The atmoschem.process R package processes atmospheric chemistry data from ASRC sites in New York State. It provides tools to generate reports and processed datasets from the ASRC’s atmospheric chemistry data, and tools to visualize the data.
Overview
The atmospheric chemistry group at the ASRC, run by Dr. Jim Schwab, collects data from instruments at 4 sites across the state of New York: Whiteface Mountain (summit and base), Pinnacle State Park, and Queens College. We maintain a variety of instruments measuring ozone and ozone precursors, airborne particulate matter, sulfur dioxide, and meteorology.
The data undergoes a variety of adjustments and quality assurance checks before being released to the public, where it is used by government agencies and atmospheric science researchers, among others. Users can access the datasets online via our website at http://atmoschem.asrc.cestm.albany.edu/.
This software, which generates the processed datasets, synthesizes advice from atmospheric monitoring, statistical programming, and data management. In terms of data processing, we tend to follow guidelines from NARSTO (Christensen et al. 2000), and we also work regularly with EPA standards. The code is organized as an R package (Marwick, Boettiger, and Mullen 2018), and we use GitHub for project management (Bryan 2018). For data management, we tend to follow Briney (2015), and we try to make the data convenient to use (White et al. 2013).
The data collection at Whiteface Mountain is described in detail in a series of publications (Schwab, Wolfe, et al. 2016; Brandt et al. 2016; Schwab, Casson, et al. 2016), and another paper describes the measurements at Pinnacle State Park (Schwab, Spicer, and Demerjian 2009).
Installation
To install the package, run (from within R)
install.packages('remotes')
remotes::install_github('ASRCsoft/atmoschem.process')To generate the processed dataset, additional dependencies are requried:
remotes::install_github('ASRCsoft/atmoschem.process', dependencies = TRUE)Reproducing the routine chemistry dataset
Creating the dataset
Download or clone the repository. The dataset package can be generated by running, from a terminal,
cd /path/to/atmoschem.process
make routine asrc_user=youruser asrc_pass=yourpassword aqs_email=youremail aqs_key=yourkey(replacing the values with your information).
Run make help to see more make options.
References
Brandt, Richard E., James J. Schwab, Paul W. Casson, Utpal K. Roychowdhury, Douglas Wolfe, Kenneth L. Demerjian, Kevin L. Civerolo, Oliver V. Rattigan, and H. Dirk Felton. 2016. “Atmospheric Chemistry Measurements at Whiteface Mountain, NY: Ozone and Reactive Trace Gases.” Aerosol and Air Quality Research 16 (3): 873–84. https://doi.org/10.4209/aaqr.2015.05.0376.
Briney, Kristin. 2015. Data Management for Researchers: Organize, Maintain and Share Your Data for Research Success. Pelagic Publishing Ltd.
Bryan, Jennifer. 2018. “Excuse Me, Do You Have a Moment to Talk About Version Control?” The American Statistician 72 (1): 20–27. https://doi.org/10.1080/00031305.2017.1399928.
Christensen, Sigurd W., Thomas A. Boden, Les A. Hook, and Meng-Dawn Cheng. 2000. “NARSTO Data Management Handbook.” NARSTO Quality Systems Science Center. https://web.archive.org/web/20030401082229/http://cdiac.esd.ornl.gov:80/programs/NARSTO/pdf/dmhb_current_version.PDF.
Marwick, Ben, Carl Boettiger, and Lincoln Mullen. 2018. “Packaging Data Analytical Work Reproducibly Using R (and Friends).” The American Statistician 72 (1): 80–88. https://doi.org/10.1080/00031305.2017.1375986.
Schwab, James J., Paul Casson, Richard Brandt, Liquat Husain, Vincent Dutkewicz, Douglas Wolfe, Kenneth L. Demerjian, et al. 2016. “Atmospheric Chemistry Measurements at Whiteface Mountain, NY: Cloud Water Chemistry, Precipitation Chemistry, and Particulate Matter.” Aerosol and Air Quality Research 16 (3): 841–54. https://doi.org/10.4209/aaqr.2015.05.0344.
Schwab, James J., John B. Spicer, and Kenneth L. Demerjian. 2009. “Ozone, Trace Gas, and Particulate Matter Measurements at a Rural Site in Southwestern New York State: 1995–2005.” Journal of the Air & Waste Management Association 59 (3): 293–309. https://doi.org/10.3155/1047-3289.59.3.293.
Schwab, James J., Douglas Wolfe, Paul Casson, Richard Brandt, Kenneth L. Demerjian, Liquat Husain, Vincent A. Dutkiewicz, Kevin L. Civerolo, and Oliver V. Rattigan. 2016. “Atmospheric Science Research at Whiteface Mountain, NY: Site Description and History.” Aerosol and Air Quality Research 16 (3): 827–40. https://doi.org/10.4209/aaqr.2015.05.0343.
White, Ethan P., Elita Baldridge, Zachary T. Brym, Kenneth J. Locey, Daniel J. McGlinn, and Sarah R. Supp. 2013. “Nine Simple Ways to Make It Easier to (Re)use Your Data.” Ideas in Ecology and Evolution 6 (2). https://doi.org/10.4033/iee.2013.6b.6.f.