posit_presentation.qmd

---
title: "Quarto: A Multifaceted Publishing Powerhouse for Medical Researchers"
format:
  clean-revealjs:
    self-contained: true
    preview-links: false
    slide-number: false
    code-line-numbers: true
    logo: images/logo.png
    css: styles.css
author:
  - name: Joshua J. Cook, M.S. DS, M.S. CRM, ACRP-PM, CCRC
    orcid: 0000-0003-3508-7065
    email: jcook0312@outlook.com
    affiliations: Adjunct Professor / Clinical Researcher / Data Scientist
date: last-modified
bibliography: refs.bib
editor: 
  markdown: 
    wrap: 72
---

## Biography {.scrollable}

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::: {.column width="40%"}
![](images/grad.jpg){fig-align="left" width="430" height="545"}
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::: {.column width="60%"}
-   **2021** - B.S., Biomedical Science, *University of West Florida*

-   **2023** - M.S., Clinical Research Management, *Wake Forest
    University*

-   **2023** - ACRP Certifications (Project Management / Clinical
    Research Coordinator)

-   **2024** - M.S., Data Science, *University of West Florida*

-   **Work History:** [Adjunct Professo]{.underline}r (Anatomy &
    Physiology), Research Quality Analyst, Clinical Research Coordinator
:::
:::
:::

# Medical Research {background-color="#40666e"}

## Medical Research {.smaller}

### Not Just Pharma!

-   Academia (Ph.D.)

-   Healthcare/Industry (M.D., D.O., RN, MSN-NP, Etc.)

-   [**OR, you are responsible for preparing these documents for someone
    in these roles.**]{.underline}

-   **General Process:**

![](images/process.png){fig-align="center" width="547" height="418"}

## Medical Research {.smaller}

### Publication Needs

1.  Statistical Report - usually #1; sometimes preceded by study
    planning analyses, such as simulations

2.  Interim Reports

3.  Interim Presentations (Regulators, Sponsors, Stakeholders,
    Conferences, Grants)

4.  Final Report

5.  Final Presentation

6.  Manuscript

7.  Website/Blogs

8.  [**NEW - Patient/Participant Material**]{.underline}

9.  Regulatory Submission

This is [**a LOT of work for medical researchers**]{.underline},
especially if changes are made to the data/analyses at any stage.

## Medical Research

### Traditional Methods {.smaller}

A mess...

![](images/process_2.png){fig-align="center" width="730" height="435"}

# Quarto {background-color="#40666e"}

## Quarto {.smaller}

### An Introduction

**Quarto** (often described as the **next generation of R Markdown**)
emerges as a promising solution capable of:

-   bridging the gaps between different programming languages

-   allowing teams to collaborate more effectively

-   enabling the efficient integration of diverse methodologies

-   with [**Quarto Projects**]{.underline}, allows for the creation of
    various project types from a single source, with multiple output
    formats.

**Quarto Project Types** refer to a type of organization of files (ex:
report, website, manuscript, or presentation) while **Quarto Project
Formats** refer to the output file type of a document (ex: HTML, PDF,
DOCX).

## Quarto {.smaller .scrollable}

### General Setup

As with any project in RStudio^®^, a [**primary folder**]{.underline}
should be setup that will be used as the working directory. This is
where the Quarto project (.*Rproj*) file will be housed, as well as any
required subfolders.

[**Quarto Projects**]{.underline} are directories that provide a central
location for all files, images, and outputs.

**This is a key concept for this presentation.**

Furthermore, Quarto Projects provide:

-   **Shared YAML** configuration and **metadata** (ex: tables of
    contents and bibliographies).

-   Organized rendering of **multiple project formats from a single
    file** (ex: PDF and HTML).

-   **Package and environment version control** (for regulatory
    purposes).

-   **Directory-specific settings and preferences** (ex: code formatting
    and view panes).

-   **Virtual Environments.**

There are *many* Quarto project types available, but for this first
example, we will create a new **Quarto Project** (in the form of a
[report]{.underline}) within RStudio^®^ using the “Create Project”
button in the toolbar. Choose any name and location for your project,
just make sure you can remember and find it!

