Skip to contents

Generate Sample Dataset for MVPA Analysis

gen_sample_dataset.Rd

Creates a synthetic dataset for testing and demonstration of MVPA analyses.

Usage

gen_sample_dataset(
  D,
  nobs,
  response_type = c("categorical", "continuous"),
  data_mode = c("image", "surface"),
  spacing = c(1, 1, 1),
  blocks = 5,
  nlevels = 5,
  external_test = FALSE,
  ntest_obs = nobs,
  split_by = NULL,
  na_cols = 0
)

Arguments

D

The data dimension(s): vector of length 2 or 3 for image data, or single number for surface data

nobs

The number of observations

response_type

Either 'categorical' or 'continuous'

data_mode

Either 'image' or 'surface'

spacing

The voxel spacing (default: c(1,1,1))

blocks

The number of 'blocks' in the data (for cross-validation)

nlevels

The number of category levels (only used if response_type='categorical')

external_test

Whether to generate an external test set

ntest_obs

The number of test observations (default: nobs)

split_by

Optional factor for splitting analyses

na_cols

The number of columns to randomly set to NA (default: 0)

Value

A list containing:

dataset

An mvpa_dataset object containing:

  • train_data: Training data as NeuroVec or ROISurface

  • test_data: Test data (if external_test=TRUE)

  • mask: Binary mask indicating valid voxels/vertices

design

An mvpa_design object containing:

  • y_train: Response variable for training

  • y_test: Response variable for test set (if external_test=TRUE)

  • block_var: Block variable for cross-validation

  • split_by: Optional splitting factor

Examples

# Generate categorical image dataset
dataset <- gen_sample_dataset(
  D = c(10,10,10),
  nobs = 100,
  response_type = "categorical",
  data_mode = "image",
  blocks = 3,
  nlevels = 2
)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'i' in selecting a method for function '[<-': could not find function "coords"

# Generate continuous surface dataset
surf_data <- gen_sample_dataset(
  D = 1000,  # number of vertices
  nobs = 50,
  response_type = "continuous",
  data_mode = "surface"
)
#> loading /Users/bbuchsbaum/Library/R/arm64/4.3/library/neuroim2/extdata/std.lh.smoothwm.asc
#> Error in assert_that(inherits(train_data, "NeuroSurfaceVector")): could not find function "assert_that"

# Generate dataset with external test set
test_dataset <- gen_sample_dataset(
  D = c(8,8,8),
  nobs = 80,
  response_type = "categorical",
  nlevels = 3,
  external_test = TRUE
)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'i' in selecting a method for function '[<-': could not find function "coords"