R for Clinical Psychology: Overview and applications

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# R for Clinical Psychology: <br> Overview and applications
## A showcase of how data science can help to develop digital health products
### <br><br><br><br><br><br>Dr. Chris Gaskell<br>Clinical Psychologist<br>2021/12/16 (last updated: 2022-01-03)

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## Chris Gaskell

## Clinical Psychologist

.fade[Non-Epileptic Attack Disorder Service<br>Northern Care Alliance NHS Foundation Trust<br>Manchester, UK]

.small[.small[
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[<svg viewBox="0 0 512 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"></path></svg> @chris-gaskell92](https://twitter.com/chris-gaskell92)
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]]

???
- Introduction
- How I got into this.

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# Contents
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<br><br><br><br>
.Large[.bold[
### R
[What is it](#-slide)

[Why use it](#-slide)

[R markdown](#-slide)

[Applications](#-slide)
]]]]

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<br><br><br><br>
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### Another title

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[Another](#-slide)

[Another](#-slide)

<a href="https://sced-for-clinicians.netlify.app/resources/">Resources</a>
]
]]]]

.footnote[.Large[**Note**: all underlined
.white[.underline[white]] text are hyperlinks!]
]

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class: left

# What is it?

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# The command line

.pull-left[

```r
2+2
## [1] 4
```
]

.footnote[
<a href="https://rdrr.io/snippets/">A place to give it a try</a>
]

???
- A fancy calculator (like spss)
- key differances is script files (syntax). 
  - transparency
  - reproducability
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# The command line

.pull-left[

```r
test = 4+2
test
## [1] 6
```
]

.footnote[
<a href="https://rdrr.io/snippets/">A place to give it a try</a>
]

???
- use website to demonstrate functions
  - sqrt
  - round
- Functions become more sophisticated
- User definable
- tricky (no GUI) but highly flexible because of arguments
- SPSS is less flexible and there is less available for paper trail.

.pull-left[

```r
sqrt(81)
## [1] 9

round(3.14159, digits = 2)
## [1] 3.14
```

.small[
- R has loads of functions built in.
- Also can be user defined.
- Groups of functions are held together within packages.
]]

.footnote[
<a href="https://rdrr.io/snippets/">A place to give it a try</a>
]

???
- Infinate number of functions.
- Not all about maths and stats.
- Packages for stats, for communicating information.

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# A Universe of Packages
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# Reasons to use R

.small[
+ Data analysis & statistics
  + Highest functionality, up to date and bug free
+ Data vizualisations (high quality)
+ Literate Programming
+ Data/web products
+ Open source
  + Free
  + Anyone code and contribute
  + Transparency & Replicability
  
And a supportive online community!
]

???
- MLM; advanced meta-analyis; machine learning;
- Visualiasation is where R really came to the table.
- Markdown is an accessible mark up language.

---
# Traditional research workflow

.small[
1. Dats stored in MS Excel <br>
2. Get it into SPSS <br>
3. Run some analayses <br>
4. Extract results? (pray they are done right) <br>
5. Write up in MS Word
]

Any problems with this?
--

.small[
lack of integration?
difficult to refine? <br>
transparency and reproducability? <br>
The time it takes to go back and repeat steps? <br>
limited functionality and flexibility?
]

???

R goes past this with literatre programming. Inregrated way to build reports.

