APRL GitLab Pages
Table of Contents
Packages
Chemoinformatic analysis of functional groups
Functional group composition for property prediction or mode/measurement intercomparisons can be harvested from molecularly-speciated measurements or model simulations.
- APRL-SSP: provides SMARTS patterns and atom-level validation tools described by Ruggeri and Takahama, Atmos. Chem. Phys., doi:10.5194/acp-16-4401-2016, 2016.
- APRL-KPP-GP: adds gas/particle partitioning to gas-phase chemistry code (Fortran 90) generated by the Kinetic Pre-Processor; described by Ruggeri et al., Atmos. Chem. Phys., doi:10.5194/acp-16-8729-2016, 2016.
- APRL-Carbontypes: carbon and functional group analysis via carbon type enumeration, described by Takahama and Ruggeri, Atmos. Chem. Phys., doi:10.5194/acp-17-4433-2017, 2017. (The relevant code has been integrated into APRL-SSP.)
Spectroscopy analysis - chemometrics and machine learning
R packages for interpretation of complex infrared spectra (measured by FT-IR) associated with atmospheric aerosols.
- AIRSpec: provides a browser-based interface (via Shiny) that consolidates many of these chemometric modules. Web version can also be accessed at http://airspec.epfl.ch. Manuscript by Reggente et al., Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2018-332, currently under open review.
- APRLspec: provides spectra object definitions and I/O functions.
- APRLssb: implements the smoothing splines baseline correction method of Kuzmiakova et al., Atmos. Meas. Tech., doi:10.5194/amt-9-2615-2016, 2016.
- APRLmpf: implements the multiple peak fitting method of Takahama et al., Aerosol Sci. Tech., doi:10.1080/02786826.2012.752065, 2013.
- APRLmvr: implements the multivariate calibration strategies summarized by Takahama et al., Atmos. Meas. Tech., doi:10.5194/amt-2018-70, 2018.
- ElnetPLS: elastic net regularization - partial least squares regression.
A vignette is available (under preparation).
Teaching - computational exercises
- ENV-320: [Bachelor course] Atmospheric Physics and Chemistry (solutions can be found in its private repository)
- ENV-400: [Master course] Air Pollution and Climate Change
Other software
Analysis tools
These programs harvest output from other numerical tools used by the atmospheric research community. Their use is illustrated by Takahama et al., Atmos. Chem. Phys., doi:10.5194/acp-11-6367-2011, 2011, among other publications.
- PSCF: implements Positive Source Contribution Function calculations from HYSPLIT back trajectories.
- PMF-tools: a set of scripts to run P. Paatero's (proprietary) executable program for Positive Matrix Factorization (PMF).
Input/output (I/O) tools
Functions for reading/exporting data.
- APRLrio: I/O library for common data formats (ICARTT, E-AIM HTML, TSI software) in R.
- APRLmio: I/O functions in MATLAB for several instruments that measure aerosol number concentrations and size distributions.
- semdsdat2itx: script for converting output of Brechtel SEMS .dat files to .itx files that can be imported into IGOR Pro.
Language tools
Tools to facilitate programming in various languages.
- libIgorPro: wrappers for shell scripting and namespace implementation with data folders for Igor Pro (Wavemetrics).
- Rfunctools: facilitates functional programming in R.
- aprl-emacs: configurations for using R, python, GNU Octave, FORTRAN, LaTeX, etc. in GNU Emacs.