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Replace partitions in prepared data

Source: R/replace_partition.R
replace_partition.Rd

Replaces the test partitions in a prepared_data object with spatial partitions generated by ENMeval or flexsdm.

Usage

replace_partition(
  data,
  new_block,
  block_source = c("ENMeval", "flexsdm"),
  enmeval_occs = NULL,
  enmeval_bg = NULL,
  tolerance = 1e-08
)

Arguments

data

A prepared_data object returned by prepare_data(). It must contain calibration_data and data_xy. The latter is available when prepare_data() is called with include_xy = TRUE.

new_block

A partition object. For block_source = "ENMeval", it must contain occs.grp and bg.grp, as returned by ENMeval::get.block(). For block_source = "flexsdm", it must contain a part data frame with x, y, pr_ab, and .part columns, as returned by flexsdm::part_sblock().

block_source

The package that generated new_block: "ENMeval" or "flexsdm".

enmeval_occs

The occurrence table supplied as occs to ENMeval::get.block(). Required when block_source = "ENMeval". It must have numeric x and y columns and retain the original row order.

enmeval_bg

The background table supplied as bg to ENMeval::get.block(). Required when block_source = "ENMeval". It must have numeric x and y columns and retain the original row order.

tolerance

Maximum absolute difference allowed between corresponding coordinate values during validation. Set to 0 to require exact numeric equality. Defaults to 1e-8.

Value

A prepared_data object with a new partition.

Details

The function checks that coordinates match in the same row order before replacing the partitions.

For ENMeval, occurrence records must precede background records in data$calibration_data. The function compares enmeval_occs and enmeval_bg with the corresponding rows of data$data_xy separately.

For flexsdm, the function compares the coordinates and occurrence/background labels in new_block$part with data$data_xy and data$calibration_data$pr_bg, respectively.

The returned object has updated part_data, partition_method, and n_partitions components.

Examples

# Load prepared data
data(sp_swd, package = "kuenm2")

# Load environmental raster layers
var <- terra::rast(system.file("extdata", "Current_variables.tif",
                               package = "kuenm2"))

# Use a spatial block partition from flexsdm
# Load example output from flexsdm::part_sblock()
data(flexsdm_block, package = "kuenm2")

# Replace the existing partitions
d_flexsdm <- replace_partition(
  data = sp_swd,
  new_block = flexsdm_block,
  block_source = "flexsdm"
)
# Explore the partitions in geographic space
pbg_flexsdm <- explore_partition_geo(d_flexsdm, raster_variables = var)
terra::plot(pbg_flexsdm)


# Use a spatial block partition from ENMeval
# Load example output from ENMeval::get.block()
data(enmeval_block, package = "kuenm2")

# Supply the same occurrence and background points, in the same order,
# that were used to generate the ENMeval blocks
occs <- sp_swd$data_xy[sp_swd$calibration_data$pr_bg == 1, ]  # Occurrences
bg <- sp_swd$data_xy[sp_swd$calibration_data$pr_bg == 0, ]  # Background

# Replace the existing partitions
d_enmeval <- replace_partition(
  data = sp_swd,
  new_block = enmeval_block,
  block_source = "ENMeval",
  enmeval_occs = occs,
  enmeval_bg = bg
)

# Explore the partitions in geographic space
pbg_enmeval <- explore_partition_geo(d_enmeval, raster_variables = var)
terra::plot(pbg_enmeval)