Chemometric tools for infrared spectra analysis
A major focus of the APRL laboratory is in algorithm development for interpretation of complex infrared spectra (measured by FT-IR) associated with atmospheric aerosols. They are released under the GNU Public License. A paper and vignette are available.
- APRLssb (R package) implements the smoothing splines baseline correction method of Kuzmiakova et al., Atmos. Meas. Tech., 2016.
- APRLmpf (R package) implements the multiple peak fitting method of Takahama et al., Aerosol Sci. Tech., 2013.
- APRLmvr (R package) provides a wrapper for multivariate regression/calibration methods as illustrated by Dillner and Takahama, Atmos. Meas. Tech., 2015 [a][b], Takahama and Dillner, J. Chemometrics, 2015, Reggente et al., Atmos. Meas. Tech., 2016, Takahama et al., Atmos. Meas. Tech., 2016, Takahama et al., Atmos. Meas. Tech., 2019.
- AIRSpec (R Shiny module): provides a browser-based interface that consolidates many of these chemometric modules. Web version can also be accessed at http://airspec.epfl.ch.
- PMF-tools (R scripts) facilitates source apportionment by factor analytic decomposition and cluster analysis of IR spectra, as described by Russell et al., J. Geophys. Res.-Atmos., 2009 (appendix) and Takahama et al., Atmos. Chem. Phys., 2011, among others.
Chemoinformatic tools for functional group analysis
Functional group composition for property prediction or mode/measurement intercomparisons can be harvested from molecularly-speciated measurements or model simulations.
- APRL-SSP (python and R scripts) provides SMARTS patterns and atom-level validation tools described by Ruggeri and Takahama, Atmos. Chem. Phys., 2016.
- APRL-KPP-GP (python and Fortran 90 code) adds gas/particle partitioning to gas-phase chemistry code (Fortran 90) generated by the Kinetic Pre-Processor; illustrated by Ruggeri et al., Atmos. Chem. Phys., 2016.
- APRL-Carbontypes (R scripts) illustrates carbon and functional group analysis via carbon type enumeration, described by Takahama and Ruggeri, Atmos. Chem. Phys., 2017. (Relevant code for reuse has been integrated into APRL-SSP.)
- PSCF (R and python scripts) implements Positive Source Contribution Function from HYSPLIT backtrajectories. Its use is illustrated by Takahama et al., Atmos. Chem. Phys., 2011, among many other publications.
- APRLrio (R package) provides a library for input/output (I/O) for common data formats (ICARTT, E-AIM HTML, TSI software).
- APRLmio (MATLAB library) provides functions for input/output (I/O) for several instruments that measure aerosol number concentrations and size distributions.
- libIgorPro (IGOR Pro library) provides convenience functions for shell scripting and implementing namespaces using IGOR Pro data folders.
- semsdat2itx (python script) provides a script for converting output of Brechtel SEMS .dat files to .itx files that can be imported into IGOR Pro.
- aprl-emacs (emacs lisp) provides configurations for using R, python, GNU Octave, Fortran, LaTeX, etc. in GNU Emacs.
- Drawings for machined parts used in electrospray-ATR FT-IR (Arangio et al., Appl. Spectrosc., doi:10.1177/0003702818821330, 2019) analysis are available here.
- Metric version of FTIR minichamber (Debus et al., Appl. Spectrosc., doi:10.1177/0003702818804574, 2019) can be found here.