eXtrem Gradient Boosted models

Usage

pipe_xgboost(
  df,
  predInput = NULL,
  responseVars = 1,
  caseClass = NULL,
  idVars = character(),
  weight = "class",
  crossValStrategy = c("Kfold", "bootstrap"),
  k = 5,
  replicates = 10,
  crossValRatio = c(train = 0.6, test = 0.2, validate = 0.2),
  params = list(),
  nrounds = 5,
  shap = TRUE,
  aggregate_shap = TRUE,
  repVi = 5,
  summarizePred = TRUE,
  scaleDataset = FALSE,
  XGBmodel = FALSE,
  DALEXexplainer = FALSE,
  variableResponse = FALSE,
  save_validateset = FALSE,
  baseFilenameXDG = NULL,
  filenameRasterPred = NULL,
  tempdirRaster = NULL,
  nCoresRaster = parallel::detectCores()%/%2,
  verbose = 0,
  ...
)

Arguments

df: a data.frame with the data.
predInput: a data.frame or a Raster with the input variables for the model as columns or layers. The columns or layer names must match the names of df columns.
responseVars: response variables as column names or indexes on df.
caseClass: class of the samples used to weight cases. Column names or indexes on df, or a vector with the class for each rows in df.
idVars: id column names or indexes on df. This columns will not be used for training.
weight: Optional array of the same length as nrow(df), containing weights to apply to the model's loss for each sample.
crossValStrategy: Kfold or bootstrap.
k: number of data partitions when crossValStrategy="Kfold".
replicates: number of replicates for crossValStrategy="bootstrap" and crossValStrategy="Kfold" (replicates * k-1, 1 fold for validation).
crossValRatio: proportion of the dataset used to train, test and validate the model when crossValStrategy="bootstrap". Default to c(train=0.6, test=0.2, validate=0.2). If there is only one value, will be taken as a train proportion and the test set will be used for validation.
params: the list of parameters to xgboost::xgb.train(). The complete list of parameters is available in the online documentation.
nrounds: max number of boosting iterations.
shap: if TRUE, return the SHAP values as shapviz::shapviz() objects.
aggregate_shap: if TRUE, and shap is also TRUE, aggregate SHAP from all replicates.
repVi: replicates of the permutations to calculate the importance of the variables. 0 to avoid calculating variable importance.
summarizePred: if TRUE, return the mean, sd and se of the predictors. if FALSE, return the predictions for each replicate.
scaleDataset: if TRUE, scale the whole dataset only once instead of the train set at each replicate. Optimize processing time for predictions with large rasters.
XGBmodel: if TRUE, return the model with the result.
DALEXexplainer: if TRUE, return a explainer for the models from DALEX::explain() function. It doesn't work with multisession future plans.
variableResponse: if TRUE, return aggregated_profiles_explainer object from ingredients::partial_dependency() and the coefficients of the adjusted linear model.
save_validateset: save the validateset (independent data not used for training).
baseFilenameXDG: if no missing, save the NN in hdf5 format on this path with iteration appended.
filenameRasterPred: if no missing, save the predictions in a RasterBrick to this file.
tempdirRaster: path to a directory to save temporal raster files.
nCoresRaster: number of cores used for parallelized raster cores. Use half of the available cores by default.
verbose: if > 0, print the state. The bigger the more information printed.
...: extra parameters for xgboost::xgb.train(), future.apply::future_replicate() or ingredients::feature_importance().