid) ```

Related Packages

Open Specy on Python

Kris Heath created a Open Specy python package! https://pypi.org/project/openspi/

Citations

Cowger W, Steinmetz Z, Gray A, Munno K, Lynch J, Hapich H, Primpke S, De Frond H, Rochman C, Herodotou O (2021). “Microplastic Spectral Classification Needs an Open Source Community: Open Specy to the Rescue!” Analytical Chemistry, 93(21), 7543–7548. doi: 10.1021/acs.analchem.1c00123.

Cowger W, Steinmetz Z, Leong N, Faltynkova A, Sherrod H (2024). “OpenSpecy: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra.” R package, 1.0.8. https://github.com/wincowgerDEV/OpenSpecy-package.

Owner

Name: Win Cowger, PhD
Login: wincowgerDEV
Kind: user
Location: Long Beach, CA
Company: Moore Institute for Plastic Pollution Research

Website: wincowger.com
Repositories: 46
Profile: https://github.com/wincowgerDEV

Win is Research Director at the Moore Institute for Plastic Pollution Research. He studies the prevention and transport of plastic pollution.

GitHub Events

Total

Create event: 4
Issues event: 16
Release event: 3
Watch event: 5
Issue comment event: 18
Push event: 86
Pull request event: 1
Fork event: 1

Last Year

Create event: 4
Issues event: 16
Release event: 3
Watch event: 5
Issue comment event: 18
Push event: 86
Pull request event: 1
Fork event: 1

Committers

Last synced: 7 months ago

All Time

Total Commits: 771
Total Committers: 7
Avg Commits per committer: 110.143
Development Distribution Score (DDS): 0.475

Past Year

Commits: 70
Committers: 2
Avg Commits per committer: 35.0
Development Distribution Score (DDS): 0.071

Top Committers

Name	Email	Commits
Win Cowger, PhD	w**r@g**m	405
Zacharias Steinmetz	s**z@u**e	202
Zacharias Steinmetz	g**t@z**e	130
nickleong20	n**k@m**g	15
hsherrod2019	h**9@g**m	9
Zacharias Steinmetz	z**z@r**e	5
hazelvaq	h**8@g**m	5

Committer Domains (Top 20 + Academic)

rptu.de: 1 mooreplasticresearch.org: 1 zsteinmetz.de: 1 uni-landau.de: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 80
Total pull requests: 77
Average time to close issues: 5 months
Average time to close pull requests: about 1 month
Total issue authors: 11
Total pull request authors: 2
Average comments per issue: 3.16
Average comments per pull request: 3.61
Merged pull requests: 67
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 10
Pull requests: 2
Average time to close issues: 11 days
Average time to close pull requests: 3 minutes
Issue authors: 3
Pull request authors: 1
Average comments per issue: 0.5
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

wincowgerDEV (63)
zsteinmetz (6)
valentinavan (2)
GCov (2)
philipp-baumann (1)
paloeffler (1)
joe007li (1)
ardcarvalho (1)
nletwin97 (1)
MPresearcher (1)
zzhui43 (1)

Pull Request Authors

zsteinmetz (47)
wincowgerDEV (30)

Top Labels

Issue Labels

enhancement (45) bug (25) Shiny app (17) R package (15) good first issue (5) documentation (4) question (4) wontfix (2)

Pull Request Labels

documentation (1) enhancement (1) Shiny app (1) codex (1)

Packages

Total packages: 3
Total downloads:
- cran 285 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 59
Total maintainers: 1

proxy.golang.org: github.com/wincowgerdev/openspecy-package

Documentation: https://pkg.go.dev/github.com/wincowgerdev/openspecy-package#section-documentation
License: cc-by-4.0
Latest release: v1.5.1
published 11 months ago

Versions: 21
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 7 months ago

proxy.golang.org: github.com/wincowgerDEV/OpenSpecy-package

Documentation: https://pkg.go.dev/github.com/wincowgerDEV/OpenSpecy-package#section-documentation
License: cc-by-4.0
Latest release: v1.5.1
published 11 months ago

Versions: 21
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 7 months ago

cran.r-project.org: OpenSpecy

Analyze, Process, Identify, and Share Raman and (FT)IR Spectra

Homepage: https://github.com/wincowgerDEV/OpenSpecy-package/
Documentation: http://cran.r-project.org/web/packages/OpenSpecy/OpenSpecy.pdf
License: CC BY 4.0
Latest release: 1.5.3
published 11 months ago

Versions: 17
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 285 Last month

Rankings

Forks count: 8.3%

Stargazers count: 16.3%

Average: 25.6%

Dependent packages count: 29.8%

Dependent repos count: 35.5%

Downloads: 37.9%

Maintainers (1)

wincowger@gmail.com

Last synced: 7 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions

actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/check-r-package v1 composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite
r-lib/actions/setup-r-dependencies v1 composite

DESCRIPTION cran

R >= 4.0.0 depends
digest * imports
dplyr * imports
hexView * imports
hyperSpec * imports
osfr * imports
rlang * imports
shiny * imports
signal * imports
DT * suggests
config * suggests
curl * suggests
data.table * suggests
ggplot2 * suggests
knitr * suggests
loggit * suggests
mongolite * suggests
plotly * suggests
rdrop2 * suggests
rmarkdown * suggests
shinyBS * suggests
shinyWidgets * suggests
shinyjs * suggests
shinythemes * suggests
testthat >= 3.0.0 suggests

.github/workflows/pkgdown.yaml actions

JamesIves/github-pages-deploy-action v4.4.1 composite
actions/checkout v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v3 composite
actions/upload-artifact v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

OpenSpecy

Science Score: 49.0%

Repository

Basic Info

Statistics

Metadata Files

README.md

Open Specy 1.0

Installation

Install from CRAN (stable version)

Install from GitHub (development version)

Install on Web Assemply through webr (experimental), you can test here: https://webr.r-wasm.org/latest/

Getting started

Simple workflow for single spectral identification

Fetch current spectral library from https://osf.io/x7dpz/

Load library into global environment

Read sample spectrum

Look at the spectrum

Process the spectra and conform it to the library format

Compare raw and processed spectra

Print the top 5 results with relevant metadata

Get all metadata for the matches

Related Packages

Open Specy on Python

Citations

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

proxy.golang.org: github.com/wincowgerdev/openspecy-package

Rankings

proxy.golang.org: github.com/wincowgerDEV/OpenSpecy-package

Rankings

cran.r-project.org: OpenSpecy

Rankings

Maintainers (1)

Dependencies