boilerplate: Generate a reproducible, copy-and-paste-ready methods...

In eyeris: Flexible, Extensible, & Reproducible Pupillometry Preprocessing

Generate a reproducible, copy-and-paste-ready methods boilerplate

Description

Auto-generates human-readable, "fMRIPrep-style" methods-section boilerplate text that describes – in plain prose – the exact preprocessing workflow that was run on an eyeris object. Because every eyeris preprocessing step records its own call stack and parameters (in eyeris$params), the pipeline is able to self-document precisely what it did to your data, ready to paste directly into the methods section of a manuscript.

This reinforces the workflow-level transparency at the heart of the eyeris "glassbox" philosophy: the code that ran and the prose that describes it are generated from one and the same source of truth.

Usage

boilerplate(
  eyeris,
  version = NULL,
  include_citation = TRUE,
  include_license = TRUE
)

Arguments

eyeris	An object of class eyeris (e.g., the output of glassbox()). Binocular objects are supported.
version	Optional character string giving the eyeris version to cite in the boilerplate. Defaults to NULL, in which case the currently installed eyeris version is used.
include_citation	Logical. Whether to append a formatted citation for eyeris. Defaults to TRUE.
include_license	Logical. Whether to append the Creative Commons CC BY 4.0 license note telling users it is safe to paste the text into a manuscript as long as they cite eyeris for attribution. Defaults to TRUE.

Details

The generated text walks the recorded pipeline steps in the canonical order in which eyeris applies them (load_asc -> deblink -> detransient -> interpolate -> lpfilt -> downsample/bin -> detrend -> zscore -> epoch) and emits one sentence per step, substituting in the actual parameter values that were used. Steps that were skipped are omitted, and any custom (user-supplied) pipeline extensions are appended at the end so that multi-step and non-default pipelines are described faithfully. Multi-block (multi-run) and binocular recordings are handled automatically.

The boilerplate also references the per-run, machine-readable .json metadata sidecar that eyeris writes for every run (source/logs/run-XX_metadata.json), which together with the reported package version is sufficient to reproduce the pipeline exactly.

License & attribution. The auto-generated boilerplate text is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license (https://creativecommons.org/licenses/by/4.0/). It is explicitly safe to copy and paste the generated Markdown content directly into your manuscript, provided that you give appropriate credit by citing eyeris (run citation("eyeris") for the reference); including that citation in your references satisfies the attribution requirement. This mirrors the approach taken by fMRIPrep and other reproducible-pipeline tools.

When you run bidsify() (or glassbox() with reporting enabled), this same boilerplate is embedded in the diagnostic HTML report and written to ⁠derivatives/.../source/logs/⁠ as a standalone Markdown file.

Value

A length-one character string of Markdown-formatted methods boilerplate (invisibly classed as eyeris_boilerplate so it prints nicely at the console). The raw string can be passed to base::cat(), base::writeLines(), or embedded directly in a report.

See Also

glassbox(), bidsify()

Examples

demo_data <- eyelink_asc_demo_dataset()

eyeris_obj <- demo_data |>
  eyeris::glassbox(verbose = FALSE)

# print the copy-and-paste-ready methods boilerplate
boilerplate(eyeris_obj)

# capture it as plain Markdown text (e.g., to write to a file)
methods_md <- boilerplate(eyeris_obj)
cat(methods_md)

eyeris documentation built on June 19, 2026, 9:08 a.m.