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Visualize Model Assessment Metrics Across Time

Source: R/plot_model_assessment.R
plot_model_assessment.Rd

Generates diagnostic plots from the per-timestep assessment table produced by generate_spatiotemporal_predictions, optionally overlaying overall reference values from the model result object.

Usage

plot_model_assessment(predictions, time_column,
                      secondary_time_mode = "combine", model_result = NULL,
                      cbp_threshold = 0.05, plot_palette = "Dark 2",
                      verbose = TRUE)

Arguments

predictions

List returned by generate_spatiotemporal_predictions, or a named list with at least a timestep_metrics element. The timestep_metrics element may also be a path to a Timestep_Assessment_Metrics.csv file produced by generate_spatiotemporal_predictions.

time_column

Character. Name of the primary time column in timestep_metrics to use as the x axis (e.g. "year"). When predictions span multiple time columns (e.g. "year" and "season"), provide all relevant column names as a character vector and control how secondary columns are handled via secondary_time_mode.

secondary_time_mode

Character. How to handle secondary time columns when time_column has length > 1. One of:

  • "combine" (default): secondary time values are appended to the primary value to form a single ordered x-axis label (e.g. 1_Spring, 1_Summer, 2_Spring, ...).

  • "facet": a separate plot is produced for each unique combination of secondary time values, with the primary time column as the x axis on every panel.

model_result

List or character. Optional. Output from a build_temporal_*() function or path to its .rds file. When supplied, overall sensitivity and specificity from model_result$fold_test_metrics are added as per-fold reference lines. Default is NULL.

cbp_threshold

Numeric. Significance threshold for CBP. Default is 0.05.

plot_palette

Character. Name of an HCL or RColorBrewer palette used to color folds in diagnostic plots. Accepts any HCL palette name (see hcl.pals) or, if RColorBrewer is installed, any Brewer palette name. Default is "Dark 2".

verbose

Logical. If TRUE (default), prints progress messages during processing.

Value

Invisibly returns a named list containing:

  • pct_suitable: Recorded plot of proportion of study area predicted suitable per time step.

  • sensitivity: Recorded plot of per-timestep sensitivity.

  • specificity: Recorded plot of per-timestep specificity (only present when pseudoabsence data were used).

  • cbp: Recorded plot of cumulative binomial probability per time step on a log scale.

  • tp_fn: Recorded plot of true positives and false negatives per time step.

  • tn_fp: Recorded plot of true negatives and false positives per time step (only present when pseudoabsence data were used).

  • timestep_summary: Data frame of per-time-step cross-fold mean and SD for each metric.

  • overall_summary: Data frame from predictions$overall_summary, when present.

Details

Plots per-fold and per-timestep diagnostic plots for data produced by generate_spatiotemporal_predictions. These quick visuals can be used by users to assess model performance and significance and decide if the model's performance warrants further interpretation of the results through post-processing analyses.

See also

Preprocessing: spatiotemporal_partition, generate_absences

Modeling: build_temporal_glm, build_temporal_gam, build_temporal_rf, build_temporal_hv,

Post-processing: generate_spatiotemporal_predictions, summarize_raster_outputs

Examples

data(tmr_predictions, package = "TemporalModelR")

plot_model_assessment(
  predictions         = tmr_predictions,
  time_column         = c("year", "season"),
  secondary_time_mode = "combine",
  verbose             = FALSE
)