Skip to content

State of Casco Bay Details

Detailed archive of State of Casco Bay data and analysis code

Casco Bay Estuary Partnership State of Casco Bay Report Details

This collection of repositories is an archive of data and data analysis conducted during preparation of the Casco Bay Estuary Partnership (CBEP) "State of Casco Bay" report.

The purpose of the collection is as an archive of methods used for analyses of State of Casco Bay data, to facilitate future projects. The collection contains full "working" versions of the data analysis workflow used to produce the State of Casco Bay report. It includes many files omitted from the companion collection found at the primary State of Casco Bay data analysis archive. Data and code were often omitted from that collection in order to simplify the repositories and clarify the principal data analysis pathway that led to figures, tables, or narrative claims presented in the final SoCB report.

Look here to find additional, often messy details of our actual data analysis process. These "working" files that have not been as carefully reviewed as files in the CBEP-SoCB-Details archive, so typographical errors and incomplete descriptions and documentation are more common. Files often include preliminary data analyses that we conducted as part of finding our way to more appropriate or more robust analyses. Analyses may be incomplete or inappropriate to the data. We offer few guideposts here regarding contents or appropriateness of specific analyses, so buyer beware.

Working data analysis repositories include the following types of files that were generally omitted from the more concise CBEP-SoCB archives:

  • Source data (data as originally accessed or downloaded),

  • Data access scripts, when relevant, and detailed of data access steps when data was accessed from online sources by hand,

  • Code documenting our data QA/QC review of source data,

  • Code that restructured source data into working data, or more detailed descriptions of data preparation steps that are not documented implicitly in R Code (e.g., for GIS workflows conducted by hand in ArcGIS).

  • Additional intermediate GIS files

  • Supplementary analyses that informed our understanding of the data, but were ultimately not referred to in State of Casco Bay,

  • Additional analyses or analyses of related data sets that we ended up not using in the final "State of Casco Bay" Report documenting,

  • Code that explored data analysis methods (e.g., for analysis of acidification data in R) or developed approaches for graphical presentation of results.

Repository Contents

State of Casco Bay 2020/2021

The 2020/2021 State of Casco Bay Report is structured into multiple Chapters. Each chapter is based on one to several data sources. The Github repositories are built around the data sources (with some variation). The following section provides a cross-walk from topics to specific repositories.

DRIVERS AND STRESSORS; "What's Affecting the Bay?"

  • A. Population and Land Use
    • Population / Census
    • Land Use
  • B. Stormwater
    • Ten years of water quality monitoring data from Long Creek, provided by the Long Creek Watershed Management District. .......... LCWMD_Monitoring
    • Geospatial data on locations of areas formally included in the "Municipal Separate Storm Sewer System" or MS4 program. .......... MS4_Areas
  • C. Combined Sewer Overflows
    • Maine DEP, City of Portland, and Portland Water District data on CSO discharges. .......... Casco_Bay_CSOs
  • D. Inland Water Quality
  • E. Climate Change
    • Analysis of eight decades of weather data from the Portland Jetport. Data accessed through NOAA online data APIs. .......... CDO_Portland_Jetport
    • Analysis of nearly a century of sea levels at the Portland tide gauge and forecasts of future tidal flooding frequencies. .......... Portland_SLR
  • F. Invasive Species
    • Review of MIMIC data on prevalence of selected invasive marine invertebrates in Casco Bay. .......... CB_Invasives

CONDITION OF THE BAY; "How is the Bay doing?"

  • G. Bay Water Quality
    • Friends of Casco Bay (FOCB) water quality monitoring data. .......... FOCB_Data
    • Bay Stratification -- Analysis of stratification in several Casco Bay subestuaries. .......... Bay_Stratification
  • H. Nutrients
    • Friends of Casco Bay (FOCB) nutrient-related data. .......... FOCB_Nutrients
    • Maine Department of Environmental Protection (DEP) nutrient-related data. .......... DEP_Nutrients
    • Combined FOCB and DEP nutrient data. .......... Combined_Nutrients
  • I. Aquatic Connectivity
  • J. Eelgrass
  • K. Coastal Acidification
    • Analysis of data collected by UNH, on behalf of CBEP, measuring OA-related parameters at the Southern Maine Community College pier, in South Portland. .......... CBEP_OA
    • Analysis of a four years of Friends of Casco Bay (FOCB) water quality data that pertains to ocean acidification. Data is from data loggers deployed off Chebeague Island. .......... FOCB_OA
  • L. Swimming Beaches and Shellfish Beds
    • Maine Department of Marine Resources (DMR) data on bacteria in shellfish. .......... Shellfish_Bacteria
    • Maine Beaches Program data on bacteria at monitored beaches. .......... Beaches_Bacteria
  • M. Toxics
    • CBEP historical data on toxics in Casco Bay Sediments. .......... CBEP_Sediments
    • Maine Surface Water Ambient Toxics (SWAT) data on toxic contaminants in blue mussels. .......... SWAT_Mussels
    • Portland Harbor Commission data on toxic contaminants in Portland harbor sediments. .......... Portland_Harbor_Toxics
    • Maine Board of Pesticides Control data on pyrethroid pesticides in intertidal sediments. .......... BPC_Pesticides

HUMAN CONNECTIONS; "What's Being Done?"

