Predict bag of models in space — bag_predict

Creates spatial predictions from a bag of models for a grid provided as a data frame or raster. It can return weighted mean predictions, weighted median/uncertainty summaries, and/or individual model predictions.

Usage

bag_predict_spat(
  bag,
  data,
  input_type = c("df", "rast")[1],
  output_type = c("df", "rast")[2],
  prediction_type = c("exp", "exponential", "linear")[1],
  standardize = FALSE,
  what = c("mean", "median", "ind"),
  gid = "gid",
  coords = c("x33", "y33"),
  crs = NULL,
  gridalign = FALSE,
  output_rescale = FALSE,
  prediction_max_quantile = 0.999,
  uncertainty_quantiles = c(0.25, 0.75),
  verbose = FALSE
)

bag_predict_spat_vars(
  bag,
  data,
  predictor_table_zoi,
  input_type = c("df", "rast")[1],
  output_type = c("df", "rast")[2],
  prediction_type = c("exp", "exponential", "linear")[1],
  standardize = FALSE,
  what = c("mean", "median", "ind"),
  gid = "gid",
  coords = c("x33", "y33"),
  crs = NULL,
  gridalign = FALSE,
  prediction_max_quantile = 0.999,
  uncertainty_quantiles = c(0.25, 0.75),
  verbose = FALSE
)

Arguments

bag: [bag,list]
A bag of models from bag_models().
data: [data.frame,SpatRaster]
Spatial grid of predictors used for prediction. All predictors in the model formula must be present.
input_type: [character(1)="df"]{"df","rast"}
Input type: data frame with predictor values ("df") or SpatRaster raster stack/layers ("rast").
output_type: [character(1)="rast"]{"df","rast"}
Output type: data frame or raster outputs.
prediction_type: [character(1)="exp"]{"exp","exponential","linear"}
Prediction scale.
standardize: [logical(1)=FALSE]
Whether to standardize predictors before prediction using bag summary statistics.
what: [character]
Prediction outputs to compute. Any combination of "mean", "median", and "ind" for the weighted mean, weighted median, and individual model predictions, respectively.
gid: [character(1)="gid"]
Name of unique pixel/grid identifier column (used for df input and output).
coords: [character(2)=c("x","y")]
Names of x/y coordinate columns. Used if input_type = "df".
crs: [character(1)=NULL]
Coordinate reference system for raster output. Only relevant if input_type = "df". For more details, check terra::crs().
gridalign: [logical(1)=FALSE]
Whether to align output grid coordinates before rasterization.
output_rescale: [logical(1)=FALSE]
Whether to rescale raster outputs to 0,1 using prediction_max_quantile clipping.
prediction_max_quantile: [numeric(1)=0.999]
Quantile used as upper truncation threshold when output_rescale = TRUE.
uncertainty_quantiles: [numeric(2)=c(0.25, 0.75)]
Quantiles used for weighted uncertainty summaries when what includes "median".
verbose: [logical(1)=FALSE]
Print progress messages.
predictor_table_zoi: [data.frame]
Predictor table with ZOI metadata (for example from add_zoi_formula() predictor_table output), used to aggregate predictions by ZOI variable groups in bag_predict_spat_vars().

Value

For bag_predict_spat(), a list with prediction outputs:

grid: prediction table in tabular form (always returned).
weights: model weights used for prediction (non-zero weight models).
r_weighted_avg_pred: raster of weighted mean prediction (if requested and output_type = "rast").
r_ind_summ_pred: raster stack with weighted median and uncertainty summaries, including the interquartile range and the quantile coefficient of variation (if requested and output_type = "rast").
r_ind_pred: raster stack of individual model predictions (if requested and output_type = "rast").

For bag_predict_spat_vars(), a list with partial prediction outputs:

vars: per-variable prediction summaries.
grid: grid-level prediction table.
weights: model weights used for prediction.
r_weighted_avg_pred: raster output for weighted means (if requested).
r_ind_summ_pred: raster output for weighted uncertainty summaries (if requested).
r_ind_pred: raster output for individual-model predictions (if requested).