Script 04 tobit analysis - see folder (04_CromTobitAnalysis)

Script 04 is the core trend-analysis step in the workflow

• preproccesess chemistry and water-level data
• assign trend periods (TERM) using cutoffs, special rules/overrides
• model on: time only or time + river stage (with lag)
  

Results may be:

• a single trend summary object, or
• a list of trend summary objects when multiple TERM periods exist

Script 05 plotting summary - see folder (05_ReportFigures)

Note: all R code functions/helpers used in 05_ReportFigures.R saved in ./r_function_extract
Script 05 is the reporting layer for the Tobit workflow.
Uses trend-analysis data from Script 04, water-level trend data, well metadata, and GIS base data, then produces:

• one PDF report per OU
• one page per well with summary table, map and plots

Main workflow

1. Load trend and water-level data
2. Load well metadata, GIS base layers
3. Group wells by OU
4. For each well, extract:
   • analyte name and units
   • well coordinates / OU
   • whether river stage is used
   • associated water-level object
   • lag(s) / regression info for each TERM
5. Choose one of two page templates:
   • pltReport(...) if trend / lag output exists
   • pltPlaceholder(...) if no regression analysis was performed

Page layout

Full report page (pltReport)

The page contains:

• header
• header summary table
• location map
• legend
• top time-series panel: observed water level + river stage
• middle panel: observed chromium concentrations + river stage
• lower-middle panel: observed + model-predicted concentrations
• bottom panel: regression summary / significance display

Placeholder page (pltPlaceholder) - if no trend reported

Uses the same upper layout:

• header
• header summary table
• location map
• legend
• optional water-level panel
• chromium observations panel

The bottom plot area is replaced with a simple No Regression Analysis Performed message.

Notes

• Chromium observations are plotted on a log scale
• Non-detects are highlighted separately (red triangle)
• Each trend TERM is shown with its own colour / symbol styling
• If water-level data exist, the top panel also shows the screened interval
• River stage is omitted for wells listed in NoRS
• Script 05 creates a report summary table for each well using tblSummary(...)