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# R Markdown workflow

.pull-left[.small[
- R offers a very different workflow.
- Literate programming approach.
  - Embed snippetes of code within a document (then hit run).
  - If the original data changes then the report will change too.
- HTML is where it gets interesting.
]
.footnote[.left[Can all be shared using GitHub <svg viewBox="0 0 448 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M400 32H48C21.5 32 0 53.5 0 80v352c0 26.5 21.5 48 48 48h352c26.5 0 48-21.5 48-48V80c0-26.5-21.5-48-48-48zM277.3 415.7c-8.4 1.5-11.5-3.7-11.5-8 0-5.4.2-33 .2-55.3 0-15.6-5.2-25.5-11.3-30.7 37-4.1 76-9.2 76-73.1 0-18.2-6.5-27.3-17.1-39 1.7-4.3 7.4-22-1.7-45-13.9-4.3-45.7 17.9-45.7 17.9-13.2-3.7-27.5-5.6-41.6-5.6-14.1 0-28.4 1.9-41.6 5.6 0 0-31.8-22.2-45.7-17.9-9.1 22.9-3.5 40.6-1.7 45-10.6 11.7-15.6 20.8-15.6 39 0 63.6 37.3 69 74.3 73.1-4.8 4.3-9.1 11.7-10.6 22.3-9.5 4.3-33.8 11.7-48.3-13.9-9.1-15.8-25.5-17.1-25.5-17.1-16.2-.2-1.1 10.2-1.1 10.2 10.8 5 18.4 24.2 18.4 24.2 9.7 29.7 56.1 19.7 56.1 19.7 0 13.9.2 36.5.2 40.6 0 4.3-3 9.5-11.5 8-66-22.1-112.2-84.9-112.2-158.3 0-91.8 70.2-161.5 162-161.5S388 165.6 388 257.4c.1 73.4-44.7 136.3-110.7 158.3zm-98.1-61.1c-1.9.4-3.7-.4-3.9-1.7-.2-1.5 1.1-2.8 3-3.2 1.9-.2 3.7.6 3.9 1.9.3 1.3-1 2.6-3 3zm-9.5-.9c0 1.3-1.5 2.4-3.5 2.4-2.2.2-3.7-.9-3.7-2.4 0-1.3 1.5-2.4 3.5-2.4 1.9-.2 3.7.9 3.7 2.4zm-13.7-1.1c-.4 1.3-2.4 1.9-4.1 1.3-1.9-.4-3.2-1.9-2.8-3.2.4-1.3 2.4-1.9 4.1-1.5 2 .6 3.3 2.1 2.8 3.4zm-12.3-5.4c-.9 1.1-2.8.9-4.3-.6-1.5-1.3-1.9-3.2-.9-4.1.9-1.1 2.8-.9 4.3.6 1.3 1.3 1.8 3.3.9 4.1zm-9.1-9.1c-.9.6-2.6 0-3.7-1.5s-1.1-3.2 0-3.9c1.1-.9 2.8-.2 3.7 1.3 1.1 1.5 1.1 3.3 0 4.1zm-6.5-9.7c-.9.9-2.4.4-3.5-.6-1.1-1.3-1.3-2.8-.4-3.5.9-.9 2.4-.4 3.5.6 1.1 1.3 1.3 2.8.4 3.5zm-6.7-7.4c-.4.9-1.7 1.1-2.8.4-1.3-.6-1.9-1.7-1.5-2.6.4-.6 1.5-.9 2.8-.4 1.3.7 1.9 1.8 1.5 2.6z"></path></svg>]]
]

???
- Don't need to know much html or css. R Markdown is a simple markup language that can handle them both but requires little of either. Packages also do a lot of the work for us.
- Literate programming
- Meta-analysis

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# .Large[.my-hot-blue[Data products]]

???
- Second part of presentation - data products
- Relevance for CP
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# Is the product of psychological therapy changing?

.pull-very-left[
CP delivery has needed to change:
1. Evidence based practice
1. Digital innovations
1. COVID-19

Issues that remain:
1. High demand
1. Acceptability
]

???
- EBP: Protocols, Standardisations
- Digital innovations: therapy Apps
- Delivery: teleconferencing through covid 19
- A good thing. Effective. Needed. Particularly 1:1.
  - However there will never be enough CPs
  - there will always be people who dont want to see one.
  - Need to consider more innovative ways to make acceptable interventions that can be easily cascaded.

- Bigger role of different intervention formats (GSH, bibliotherapy, apps, websites, resources)
- Quality of resources and handouts in NHS are terrible!

