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Generate Spatiotemporal Predictions from Temporal Models

Source: R/generate_spatiotemporal_predictions.R
generate_spatiotemporal_predictions.Rd

Generates temporally explicit habitat suitability predictions by projecting fitted models onto environmental raster stacks matching each time period. Accepts output from any of the four TemporalModelR modeling functions. Produces per-time-step assessment metrics showing how predictions and test point coverage vary over time.

Usage

generate_spatiotemporal_predictions(partition_result, model_result,
                                    pseudoabsence_result = NULL, raster_dir,
                                    variable_patterns, time_cols, time_steps,
                                    output_dir = file.path(tempdir(), "Predictions"),
                                    overwrite = FALSE,
                                    verbose = TRUE)

Arguments

partition_result

List or character. Output from spatiotemporal_partition or path to an .rds file containing that output.

model_result

List or character. Output from any of build_temporal_hv, build_temporal_glm, build_temporal_gam, or build_temporal_rf, or a path to an .rds file. Model type is detected automatically from the model_type field.

pseudoabsence_result

List, character, or NULL. Optional. Output from generate_absences or path to an .rds file. When supplied for presence/absence models (GLM, GAM, RF), the held-out pseudoabsence test points for each fold are filtered to the current time step and used alongside presence test points to compute per-timestep TN, FP, Specificity, and TSS. These columns are added to the timestep metrics table when pseudoabsences are available. Ignored for hypervolume models. Default is NULL.

raster_dir

Character. Directory containing environmental raster files (.tif), typically the output of raster_align or scale_rasters. File names must follow the patterns supplied in variable_patterns, with any time placeholder substituted for the corresponding value from time_cols.

variable_patterns

Named character vector mapping clean variable names to raster filename patterns. For time-varying variables include the time placeholder in the pattern (e.g. "forest_cover" = "forest_cover_YEAR"); for static variables omit it (e.g. "elevation" = "elevation"). Time placeholders must match entries in time_cols.

time_cols

Character. Name of the column(s) containing year or time step values in the occurrence data. Must match time_cols used in spatiotemporal_partition and the time placeholders used in variable_patterns.

time_steps

Vector, data frame, or matrix of time periods for which to generate predictions.

output_dir

Character. Directory to write prediction rasters and the assessment metrics CSV. Default is file.path(tempdir(), "Predictions").

overwrite

Logical. If TRUE, overwrites existing output files. If FALSE (default), existing files are skipped.

verbose

Logical. If TRUE (default), prints progress messages during processing. Includes per-time-step prediction progress.

Value

Invisibly returns a list containing:

  • timestep_metrics: data frame of per-fold per-time-step metrics. Columns always present: Fold, the time column(s), Pct_Suitable, N_Pres, TP, FN, Sensitivity, CBP. When pseudoabsence_result is supplied for parametric models, additionally: N_Abs, TN, FP, Specificity, TSS. Saved as Timestep_Assessment_Metrics.csv.

  • overall_summary: data frame of pooled metrics per fold. Columns: Fold, N_Timesteps, Mean_Pct_Suitable, Total_TP, Total_FN, Overall_Sensitivity, Overall_CBP. When pseudoabsences available: additionally Total_TN, Total_FP, Overall_Specificity, Overall_TSS.

  • prediction_files: character vector of paths to saved prediction rasters.

  • model_type: character string recording the model type used.

Details

G-space predictions are produced as rasters for each time-step and fold of an input model.

Per-timestep metrics are computed per fold per time step by extracting raster predictions at the held-out presence points that fall within that time step. Pct_Suitable records the proportion of the study area predicted suitable. Sensitivity shows how consistently test points are captured. CBP (cumulative binomial probability) tests whether the observed number of correctly predicted test points is better than expected by random placement: under the null, each point has Pct_Suitable probability of falling in suitable area, so dbinom(TP, N_Test_Pts, Pct_Suitable) gives the probability of observing exactly TP correct by chance. Small values indicate predictions are better than random.

See also

Preprocessing: scale_rasters, spatiotemporal_partition

Modeling: build_temporal_hv, build_temporal_glm, build_temporal_gam, build_temporal_rf

Post-processing: summarize_raster_outputs, plot_model_assessment

Examples

data(tmr_partition, package = "TemporalModelR")

data(tmr_glm,       package = "TemporalModelR")

data(tmr_absences,  package = "TemporalModelR")

scl_dir    <- system.file("extdata/rasters_scaled",
                          package = "TemporalModelR")

time_steps <- expand.grid(
  year             = 1:15,
  season           = "Spring",
  stringsAsFactors = FALSE
)

generate_spatiotemporal_predictions(
  partition_result     = tmr_partition,
  model_result         = tmr_glm,
  pseudoabsence_result = tmr_absences,
  raster_dir           = scl_dir,
  variable_patterns    = c(
    "elevation"    = "elevation",
    "forest_cover" = "forest_cover_YEAR",
    "prseas"       = "prseas_YEAR_SEASON"
  ),
  time_cols            = c("year", "season"),
  time_steps           = time_steps,
  output_dir           = tempdir(),
  overwrite            = TRUE,
  verbose              = FALSE
)