Casco Bay Estuary Partnership (CBEP) staff was involved with a project to look at carbonate chemistry parameters from several National Estuaries,including CBEP. The project we being led principally by Nick Rosenau, of the U.S. Environmental Protection Agency, in Washington D.C. The effort has produuced a draft scientific paper, which will be submitted for publication soon (fall 2020).

The files included in this Github repository were part of CBEP's effort to explore analytic methods and graphics for the scientific paper.

These files were all "preliminary" in the sense that they were part of our efforts to improve our understanding of carbonate chemistry, explore analytic methods, or look at ideas for graphic presentation of results. None of the code included here was used to produce final graphics or figures for the paper.

CBEP is committed to the ideal of open science. Our data archives ensure our science is documented and reproducible by others. The purpose of these archives is to release raw data and data analysis code whenever possible to allow others to review, critique, learn from, and build upon CBEP science.

• Original Data. Original data, with a "DATA_SOURCES.md" file that documents data sources. DATA IN THIS FOLDER IS AS ORIGINALLY PROVIDED.

• Complete NEP Data Additional Original data, with a "DATA_SOURCES.md" file that documents data sources. DATA IN THIS FOLDER IS AS ORIGINALLY PROVIDED.

• Derived Data. Data derived from the original raw data. Includes R notebooks that embody data transformation and reorganization, along with CSV files containing data used elsewhere in the repository.

• Temperature_Dependence. Contains a long R Markdown file documenting my current understanding of temperature dependence of pCO2. The R Markdown document produced a PDF summary, also stored here.

• Analysis. Contains R Notebooks proceeding through one approach to analysis of pCO2 data using generalized additive mixed models (GAMMs). GAMMs are well suited to this problem, as they easily integrate non-linear terms, and properly address the high serial autocorrelation common in data from automated sensors. Files presented here walk through a simplified GAMM analyses of pCO2 data. The files are a subset of analyses we conducted. Other analyses follow similar methods, looking at different dependent variables (temperature corrected pCO2 and pH) and more complex models incorporating a richer set of nonlinear and interaction terms. Additional analysis examples can be found in our CBEP_OA Github repository.

• Analysis_Daily. Contains files related to analysis of, or preparation of graphics from, daily summaries of hourly pCO2 and pH data. Analysis and graphics focus on diurnal range and daily medians. One file, Diurnal Range Graphics All NEPs.Rmd analyses data from all the NEPs with available data from the EPA study.

Data was either derived from CBEP OA data analyzed as part of our 2020 State of the Bay report, or e-mailed to Curtis C. Bohlen by Nick Rosenau of the U.S. Environmental Protection Agency (EPA), who was coordinating an effort to compare carbonate chemistry in National Estuary Waters.

Data sets were gathered through projects coordinated by, and often funded by, National Estuary Programs around the U.S. Data was assembles by staff at U.S. EPA. CBEP did not produce the data, but participated in efforts to consolidate data analysis and review. CBEP was not the producer of the data, cannot vouch for its accuracy, does not hold copyright, and cannot grant useage rights to others.

Data is provided here on an "AS IS" basis for study only. Data was provided to CBEP on a preliminary basis as part of collaborative research. Users are cautioned that data may not have gone through complete QA/QC processes and may contain inaccurate information.