author_guide.qmd

---
title: "Journal of Math 615 Guide for Authors"
output: 
  html_document:
    toc: true
    toc_float: true
    # includes:
    #   in_header:
    #     - header.html
    #     - header-tracker.html
---

## Introduction
The *Journal of MATH 615* is the official internal publication of the Data Analysis for Graduate Research course at California State University at Chico. Specific details as to project deadlines, rubrics, and more can be found for current students on the Canvas course page. The details below are meant to mimic those of real journal websites for submission to provide practice for future submissions.


## Manuscript Preparation

All new submissions must provide the following documents:

* PDF manuscript in the journal style outlined below
* Self-contained HTML version manuscript with code folding enabled. showing

To ensure reproducibility and provide transparency, all results from the manuscript must be generated via a single, commented standalone replication script. This includes any necessary data preparation steps. Code that was ultimately not used in the final report should be excluded. To facilitate authoring manuscripts in the required style, we recommend using the [jasa Quarto template extension](https://quarto.org/docs/extensions/listing-journals.html). You can see a video tutorial on how to install this template [here](https://youtu.be/uJy45by8HFI). 

Manuscripts must be written in English using the Quarto R and text processing system. The journal Style Guide must be followed for formatting manuscripts. Only PDF and HTML files can be submitted. It is the responsibility of the authors to provide a submission in the appropriate format, paying very close attention to the style instructions. Manuscripts not meeting these requirements will be returned to the authors immediately.


## Style Guide

The [Quarto Authoring guide](https://quarto.org/docs/guide/) has many helpful pages for authors including how to write markdown, figure and table captions, side by side text or images, and how to globally hide code. 


### Page Limits

Articles have an expected page length of at least 3 pages and no more than 5 pages. These pages limits include the required figure(s) and table(s), but not references or acknowledgements. 


### Font Size and Spacing
Use a standard font size and any standard font. Articles should be single spaced.


### Title and Author Information
The article should have an informative title. Additionally, author information should include:

* Author name
* Author degrees
* Author affiliation (e.g., BIOL MS Student, MSDSA Student, Center for Regenerative Agriculture, etc.)


### Abstract and Keywords
A short abstract should describe the problem, data, and results.

Immediately after the abstract, provide a maximum of 5 keywords, avoiding general and plural terms and multiple concepts (avoid, for example, 'and', 'of'). These keywords will be used for indexing purposes.


### Article Body Structure
Articles should follow a similar structure to that outlined below:

* Introduction, Background
* Study Design and Data collection
* Data Preparation and Statistical Analysis Methods
* Results
* Discussion, Conclusion

Note, these exact names do not need to be used and can be customized to your given article, analysis, and context.


### Tables and Figures

A minimum of one table and one figure is required for all publications. 

All tables and figures should be "publication ready" with informative titles, labels, and captions. Where applicable, units of measurement should be included. Variable names from code should be replaced with meaningful labels (e.g., instead of `outcome_variable4` write the actual outcome). 

Articles must include a "Table 1" that describes the study population in a tabular format. Additional tables and figures may be included as necessary to present and summarize results. These count towards the page limit. 


### Decimal Numerals
To enhance readability and clarity of the text as well as tables and figures, decimal numerals should - with the obvious exception of P-values - be rounded to the unit whenever possible (i.e. in all cases in which the rounding procedure does not change the meaning). 


### Acknowledgments
Collate acknowledgements in a separate section at the end of the article before the references and do not, therefore, include them on the title page, as a footnote to the title or otherwise. List here those individuals who provided help during the research (e.g., providing language help, writing assistance or proof reading the article, etc.). 


### References
Any style of reference is acceptable as long as formatting is consistent. See [the Citations section of the Quarto authoring guide](https://quarto.org/docs/authoring/citations.html) for information on how to cite references in Quarto. 

## Supplemental Materials

Given the small page limits, it is acceptable to include *additional* tables and figures beyond the required minimum of one table and one figure in a Supplemental Materials section if needed. These figures and tables should be referenced in the text as **Figure S1**, **Table S1**, etc. 

While you should direct the reader to the Supplemental Materials to access the additional tables, figures, or information, the paper itself should be able to be largely understood as though a reader did not have access to the supplement.

## Blind review and submission process

You will submit a draft manuscript for blind peer review prior to submission. To help the reviewers identify specific places in your manuscript to discuss, please add the following code to the top of your YAML header (PDF submissions only) to add the line numbers to your compiled document. This is for the review period only, and not to be used in the final version. 

```
format: 
  pdf:
    include-in-header: 
      text: '\usepackage{lineno}\linenumbers'
```