You R What You Measure

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<br>
.right[
# You R What You Measure
### Digital biomarkers for insights in personalized health
]
<br> <br> <br> <br> 
.left[Irene van den Broek | R/Medicine 2021 | August 27]
<hr>

.left[.footnote[[<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"/></svg>  www.jebentwatjemeet.nl](https://www.jebentwatjemeet.nl) <br>
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---
name: intro
class: top

## You are what you measure: My Quantified Self Project
<br>
.pull-left[.center[<img src="img/Logo_8factors.png" width="90%">]]

.pull-right[.center[Collecting data about my .darkpink.large[Health] and .darkpink.large[Habits] using apps, sensors and wearable devices]]

---
name: apps

## Wearables and apps for tracking .darkpurple[Health] and .darkpurple[Habits]

.left-col[<img src="img/devices/Oura.png", width = "35%", style="padding:10px"> Oura Ring
<br><br>
<img src="img/apps/RescueTime.png", width = "35%", style="padding:10px; border-radius:30%"> RescueTime
<br><br>
<img src="img/apps/Strava.png", width = "35%", style="padding:10px; border-radius:25%"> Strava]

.center-col[<img src="img/apps/HRV4Training.png", width = "35%", style="padding:10px"> HRV4Training
<br><br>
<img src="img/devices/Dreem.png", width = "35%", style="padding:10px"> Dreem
<br><br>
<img src="img/devices/FreeStyleLibre.png", width = "35%", style="padding:10px"> FreeStyle Libre]

.right-col[<img src="img/devices/AppleWatch.png", width = "35%", style="padding:10px"> Apple Watch
<br><br>
<img src="img/devices/CorSense.png", width = "35%", style="padding:10px"> CorSense
<br><br>
<img src="img/apps/cronometer.png", width = "35%", style="padding:10px; border-radius:25%"> Cronometer]

---
name: aim
class: center

## .left[Let's talk biomarkers. Let's talk health tech. Let's talk R!]

<br>
.pull-left[<svg aria-hidden="true" role="img" viewBox="0 0 320 512" style="height:7em;width:4.38em;vertical-align:-0.125em;margin-left:1em;margin-right:1em;font-size:inherit;fill:#586CC4;overflow:visible;position:relative;"><path d="M272 0H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h224c26.5 0 48-21.5 48-48V48c0-26.5-21.5-48-48-48zM160 480c-17.7 0-32-14.3-32-32s14.3-32 32-32 32 14.3 32 32-14.3 32-32 32zm112-108c0 6.6-5.4 12-12 12H60c-6.6 0-12-5.4-12-12V60c0-6.6 5.4-12 12-12h200c6.6 0 12 5.4 12 12v312z"/></svg> <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:7em;width:7em;vertical-align:-0.125em;margin-left:1em;margin-right:1em;font-size:inherit;fill:#586CC4;overflow:visible;position:relative;"><path d="M320.2 243.8l-49.7 99.4c-6 12.1-23.4 11.7-28.9-.6l-56.9-126.3-30 71.7H60.6l182.5 186.5c7.1 7.3 18.6 7.3 25.7 0L451.4 288H342.3l-22.1-44.2zM473.7 73.9l-2.4-2.5c-51.5-52.6-135.8-52.6-187.4 0L256 100l-27.9-28.5c-51.5-52.7-135.9-52.7-187.4 0l-2.4 2.4C-10.4 123.7-12.5 203 31 256h102.4l35.9-86.2c5.4-12.9 23.6-13.2 29.4-.4l58.2 129.3 49-97.9c5.9-11.8 22.7-11.8 28.6 0l27.6 55.2H481c43.5-53 41.4-132.3-7.3-182.1z"/></svg>
<br>
<br>
.xlarge[The potential of digital biomarkers to advance personalized health]
<br><br>
Personal use <br> Clinical trials <br> Clinical practice]

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<br>
<br>
.xlarge[The power of R to support digital health data] 
<br><br>
Data collection <br> Data analysis <br> Data communication]