  • N. Conserved Lands
  • O. Coastal Habitats
  • P. Economics
    • Analysis of recent (pre-pandemic) data on number of cruise ships and cruise ship visitors visiting Portland, Maine. .......... Portland_Cruise_Ships
  • Q. Education
  • R. Stewardship
  • S. Climate Preparedness

Reusable Code and Utilities

  • Small package to facilitate use of maximum likelihood estimates of (unobserved) "non-detects" in left censored data, such as observations of concentrations of contaminants or bacteria. .......... LCensMeans
  • Utility package to facilitate uniformity in graphic design for the 2020-2021 State of Casco Bay report. Defines a default graphic style, fonts and six preferred colors. .......... CBEPgraphics
  • Package to generate several varieties of ggplot style graphics from depth profile data, including interpolated two dimensional depth by time or depth by location color plots. .......... tdggraph

General Data Sources and Information

  • Watershed Boundary
  • Impervious Cover
  • NHD hydrography
  • Others

About Casco Bay and Casco Bay Estuary Partnership

Casco Bay Estuary Partnership (CBEP) is one of twenty eight National Estuary Programs. Each National Estuary Program is a locally led, non-regulatory, science-based collaborative organization that works to address challenges facing Estuaries of National Significance and the communities on their shores.

CBEP works with dozens of partner organizations, including federal, state, and local government; colleges and universities; non-profits and interest groups; local businesses and private citizens on behalf of Casco Bay, a coastal embayment in southern Maine.

You can find more information about CBEP on our web site.

Casco Bay is approximately 160 square miles in size, dotted with hundreds of islands. The roughly 980 square mile watershed is long and narrow, extending as far as the mountains of Western Maine. Forty eight towns and cities touch the watershed. Twelve are coastal communities with marine shorelines. Our largest urban center is Portland, Maine, located on the South West corner of the Bay. Dozens of lakes dot the watershed including Sebago Lake, Maine's deepest, and second largest. The climate is cool-temperate. On the order of a meter of precipitation falls in most years, spread more or less evenly over twelve months. Most of that precipitation falls as rain, but snow predominates in the winter months.

The Casco Bay watershed represents on the order of four and a half percent of the land area of Maine, but close to a quarter of the state's population, and a third of employment and economic activity. The regional economy is dominated by the service economy of Portland, but marine-related industries represents about four percent of jobs and economic activity in the region. That share is substantially higher for our island and peninsula communities.

Casco Bay supports a robust lobster fishery, substantial clam harvests, a growing aquaculture industry(principally blue mussels, american oyster, and sugar kelp). Portland Harbor handles both container ships and oil tankers. Land-based businesses on the waterfront support Maine's fishing industry, but also support a burgeoning restaurant scene. In fact, tourism (including restaurants, lodging, cruise ships, tour operations, etc. (but omitting property rentals and real estate) represents close to three quarters of all marine-related economic activity of the region.

The Team

The primary author of this archive is Curtis C. Bohlen, Director and lead scientist of the Casco Bay Estuary Partnership. Other members of the CBEP staff, including Marti Blair, Victoria Boundy, Matthew Craig, and Thomas Gilmartin have made additional contributions.

You can find more information about us at the CBEP website.

Popular repositories Loading

  1. BPC_Pesticides BPC_Pesticides Public

    Analysis of data from 2014 and 2015 Maine Board of Pesticides Control marine sediment and water sampling for selected pesticides

    HTML 1

  2. Presumpscot_WQ Presumpscot_WQ Public

    Analysis of volunteer water quality monitoting data from Presumpscot River Watch and Presumpscot Land Trust

    HTML 1

  3. Bay_Stratification Bay_Stratification Public

    Graphics to show vertical stratification in water quality in Casco Bay, Maine, based on DEP and FOCB data


  4. Portland_Harbor_Toxics Portland_Harbor_Toxics Public


  5. SWAT_Mussels SWAT_Mussels Public


  6. Beaches_Bacteria Beaches_Bacteria Public



Showing 10 of 31 repositories
  • CBEP-SoCB-Details/LCWMD_Monitoring’s past year of commit activity
    Python 0 1 0 0 Updated Jun 2, 2022
  • CBEP-SoCB-Details/Analysis_Biomonitoring’s past year of commit activity
    0 1 0 0 Updated Jan 26, 2022
  • Access_Biomonitoring Public

    Code, largely in python, for accessing and organizing Maine stream biomonitoring data for further data analysis.

    CBEP-SoCB-Details/Access_Biomonitoring’s past year of commit activity
    Python 0 1 0 0 Updated Jan 26, 2022
  • .github Public
    CBEP-SoCB-Details/.github’s past year of commit activity
    0 MIT 1 0 0 Updated Jan 14, 2022
  • CBEP-SoCB-Details/CB_Aquaculture’s past year of commit activity
    0 1 0 0 Updated Dec 17, 2021
  • FOCB_WQ Public
    CBEP-SoCB-Details/FOCB_WQ’s past year of commit activity
    0 1 0 0 Updated Dec 11, 2021
  • CBEP-SoCB-Details/DEP_nutrients’s past year of commit activity
    0 1 0 0 Updated Dec 11, 2021
  • CBEP-SoCB-Details/Shellfish_Bacteria’s past year of commit activity
    HTML 0 1 0 0 Updated Dec 11, 2021
  • CBEP-SoCB-Details/Portland_SLR’s past year of commit activity
    Python 0 1 0 0 Updated Dec 11, 2021
  • FOCB_OA Public
    CBEP-SoCB-Details/FOCB_OA’s past year of commit activity
    Python 0 1 0 0 Updated Dec 9, 2021


This organization has no public members. You must be a member to see who’s a part of this organization.

Top languages


Most used topics