manage_lib: Manage spectral libraries

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

Manage spectral libraries

Description

These functions will import the spectral libraries from Open Specy if they were not already downloaded. The CRAN does not allow for deployment of large datasets so this was a workaround that we are using to make sure everyone can easily get Open Specy functionality running on their desktop. Please see the references when using these libraries. These libraries are the accumulation of a massive amount of effort from independant groups and each should be attributed when you are using their data.

Usage

check_lib(
  type = c("derivative", "nobaseline", "raw", "mediod", "model"),
  path = "system",
  condition = "warning"
)

get_lib(
  type = c("derivative", "nobaseline", "raw", "mediod", "model"),
  path = "system",
  node = "x7dpz",
  conflicts = "overwrite",
  ...
)

load_lib(type, path = "system")

rm_lib(
  type = c("derivative", "nobaseline", "raw", "mediod", "model"),
  path = "system"
)

Arguments

type	library type to check/retrieve; defaults to c("derivative", "nobaseline", "raw", "mediod", "model") which reads everything.
path	where to save or look for local library files; defaults to "system" pointing to system.file("extdata", package = "OpenSpecy").
condition	determines if check_lib() should warn ("warning", the default) or throw and error ("error").
node	the OSF node to be retrieved; should be "x7dpz" unless you maintain your own OSF node with spectral libraries.
conflicts	determines what happens when a file with the same name exists at the specified destination. Can be one of the following (see osf_download() for details): "error" throw an error and abort the file transfer operation. "skip" skip the conflicting file(s) and continue transferring the remaining files. "overwrite" (default) replace the existing file with the transferred copy.
...	further arguments passed to osf_download().

Details

check_lib() checks to see if the Open Specy reference library already exists on the users computer. get_lib() downloads the Open Specy library from OSF (\Sexpr[results=rd]{tools:::Rd_expr_doi("10.17605/OSF.IO/X7DPZ")}). load_lib() will load the library into the global environment for use with the Open Specy functions. rm_lib() removes the libraries from your computer.

Value

check_lib() and get_lib() return messages only; load_lib() returns an OpenSpecy object containing the respective spectral reference library.

Author(s)

Zacharias Steinmetz, Win Cowger

References

Bell IB, Clark RJH, Gibbs PJ (2010). “Raman Spectroscopic Library.” Christopher Ingold Laboratories, University College London, UK. https://www.chem.ucl.ac.uk/resources/raman/.

Berzinš K, Sales RE, Barnsley JE, Walker G, Fraser-Miller SJ, Gordon KC (2020). “Low-Wavenumber Raman Spectral Database of Pharmaceutical Excipients.” Vibrational Spectroscopy 107, 103021. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5281/zenodo.3614035")}.

Cabernard L, Roscher L, Lorenz C, Gerdts G, Primpke S (2018). “Comparison of Raman and Fourier Transform Infrared Spectroscopy for the Quantification of Microplastics in the Aquatic Environment.” Environmental Science & Technology 52(22), 13279–13288. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1021/acs.est.8b03438")}.

Caggiani MC, Cosentino A, Mangone A (2016). “Pigments Checker version 3.0, a handy set for conservation scientists: A free online Raman spectra database.” Microchemical Journal 129, 123–132. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.microc.2016.06.020")}.

Chabuka BK, Kalivas JH (2020). “Application of a Hybrid Fusion Classification Process for Identification of Microplastics Based on Fourier Transform Infrared Spectroscopy. Applied Spectroscopy.” Applied Spectroscopy 74(9), 1167–1183. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1177/0003702820923993")}.

Cowger, W (2023). “Library data.” OSF. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.17605/OSF.IO/X7DPZ")}.

Cowger W, Gray A, Christiansen SH, De Frond H, Deshpande AD, Hemabessiere L, Lee E, Mill L, et al. (2020). “Critical Review of Processing and Classification Techniques for Images and Spectra in Microplastic Research.” Applied Spectroscopy, 74(9), 989–1010. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1177/0003702820929064")}.

Cowger W, Roscher L, Chamas A, Maurer B, Gehrke L, Jebens H, Gerdts G, Primpke S (2023). “High Throughput FTIR Analysis of Macro and Microplastics with Plate Readers.” ChemRxiv Preprint. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.26434/chemrxiv-2023-x88ss")}.