---

# Applications of R to digital healthcare

.small[
- There is a need for improving how we cascade information/intervention (both for research and clinical purpposes).

- Greater quality of information.

- Data products, resources, worksheets, teaching slides that people **actually** want to use.

- R is a good fit because it can produce good quality html products without the need to be an expert in html

- html is flexible, accessible and lightweight
]

???
- Traditionally, this is out the skillset set of a psychologist. But as the digital landscape is developing there is an increasing need to bring it into our thinking, and perhaps remit. NHS mental health service often lack the infrastructure or expertise to think in this way.
- Psychologists need to start considering innovation around digital delivery because the people in management, who should be thinking about this, wont.

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background-size: cover

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# Embed Tweets

<blockquote class="twitter-tweet" data-width="550" data-lang="en" data-dnt="true" data-theme="light"><p lang="en" dir="ltr">Really exciting developments! We are now able to provide fostering-specific norms and more detailed reports through BERRI to better support foster carers, fostering agencies and local authorities to identify and meet the psychological needs of the children in their care <a href="https://t.co/rYliPjgUyh">https://t.co/rYliPjgUyh</a></p>— BERRI - Outcome Measure (@BerriPrime) <a href="https://twitter.com/BerriPrime/status/1466732253304832004?ref_src=twsrc%5Etfw">December 3, 2021</a></blockquote>

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# Embed Videos & Gifs

.pull-left[
<div class="vembedr">
<div>
<iframe src="https://www.youtube.com/embed/9kYUGMg_14s?start=4" width="400" height="450" frameborder="0" allowfullscreen="" data-external="1"></iframe>
</div>
</div>
]

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background-position:10% 70%, 90% 70%
background-size: 525px 400px, 525px 400px

# Great data visualization!

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# Which can even me animated

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# Applications

.left[
.large[
- Presentations

- Books

- Websites

- Shiny applications

- Automated Reports
]]

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background-size: 300px 375px
# Presentations

.pull-very-left[
- Lightweight (embed videos, gifs, HD imgs).
- Host online (No need to send files). <br>
<a href="www.r-for-cp.netlify.app">www.r-for-cp.netlify.app</a>

<a href="http://fnd-for-paramedics.netlify.app"> Clinical teaching about dissociative seizures</a>

<a href="http://chris-gaskell.github.io/uos-sced/day-one/index.html"> Academic teaching about practice based research</a>
]

???
- Scribble.
- Webcam.
- Panelset.
- Videos
- contact cards
-

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# Websites

.pull-very-left[
Static webistes:
- Personal academic websites.
- Websites for teaching staff and students.
- Hosting resources.

<a href="https://leo-the-lurcher.netlify.app">My dog's website (bit of fun)</a>

<a href="http://sced-for-clinicians.netlify.app">Teaching workshop website</a>

<a href="http://chris-gaskell.com">My personal site</a>

]

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# E-Books

.pull-very-left[
Books that are: <br>
- Polished, professional and interactive
- Can output to html, MsWord or pdf
- Protocols & treatment manuals
- Workbooks & resources for carers and patients.

<a href="https://bookdown.org/yihui/bookdown/">The Bookdown example</a>

<a href="https://nead-gsh.netlify.app">An example book I made earlier for work</a>
]

???
- Looks just like an online book.
- Sidebar contents table
- Search function
- Embded images, videos, tweets, downloadable files.

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# Applications

.pull-very-left[
Apps that are interactive and reactive:

- <a href="http://neuro-tests.netlify.app">Neuropsychology Test Catalogue</a>

- <a href="https://shiny.rstudio.com/gallery/">Gallery of applications</a>

- <a href="https://www.rstudio.com/blog/winners-of-the-2020-rstudio-table-contest/">Great looking data tables</a>
]

---
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background-image: url(https://i.pinimg.com/originals/d6/4f/60/d64f60c95354b0ae5fb447ff942eb20b.png)
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# Academic Posters

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