![](images/create.png){width="418" height="336"}

![](images/type.png){width="420"}

## Quarto {.smaller .scrollable}

### Quarto Project Defaults & Layout

-   Your Quarto Project will open to a [template Quarto
    Markdown]{.underline} *(.qmd)* file with a [YAML
    header]{.underline}, some [markdown text]{.underline}, and an
    [example R code chunk.]{.underline}

-   If another programming language is preferred, {r} can be changed to
    {python}, etc.

-   The tool bar gives text-editing options for markdown and allows for
    the creation of more chunks as needed.

-   This is just the basic layout, and many more components can be added
    to a Quarto Markdown to enrich content.

![](images/clipboard-480932952.png){width="690" height="251"}

## Quarto {.smaller .scrollable}

### The Importance of YAML

Every Quarto Markdown *(.qmd*) file begins with a **YAML** (Yet Another
Markup Language) header, which is a versatile human-readable data
serialization language.

YAML is primarily used in [configuration files]{.underline} and data
representation in the form of [**maps**]{.underline} (key-value pairs)
and [**lists**]{.underline} (sequences of values).

YAML is delineated with three dashes (—) and provides the configuration
of a Quarto document with many fields available for specification
depending on the quarto project format (ex: HTML and PDF).

Some examples of YAML fields that we have found especially helpful
include:

-   **Title/subtitle** – titles of the document.

-   **Date** – date of the document (*can be “today”).*

-   **Author** – listing of authors for the document.

-   **Abstract** – provides a summary of the document.

-   **Theme** – theme of the entire document (*many formats available*).

-   **Toc** – table of contents (*many formats available*).

-   **Bibliography** – document bibliography (*BibTeX or CSL*).

-   **Crossref** – configuration for cross-reference labels and
    prefixes.

-   **Format** – designates the output format (*HTML by default*).

-   **Embed-resources** - incorporates external dependencies into a
    standalone HTML file (i*.e., self-contained files*).

For the full list of YAML options, please refer to the Quarto
documentation ([Quarto –
Reference](https://quarto.org/docs/reference/)).

# Medical Research Case Example {background-color="#40666e"}

## Quarto Case Example

### File Structure

``` plaintext
/positconf
├── /Data
│   ├── 2022_data.rds
│   └── 2021_data.rds
├── /Analysis
│   ├── data_processing.qmd
│   └── data_missing.qmd
├── /Images
│   ├── logo.jpg
│   └── logo_2.jpg
├── /Manuscript
│   ├── Manuscript.Rproj
│   └── index.qmd
│   └── quarto.yml
├── /Presentation
│   ├── Presentation.Rproj
│   └── index.qmd
│   └── quarto.yml
├── Report.Rproj
├── index.qmd
├── quarto.yml
```

## Quarto Case Example

### YAML for a Report

``` plaintext
/positconf
├── Report.Rproj
├── index.qmd
├── quarto.yml
```

```{r}
#| eval: FALSE
#| echo: TRUE
#| code-line-numbers: "1-7|8-11"

---
title: |
  ![](Images/logo.jpg){fig-align="left" width="500"}  \  
    \  
    Project BRFSS Weekly Update
author: "Joshua J. Cook, M.S. DS, M.S. CRM, \ ACRP-PM, CCRC, Swann A. Adams Ph.D., M.S., FACE"
date: today
format:
  html:
    html-table-processing: none
embed-resources: true
toc: true
---
```

## Quarto Case Example {.smaller .scrollable}

### The Report

![](images/clipboard-2136297575.png)

![](images/clipboard-1619737040.png)

![](images/clipboard-3064409893.png){width="687"}

**Importantly:** the code nor figure are not being generated in within
the report itself!

## Quarto Case Example

### The Report

Goal in a nutshell: [maintain quality and consistency through
modularity.]{.underline}

**Quarto Shortcodes:** special markdown directives that generate
content.

**Key Shortcodes:**

-   **embed** - embeds cells from Quarto markdown (.qmd) file or a
    Jupyter (.ipynb) notebook.

