Data and Code for High Throughput FTIR Analysis of Macro and Microplastics with Plate Readers

Data and source code for reproducing the analysis conducted in "High Throughput FTIR Analysis of Macro and Microplastics with Plate Readers"

All materials are licensed for noncommercial purposes https://creativecommons.org/licenses/by-nc/4.0/

HIDA_Publication.R has source code for doing data cleanup and analysis on data in database.zip. 

databasedata.zip holds all raw and analyzed data. 

- ATR, Reflectance, and Transmission folders has all data used in the manuscript. In a raw (.0) and combined (export.csv) format for each of the plates analyzed (folder numbers). 

- Plots folder has images of each spectrum. 

- cell_information.csv has the raw ids and comments made at the time the particles were assessed. 

- classes_reference_2.csv has the transformations used to standardize open specy's terms to polymer classes. 

- CleanedSpectra_raw.csv has the total cleaned up database of all spectral intensities in long format.  

- joined_cell_metadata.csv has the metadata for each plate well analyzed. 

- library_metadata.csv has metadata for each spectrum in raw form for each particle id. 

- Lisa_Plate_6.csv has the metadata from Lisa Roscher used in this study. 

- Metadata_raw.csv has the conformed metadata that can be paired with the CleanedSpectra_raw.csv file. 

- OpenSpecy_Classification_Baseline.csv has the particle metadata combined with Open Specy's classes identified after baseline correcting and smoothing the spectra with the standard Open Specy routine.

- OpenSpecy_Classification_Raw.csv has the particle metadata combined with Open Specy's identified classes if using the raw spectra. 

- particle_spectrum_match.csv converts particle ids to their reference in the Polymer_Material_Database_AWI_V2_Win.xlsx file. 

- Polymer_Material_Database_AWI_V2_Win.xlsx metadata on materials from Primpke's database. 

- polymer_metadata_2.csv can be used to crosswalk polymer categories to more or less specific terminology. 

- spread_os.csv is the reference database used in CleanedSpectra_raw.csv that has been spread to wide format.

- Top Correlation Data20221201-125621.csv is a download of results from Open Specy's beta tool that provides the top ids from the reference database.