SEACAR Trend Analyses

The SEACAR Trend Analyses repository contains the analysis scripts used to generate habitat-specific reports. Updated forms of these scripts can be found in the MA Report Generation/scripts/ sub-folder where they are used to generate Managed Area Reports for each Managed Area which include analyses for each habitat (except Oyster - in development).

Managed Area Reports overview

The Managed Area Reports Directory can be used to easily locate HTML and PDF versions for each Managed Area.

The Managed Area Reports are located in the MA Report Generation/output/Reports/ sub-folder, in both HTML and PDF formats.

Managed Area Reports contain the following information and visualizations if the habitats are included for a given Managed Area:

• Introduction
  • Threshold filtering
  • Value Qualifiers overview
• Discrete Water Quality / Water Clarity (by parameter)
  • Seasonal Kendall-Tau trend analysis ("discrete trendplots")
  • Map of discrete sample locations ("discrete maps")
  • Programs contributing data ("program tables"):
    • ProgramID
    • N_Data
    • Year Min & Max
  • Overview of value qualifiers by year ("VQ tables")
    • Year
    • N_Total (total data for that parameter in that year)
    • N_* (count of data entries with a given VQ in that year)
    • Perc_* (percent of data entries flagged with a given VQ compared to total for that year)
• Continuous Water Quality / Water Clarity (by parameter)
  • Station overview table ("continuous station table")
    • ProgramLocationID
    • Years of Data
    • Use in Analysis (True or False)
    • Parameters measured
  • Map of continuous sites with visual indicators showing if they are used in analysis ("continuous maps")
  • Seasonal Kendall-Tau trend analyses:
    • For each station/ProgramLocationID ("continuous trendplots")
    • All stations combined for each parameter ("combined continuous trendplots")
    • For MAs with lots of continuous stations, the combined trendplots will be combined by ProgramID
• Submerged Aquatic Vegetation (SAV)
  • Spatio-temporal sample locations plot ("SAV temporal scope plot")
  • Map of SAV sample locations ("SAV maps")
  • Program Summary tables / program-level overview
    • N_Data, Year Min and Max, Collection method, Number of sample locations
    • Individual tables provided for each program
  • Median Percent Cover species trend plots (Linear Mixed Effects)
    • Plots for all available species with LME trendlines laid upon scatterplots of median percent cover ("SAV multiplots")
    • Combined species trendlines with their significance indicated, simplified form of above plot ("SAV trendplots")
    • LME Trend Results table provides statistical information behind SAV multiplots and SAV trendplots
  • Frequency of Occurrence plots ("SAV barplots")
  • GAM species plots - Median % Cover ("SAV GAM plots")
• Nekton
  • Species richness plots (LME trend analysis)
• Coral
  • Species richness plots (LME trend analysis)
  • Percent cover plots (LME trend analysis)
• Coastal Wetlands
  • Species richness plots (LME trend analysis)
• Oyster (currently unavailable, in development)