Open Specy

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

Raman and (FT)IR spectral analysis tool for plastic particles and other environmental samples. Supported features include reading spectral data files (.asp, .csv, .jdx, .spc, .spa, .0), Savitzky-Golay smoothing of spectral intensities with smooth_intens(), correcting background noise with subtr_bg() in accordance with Zhao et al. (2007, doi: dbhfsj), and identifying spectra using an onboard reference library (Cowger et al. 2020, doi: f3sk). Analyzed spectra can be shared with the Open Specy community. A Shiny app is available via run_app() or online at http://www.openspecy.org.

Installation

OpenSpecy is available from CRAN and GitHub.

Install from CRAN (stable version)

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

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):

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

Getting started

library(OpenSpecy)
run_app()

See package vignette for a detailed standard operating procedure.

Workflow

library(dplyr)

# Fetch current spectral library from https://osf.io/x7dpz/
get_lib()

# Load library into global environment
spec_lib <- load_lib()

# Read sample spectrum
raman_hdpe <- read_text(read_extdata("raman_hdpe.csv"))

# Share your spectrum with the Open Spey community
share_spec(raman_hdpe,
           metadata = c(user_name = "Win Cowger",
                        contact_info = "wincowger@gmail.com",
                        spectrum_type = "Raman",
                        spectrum_identity = "HDPE")
           )

# Adjust spectral intensity
raman_adj <- raman_hdpe %>%
  adj_intens()

# Smooth and background-correct spectrum
raman_proc <- raman_adj %>% 
  smooth_intens() %>% 
  subtr_bg()

# Match spectrum with library and retrieve meta data
match_spec(raman_proc, library = spec_lib, which = "raman")

find_spec(sample_name == 5381, library = spec_lib, which = "raman")

Citation

To cite the R package OpenSpecy use:

Win Cowger and Zacharias Steinmetz (2021). OpenSpecy: Analyze, Process, Identify, and Share, Raman and (FT)IR Spectra. R package version 0.9.1. https://github.com/wincowgerDEV/OpenSpecy

A BibTeX entry for LaTeX users is

@Manual{,
  title = {OpenSpecy: Analyze, Process, Identify, and Share, Raman and (FT)IR Spectra},
  author = {Win Cowger and Zacharias Steinmetz},
  year = {2021},
  note = {R package version 0.9.1},
  url = {https://github.com/wincowgerDEV/OpenSpecy},
}

ardcarvalho/OpenSpecy