Journal of Math 615 Guide for Authors

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.

Article Preparation

Article 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 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.

Reproducibility

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.

Required template

To facilitate authoring manuscripts in the required style, we require authors to use this custom quarto template and bibliography file.

Cover image

Authors are encouraged to submit a .jpg or .png image that would be used as a cover image in the publication.

Style Guide

The Quarto Authoring 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 are expected to be between 10 and 15 pages. These pages limits include the required figures and tables, but not references nor the Appendix.

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.

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). Consider using the scales::label_pvalue function as applicable.

Captions

For Tables use tbl-

```{r}
#| label: tbl-lm
#| tbl-cap: "A regression model."

pen <- palmerpenguins::penguins
lm(body_mass_g ~ island + bill_length_mm, data = pen) |>
  gtsummary::tbl_regression()
```
Table 1: A regression model.
Characteristic Beta 95% CI p-value
island


    Biscoe — —
    Dream -919 -1,034, -804 <0.001
    Torgersen -523 -692, -355 <0.001
bill_length_mm 77 67, 88 <0.001
Abbreviation: CI = Confidence Interval

For Figures use fig-

```{r}
#| label: fig-scatter
#| fig-cap: "A scatterplot"
#| fig-width: 4
#| fig-height: 4

ggpubr::ggscatter(pen, x = "bill_length_mm", y = "body_mass_g", 
                  color = "island",
                  add = "loess", conf.int = TRUE)
```
Figure 1: A scatterplot

Cross-references

Markdown Format Output 
@fig-scatter is pretty.
 is pretty. 
@tbl-lm was created from code.
 was created from code. 
@sec-crf is this section.
 is this section. 
@eq-black-scholes is above.
 ?@eq-black-scholes is above.

See the Quarto documentation on cross-references for more info.

Citation Syntax

The journal template contains a Bibtex .bib file for you to use. Any style of reference is acceptable as long as formatting is consistent. See the Quarto section of the BibTeX guide and the Citation guide from the Quarto documentation for information on how to cite articles and include a reference section in Quarto.

Markdown Format Output 
Blah Blah [see @knuth1984, pp. 33-35;
also @wickham2015, chap. 1]
 Blah Blah (see ; also ) 
Blah Blah [@knuth1984, pp. 33-35,
38-39 and passim]
 Blah Blah ( and passim) 
Blah Blah [@wickham2015; @knuth1984].
 Blah Blah (; ). 
Wickham says blah [-@wickham2015]
 Wickham says blah ()

You can also write in-text citations, as follows:

Markdown Format Output 
@knuth1984 says blah.
 Knuth () says blah. 
@knuth1984 [p. 33] says blah.
 Knuth () says blah.

Article Body Structure

Articles must contain the following sections.

Introduction and Background

This section sets the stage for your study by explaining the context, importance, and purpose of your work. It should give the reader enough background to understand why your research matters.

  • Briefly describe the problem or topic and why it is important.
  • Summarize relevant literature and clearly state your research question or hypothesis.

Study Design and Data collection

Here you explain how the study was planned and how data were obtained. This ensures the reader can understand and evaluate the reliability of your results.

  • Describe the type of study (e.g., observational, experimental) and its key features.
  • Explain how data were collected, including sources, time frames, and any selection criteria.

Methods

Use separate sub-sections for data preparation and statistical analysis methods.

Data Preparation

This part details the steps taken to clean, organize, and prepare the data before analysis.

  • Describe any data cleaning procedures (e.g., handling missing values, correcting errors).
  • Explain how variables were defined, transformed, or categorized.

Statistical Analysis

This section explains the techniques and tools used to answer your research question.

  • Identify the statistical methods and justify why they were appropriate.
  • Specify the software or packages used for analysis.

Results

Present your findings clearly and objectively, without interpretation or speculation. Use separate sub-sections for descriptive statistics and results of statistical models.

  • Report key results in text, tables, or figures, focusing on what is most relevant to the research question.
  • Include appropriate summary statistics and measures of uncertainty (e.g., confidence intervals, p-values).

Discussion, Conclusion

Interpret your results, explain their meaning, and place them in context with existing knowledge.

  • Summarize the main findings and discuss their implications or applications.
  • Address limitations of the study and suggest directions for future research.

References

The journal template contains a Bibtex .bib file for you to use. Any style of reference is acceptable as long as formatting is consistent. See the Quarto section of the BibTeX guide and the Citation guide from the Quarto documentation for information on how to cite articles and include a reference section in Quarto.

Appendix

All of the code used for this report should be included and executed here. Do not include extreneous code or output not directly relevant to the results reported in this research report.

References

Knuth, Donald E. 1984. “Literate Programming.” The Computer Journal 27 (2): 97–111.
Wickham, Hadley. 2015. R Packages. 1st ed. O’Reilly Media, Inc.