-   **include** - direct copy/paste of content from another Quarto
    markdown or Jupyter notebook.

```{r}
#| eval: false
#| echo: true
#| code-line-numbers: "1|3"

{{< include Analysis/data_processing.qmd >}} # will include EVERYTHING from the file

{{< embed Analysis/data_missing.qmd#fig-missing-1 >}} # will only include a SPECIFIC figure
```

## Quarto Case Example {.smaller .scrollable}

### YAML for a Manuscript

``` plaintext
/positconf
├── /Manuscript
│   ├── Manuscript.Rproj
│   └── index.qmd
│   └── quarto.yml
```

```{r}
#| eval: FALSE
#| echo: TRUE
#| code-line-numbers: "1-13|14-15|16-20"

---
title: Assessment of Temporal Trends in HPV Vaccination, Cervical Cancer Screening, and Diagnosis Among LGBTQ+ Individuals
authors:
  - name: Joshua J. Cook, M.S. DS, M.S. CRM, ACRP-PM, CCRC
    affiliation: The University of South Carolina
    roles: data analysis, manuscript writing
    corresponding: true
  - name: Swann Arp Adams, Ph.D., FACE, M.S.
    affiliation: The University of South Carolina
    roles: data analysis, manuscript writing
    corresponding: true
bibliography: references.bib
abstract: "The full progress of our project can be followed in the attached Chill and Chat log. In summary, we have extracted 2022-2014 data from the Centers for Disease Control (CDC) Behavioral Risk Factor Surveillance System (BRFSS) datasets. The cutoff for 2014 was determined based on initial exploratory data analysis (EDA), which revealed that Sexual Orientation and Gender Identity (SOGI) data collection began in that year. The initial report (also attached) shows the progress in our EDA for identify our variables of interest, which includes 38 of the 200+ variables in the BRFSS dataset. Only 3 variables have missing values, which we plan to impute before analysis. We are also awaiting 2023 data to be released within the next month, which will complete our 10-year dataset which is often required for temporal studies of this nature. In the meantime, we are continuing to develop our analysis methodology via the technical papers and complete initial analyses which we will expand to 2023 once released. We plan on submitting our abstract to ASPO in September when calls open, and the draft manuscript over the next 6 months."
format:
  pdf: default
  plos-pdf:
    journal: 
      id: globalpublichealth
    keep-tex: true  
---
```

## Quarto Case Example {.smaller .scrollable}

### The Manuscript

![](images/clipboard-1827865736.png){width="595" height="639"}

![](images/clipboard-1022182594.png){width="595" height="597"}

Again, using shortcodes:

```{r}
#| eval: false
#| echo: true

{{< embed Analysis/data_missing.qmd#fig-missing-1 >}} # will only include a SPECIFIC figure
```

## Quarto Case Example {.smaller .scrollable}

### YAML for a Presentation

``` plaintext
/positconf
├── /Presentation
│   ├── Presentation.Rproj
│   └── index.qmd
│   └── quarto.yml
```

```{r}
#| eval: FALSE
#| echo: TRUE
#| code-line-numbers: "|3-10"

---
title: "Assessment of Temporal Trends in HPV Vaccination, Cervical Cancer Screening, and Diagnosis Among LGBTQ+ Individuals"
format:
  clean-revealjs:
    self-contained: true
    preview-links: true
    slide-number: false
    code-line-numbers: true
    logo: ../Images/logo_2.jpg
    css: styles.css
author:
  - name: Joshua J. Cook
    orcid: 0000-0003-3508-7065
    email: jcook0312@outlook.com
    affiliations: Adjunct Professor / Clinical Researcher / Data Scientist
date: last-modified
bibliography: refs.bib
editor: 
  markdown: 
    wrap: 72
---
```

## Quarto Case Example {.smaller .scrollable}

### The Presentation

![](images/clipboard-1088875303.png){width="638"}

![](images/clipboard-2851995800.png){width="640"}

```{r}
#| eval: false
#| echo: true

{{< embed Analysis/data_missing.qmd#fig-missing-1 >}} # will only include a SPECIFIC figure
```

