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Plot Raw vs Calibrated Environmental Suitability (psi vs psi*)

Source: R/plot_psi_star_diagnostic.R
plot_psi_star_diagnostic.Rd

The psi_star parameters recalibrate the LSTM suitability signal on the logit scale before it enters the transmission model. Without this plot there is no routine way to see how much the calibration suppresses or reshapes the LSTM output. The subtitle reports the mean suppression percentage, making it immediately clear whether psi is acting as a meaningful seasonal driver or being effectively disabled.

Usage

plot_psi_star_diagnostic(dirs, PATHS = NULL, location_names, verbose = TRUE)

Arguments

dirs

Named list of output directory paths as returned by the internal .mosaic_ensure_dir_tree() helper inside run_MOSAIC(). Required entries: dirs$res_fig_diag (output), dirs$inputs (for config.json), dirs$res_posterior (for parameter_estimates.csv).

PATHS

Optional named list of project paths as returned by get_paths(); used only as a fallback to read PATHS$MODEL_INPUT/pred_psi_suitability_day.csv when the run's config.json carries no usable psi_jt. Default NULL.

location_names

Character vector of ISO3 location codes (e.g. "MOZ"). One plot is generated per location.

verbose

Logical; if TRUE (default) emits progress messages.

Value

Invisibly returns a named list of ggplot objects, one per location. Saves PNG files to dirs$res_fig_diag with filenames psi_raw_vs_psi_star_{j}.png.

Details

Creates a time-series plot comparing the raw LSTM-predicted environmental suitability psi with the calibrated psi* after applying the posterior psi_star parameters (psi_star_a, psi_star_b, psi_star_z, psi_star_k) via calc_psi_star.

The raw series is the psi_jt row the run actually calibrated on, read from 1_inputs/config.json over its daily date_start..date_stop grid, so the figure is a pure read of the run directory and renders post-hoc on any machine. Only when config.json has no psi_jt of matching length does it fall back to the psi column of PATHS$MODEL_INPUT/pred_psi_suitability_day.csv.

The plot is skipped gracefully (with a message) for any location where:

  • the psi_star posterior parameters are absent from parameter_estimates.csv (e.g. parameters were frozen or not sampled),

  • neither psi_jt nor the fallback CSV is available, or

  • the suitability data contains no rows for the location or calibration window.

See also

calc_psi_star for the transformation applied.