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Plot GLM-AED diagnostic variables to debug unrealistic oxygen values

Source: R/plot_glm_diagnostics.R
plot_glm_diagnostics.Rd

Reads model output using read_model_outputs() and produces a multi-panel diagnostic plot organised into thematic groups: oxygen budget, physical drivers, mixing, biological demand, and sediment fluxes.

Usage

plot_glm_diagnostics(
  aeme,
  lake_dir,
  surface_depth = 0.5,
  bottom_depth = NULL,
  dates = NULL,
  phyto_pars = NULL,
  output_dir = NULL
)

Arguments

aeme

An AEME object. Required if lake_dir is not provided.

lake_dir

Character. Path to the lake model output directory. If missing, derived from aeme and path.

surface_depth

Numeric. Depth (m) to extract for "surface" values. Defaults to 0.5.

bottom_depth

Numeric or NULL. Depth (m) to extract for "bottom" values. If NULL, the deepest available layer is used. Defaults to NULL.

dates

Date vector or NULL. Subset of dates to plot. NULL = all.

phyto_pars

Dataframe of phytoplankton parameters (passed through to read_model_outputs). Defaults to NULL.

output_dir

Character or NULL. Directory to save PDF output. If NULL, plots are displayed interactively. Defaults to NULL.

Value

Invisibly returns a list containing the out object from read_model_outputs and the assembled ggplot page objects.