EcoConsModPreReg Format: A Quarto Template for Adaptive Preregistration of Ecological Models

Here we present a preregistration template for ecological models in ecology, conservation and related fields. This template is based on the EcoConsPreReg: A Guide to Adaptive Preregistration for Model-Based Research in Ecology and Conservation (v1.0.2) by Gould et al. (2024)[^readme-1].

[^readme-1]: Gould, E., Jones, Christopher, S., Yen, J. D. L., Fraser, Hannah, S., Wootton, H., Vivian, L., Good, M., Duncan, David, H., Rumpff, L., & Fidler, F. (2024). EcoConsPreReg: A Guide to Adaptive Preregistration for Model-Based Research in Ecology and Conservation (v1.0.2). Zenodo. https://doi.org/10.5281/zenodo.10884635

For non-trivial modelling studies, especially where model parameter and structure is in any way data-contingent, we recommend taking an Adaptive Preregistration approach (insert cross-ref to preprint). However, this template may be used with any mode of preregistration.

Creating a New Preregistration

bash quarto use template egouldo/EcoConsModPreReg

This command will install the EcoConsPreReg extension in your project workspace, including a quarto template that can be used as a starting point for your preregistration. The template source code is located here: template.qmd. When you execute the command you will be prompted to choose an installation location---either in the working (root) directory, or in a subdirectory (existing or new). By default, the installation will create the quarto template file template.qmd in the working (root) directory. If you specify a subdirectory location the installation process will rename the template file to match the name of the enclosing directory (e.g., specified_subdirectory/specified_subdirectory.qmd).

Use with Existing Preregistration Document

To use the quarto template with an existing project or document, run the following command in the terminal:

bash quarto add egouldo/EcoConsModPreReg

Usage

Editing

Edit the template file: Replace author, author-affiliations, keywords, title and abstract yaml metadata as relevant to your study. All preregistration items should be completed unless marked as optional, or are not applicable to your study.

Format Options

The EcoConsModPreReg format can be rendered to html, pdf, or docx. Standard Quarto formatting options are also available, and can be overridden in the document's yaml metadata, see the quarto scholarly writing guide.

To use the pdf extension with an existing document, add the following in your document yaml:

yaml format: pdf: default ecoconsmodprereg-pdf: keep-tex: true

Author Affiliations

To output multiple author affiliations with footnotes when rendering to pdf, the yaml tag affil-id: must be provided for each author rather than using the default quarto affiliations: tag as for html and docx formats. This is because the pdf output uses the LaTeX authblk package to format author affiliations. For details, see https://stackoverflow.com/a/76016913/4593464.

The CRediT taxonomy

Each listed author / contributor's intended contribution should be provided with the CRediT taxonomy. For details, see: quarto yaml options for CRediT role values.

Citations

EcoConsModPreReg documents default to using the Methods in Ecology and Evolution journal citation style. This can be overridden by adding your own .csl file to the document directory, and updating the quarto document yaml metadata to point to the new .csl file, see the quarto citations authoring guide for details.