De Frond H, Rubinovitz R, Rochman CM (2021). “µATR-FTIR Spectral Libraries of Plastic Particles (FLOPP and FLOPP-e) for the Analysis of Microplastics.” Analytical Chemistry 93(48), 15878–15885. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1021/acs.analchem.1c02549")}.

El Mendili Y, Vaitkus A, Merkys A, Gražulis S, Chateigner D, Mathevet F, Gascoin S, Petit S, Bardeau JF, Zanatta M, Secchi M, Mariotto G, Kumar A, Cassetta M, Lutterotti L, Borovin E, Orberger B, Simon P, Hehlen B, Le Guen M (2019). “Raman Open Database: first interconnected Raman–X-ray diffraction open-access resource for material identification.” Journal of Applied Crystallography, 52(3), 618–625. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1107/s1600576719004229")}.

Johnson TJ, Blake TA, Brauer CS, Su YF, Bernacki BE, Myers TL, Tonkyn RG, Kunkel BM, Ertel AB (2015). “Reflectance Spectroscopy for Sample Identification: Considerations for Quantitative Library Results at Infrared Wavelengths.” International Conference on Advanced Vibrational Spectroscopy (ICAVS 8). https://www.osti.gov/biblio/1452877.

Lafuente R, Downs RT, Yang H, Stone N (2016). “The power of databases: The RRUFF project.” Highlights in Mineralogical Crystallography. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1515/9783110417104-003")}.

Munno K, De Frond H, O’Donnell B, Rochman CM (2020). “Increasing the Accessibility for Characterizing Microplastics: Introducing New Application-Based and Spectral Libraries of Plastic Particles (SLoPP and SLoPP-E).” Analytical Chemistry 92(3), 2443–2451. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1021/acs.analchem.9b03626")}.

Myers TL, Brauer CS, Su YF, Blake TA, Johnson TJ, Richardson RL (2014). “The influence of particle size on infrared reflectance spectra.” Proceedings Volume 9088, Algorithms and Technologies for Multispectral, Hyperspectral, and Ultraspectral Imagery XX, 908809. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1117/12.2053350")}.

Myers TL, Brauer CS, Su YF, Blake TA, Tonkyn RG, Ertel AB, Johnson TJ, Richardson RL (2015). “Quantitative reflectance spectra of solid powders as a function of particle size.” Applied Optics 54(15), 4863–4875. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1364/ao.54.004863")}.

Primpke S, Wirth M, Lorenz C, Gerdts G (2018). “Reference database design for the automated analysis of microplastic samples based on Fourier transform infrared (FTIR) spectroscopy.” Analytical and Bioanalytical Chemistry 410, 5131–-5141. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/s00216-018-1156-x")}.

Roscher L, Fehres A, Reisel L, Halbach M, Scholz-Böttcher B, Gerriets M, Badewien TH, Shiravani G, Wurpts A, Primpke S, Gerdts G (2021). “Abundances of large microplastics (L-MP, 500-5000 µm) in surface waters of the Weser estuary and the German North Sea.” PANGAEA. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1594/PANGAEA.938143")}.

“Handbook of Raman Spectra for geology” (2023). http://www.geologie-lyon.fr/Raman/.

“Scientific Workgroup for the Analysis of Seized Drugs.” (2023). https://swgdrug.org/ir.htm.

Further contribution of spectra: Suja Sukumaran (Thermo Fisher Scientific), Aline Carvalho, Jennifer Lynch (NIST), Claudia Cella and Dora Mehn (JRC), Horiba Scientific, USDA Soil Characterization Data (https://ncsslabdatamart.sc.egov.usda.gov), Archaeometrielabor, and S.B. Engelsen (Royal Vet. and Agricultural University, Denmark). Kimmel Center data was collected and provided by Prof. Steven Weiner (Kimmel Center for Archaeological Science, Weizmann Institute of Science, Israel).

Examples

## Not run: 
check_lib("derivative")
get_lib("derivative")

spec_lib <- load_lib("derivative")

## End(Not run)

OpenSpecy documentation built on Nov. 26, 2023, 1:09 a.m.