mlr_resamplings_spcv_block function

(blockCV) Spatial block resampling

This function creates spatially separated folds based on a distance to number of row and/or column. It assigns blocks to the training and testing folds randomly , systematically or in a checkerboard pattern . The distance (size) should be in metres , regardless of the unit of the reference system of the input data (for more information see the details section). By default, the function creates blocks according to the extent and shape of the spatial sample data (x e.g. the species occurrence), Alternatively, blocks can be created based on r assuming that the user has considered the landscape for the given species and case study. Blocks can also be offset so the origin is not at the outer corner of the rasters. Instead of providing a distance, the blocks can also be created by specifying a number of rows and/or columns and divide the study area into vertical or horizontal bins, as presented in Wenger & Olden (2012) and Bahn & McGill (2012). Finally, the blocks can be specified by a user-defined spatial polygon layer.

Details

To maintain consistency, all functions in this package use meters as their unit of measurement. However, when the input map has a geographic coordinate system (in decimal degrees), the block size is calculated by dividing the size parameter by deg_to_metre (which defaults to 111325 meters, the standard distance of one degree of latitude on the Equator). In reality, this value varies by a factor of the cosine of the latitude. So, an alternative sensible value could be cos(mean(sf::st_bbox(x)[c(2,4)]) * pi/180) * 111325.

The offset can be used to change the spatial position of the blocks. It can also be used to assess the sensitivity of analysis results to shifting in the blocking arrangements. These options are available when size is defined. By default the region is located in the middle of the blocks and by setting the offsets, the blocks will shift.

Roberts et. al. (2017) suggest that blocks should be substantially bigger than the range of spatial autocorrelation (in model residual) to obtain realistic error estimates, while a buffer with the size of the spatial autocorrelation range would result in a good estimation of error. This is because of the so-called edge effect (O'Sullivan & Unwin, 2014), whereby points located on the edges of the blocks of opposite sets are not separated spatially. Blocking with a buffering strategy overcomes this issue (see cv_buffer).

mlr3spatiotempcv notes

By default blockCV::cv_spatial() does not allow the creation of multiple repetitions. mlr3spatiotempcv adds support for this when using the size

argument for fold creation. When supplying a vector of length(repeats) for argument size, these different settings will be used to create folds which differ among the repetitions.

Multiple repetitions are not possible when using the "row & cols" approach because the created folds will always be the same.

The 'Description' and 'Details' fields are inherited from the respective upstream function.

For a list of available arguments, please see blockCV::cv_spatial .

blockCV >= 3.0.0 changed the argument names of the implementation. For backward compatibility, mlr3spatiotempcv is still using the old ones. Here's a list which shows the mapping between blockCV < 3.0.0 and blockCV >= 3.0.0:

• range -> size
• rasterLayer -> r
• speciesData -> points
• showBlocks -> plot
• cols and rows -> rows_cols

The default of argument hexagon is different in mlr3spatiotempcv (FALSE instead of TRUE) to create square blocks instead of hexagonal blocks by default.

Examples

if (mlr3misc::require_namespaces(c("sf", "blockCV"), quietly = TRUE)) {
  library(mlr3)
  task = tsk("ecuador")

  # Instantiate Resampling
  rcv = rsmp("spcv_block", range = 3000L, folds = 3)
  rcv$instantiate(task)

  # Individual sets:
  rcv$train_set(1)
  rcv$test_set(1)
  intersect(rcv$train_set(1), rcv$test_set(1))

  # Internal storage:
  rcv$instance
}

References

Valavi R, Elith J, Lahoz-Monfort JJ, Guillera-Arroita G (2018). blockCV: an R package for generating spatially or environmentallyseparated folds for k-fold cross-validation of species distributionmodels.

bioRxiv. tools:::Rd_expr_doi("10.1101/357798") .

Super class

mlr3::Resampling -> ResamplingSpCVBlock

Public fields

• blocks: sf | list of sf objects

   Polygons (`sf` objects) as returned by `blockCV` which grouped observations into partitions.
  

Active bindings

• iters: integer(1)

   Returns the number of resampling iterations, depending on the values stored in the `param_set`.
  

Methods

Public methods

• list("ResamplingSpCVBlock$new()")

• list("ResamplingSpCVBlock$instantiate()")

• list("ResamplingSpCVBlock$clone()")

Method new()

Create an "spatial block" resampling instance.

For a list of available arguments, please see blockCV::cv_spatial().

Usage

ResamplingSpCVBlock$new(id = "spcv_block")

Arguments

• id: character(1)

   Identifier for the resampling strategy.
  

Method instantiate()

Materializes fixed training and test splits for a given task.

Usage

ResamplingSpCVBlock$instantiate(task)

Arguments

• task: mlr3::Task

   A task to instantiate.
  

Method clone()

The objects of this class are cloneable with this method.

Usage

ResamplingSpCVBlock$clone(deep = FALSE)

Arguments

• deep: Whether to make a deep clone.