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

A 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)