Furthermore, if the researcher prefers PowerPoint, the **format can be
changed to output to .pptx.**

Importantly, the updated figures, tables, etc. will still be cleanly
output **for them to use in their presentations.**

## Quarto Case Example

### The Key Points

1.  All of these **documents are frequently used by medical
    researchers.**

2.  If an error is identified, or something about the data, tables, or
    figures needs to be changed, **simply altering the files in
    /Analysis will prompt all the documents to update when they are next
    rendered.**

3.  If **another template is needed** (ex: when being rejected from one
    journal), it is easy to switch while retaining all original content.

4.  Even if the researcher prefers traditional PowerPoint or Word
    methods, this system still offers **protection against redundancy
    when updates to analysis code are needed.**

5.  In other words, [**we are effectively moving beyond
    copy/paste.**]{.underline}

# Wrapping Up {background-color="#40666e"}

## Advanced Features {.smaller .scrollable}

### Just a Few

**1. In-line Programming**

```{r}
#| echo: true

x <- 2+2
```

`r x` is currently the value of x.

**2. Dynamically Updating -** using quarto.yml

![](images/clipboard-557801892.png){width="605" height="187"}

**3. Templates** (Two used here - just install using terminal and define
in YAML as above):

-   [quarto-journals/plos: Quarto template for Public Library of Science
    (github.com)](https://github.com/quarto-journals/plos) (Manuscript)

-   <https://github.com/grantmcdermott/quarto-revealjs-clean#readme>
    (Presentation)

**4. Collaboration Tools Available -** notes, highlighting, commenting
with Hypothesis

**5. Works with Zotero Libraries -** possibly some compatibility with
EndNote

**6. Enhancing Participant Communication** - very quick release of
presentation material to providers

**7. Speeding up the Delivery of Treatments** - accelerating the
conversion of statistical reports into manuscripts and regulatory
documents (which can follow templates and get updated after content is
altered!)

## Conclusion

### Quarto is a Multifaceted Publishing Powerhouse for Medical Researchers

-   Allows us to **efficiently create various polished formats from a
    single source** document (in this case, stored in the /Analysis
    folder).

-   **Templates** available to support a wide array of submission
    requirements (reports, manuscripts, presentations) with **tools for
    collaboration** (notes, highlighting, commenting).

-   **Enhances participant communication** and **(hopefully) speeds up
    the delivery of treatments** by reducing time-spent converting
    between document types.

## Conclusion

### Limitations

-   Setup and organization **may not be appropriate for all projects**
    especially if smaller and publication needs are not extensive.

-   **Tables seem to have a hard time being embed** from another file
    (workaround: programmed into the primary .qmd).

-   Thinking about ways to **reuse markdown text** similar to the
    embedding process for code/figures (LLMs?).

## Acknowledgements & Contact Information {.smaller}

### \*Actively seeking a full-time position\*

Joshua J. Cook thanks Nathaniel Nicklaus, as well as his mentors, Dr.
Swann Adams, Louise Hadden, Dr. Achraf Cohen, and Kirk Paul Lafler, as
well as Richann Watson and Troy Martin Hughes for their general guidance
and mentorship.

Special thanks to Mine Cetinkaya-Rundel, who gave an hour-long
presentation on this topic at R/Medicine 2024. [R/Medicine: Quarto for
Reproducible Medical Manuscripts
(youtube.com)](https://www.youtube.com/watch?v=NK1onTLcgY4)

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**Your comments and questions are valued and encouraged. Contact the
author at:**

Joshua J. Cook, M.S. DS, M.S. CRM, ACRP-PM, CCRC

Adjunct Professor / Clinical Researcher / Data Scientist

Website: <https://joshua-j-cook-portfolios.netlify.app/>

Email: [jcook0312\@outlook.com](mailto:jcook0312@outlook.com)
:::

::: {.column width="60%"}
![](images/contact.png){fig-align="center" width="223" height="207"}
:::
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