---
name: Digital Biomarkers
class: left

## Digital Biomarkers

** Digital Biomarkers**: _Objective, quantifiable physiological and behavioral data that are collected and measured by means of digital devices such as apps, sensors and wearables._

<br>
.center[<img src="img/PersonalizedHealth.png" width="100%">]

---

## Blood Glucose Monitoring in Diabetes Management

<div style="vertical-align:top; display:inline-block; text-align:center; width:24%;">
    <img src="img/devices/Dexcom.png" height="200px"/>
    <span style="display:block;">Dexcom</span>
</div>

<div style="vertical-align:top; display:inline-block; text-align:center; width:24%;">
    <img src="img/devices/Eversense.png" height="200px"/>
    <span style="display:block;">Eversense</span>
</div>

<div style="vertical-align:top; display:inline-block; text-align:center; width:24%;">
    <img src="img/devices/FSL.png" height="200px"/>
    <span style="display:block;">FreeStyle Libre</span>
</div>

<div style="vertical-align:top; display:inline-block; text-align:center; width:24%;">
    <img src="img/devices/MedtronicGL3.png" height="200px"/>
    <span style="display:block;">Medtronic</span>
</div>

---
name: R-R intervals
class: left

## Heart Rate Variability: a non-invasive marker of .darkpurple[Stress]

**HRV** is the variation in time between consecutive heart beats and reflects the heart's capacity to adapt to changes

<br>
.center[<img src="img/ECG_RR.png" width="100%">]

---
name: HRV applications
class: center

## .left[Daily HRV measurement to monitor .darkpurple[Stress] and .darkpurple[Recovery]]

.left-column[Using **Corsense** and **HRV4Training** app <br><br>
<img src="img/devices/CorSense.png" width = "40%"> <br><br>
<img src="img/apps/HRV4Training.png" width = "40%" style="padding:10px">
]

.right-column[
<iframe src="data/eTrend_HRV4T_H250.html" width="100%" height="450" id="igraph" scrolling="no" seamless="seamless" frameBorder="0"> </iframe>
]

---
name: timeseries
class: center

## .left[More .darkpurple[Long-term] Trends: Step Count, Body Weight and Sleep]

.panelset[

.panel[.panel-name[Step Count]

.left-column[
Using **Apple Watch** <br><br>
<img src="img/devices/AppleWatch.png" width="100px">
<br><br>
<img src="img/apps/applewatch.jpg" width="100px"; style="padding:10px; border-radius:25%;">
]

.right-column[
<iframe src="data/eTrend_Steps.html" width="100%" height="400" id="igraph" scrolling="no" seamless="seamless" frameBorder="0"> </iframe>
]

]

.panel[.panel-name[Body Weight]

.left-column[
Using **QardioBase** smart scale <br><br>
<img src="img/devices/QardioBase.png" width="100px">
<br><br>
<img src="img/apps/Qardio.png" width="100px"; style="padding:10px; border-radius:25%;">
]

.right-column[
<iframe src="data/eTrend_Weight.html" width="100%" height="400" id="igraph" scrolling="no" seamless="seamless" frameBorder="0"> </iframe>
]

]

.panel[.panel-name[Sleep]

.left-column[
Using **Dreem** headband <br><br>
<img src="img/devices/Dreem.png" width="100px">
<br><br>
<img src="img/apps/dreem.png" width="100px"; style="padding:10px; border-radius:25%;">
]

.right-column[
<iframe src="data/eTrend_Sleep.html" width="100%" height="400" id="igraph" scrolling="no" seamless="seamless" frameBorder="0"> </iframe>
]

]

] 
---
name: Nightly patterns
class: center

## .left[More about .darkpurple[Sleep]: the Easiest way to collect data!]

.panelset[

.panel[.panel-name[Sleep Phases]
.left-column[
Using **Dreem Headband**<br>
<img src="img/devices/Dreem.png" width="100px">
<br>
<img src="img/apps/dreem.png" width="100px"; style="padding:10px; border-radius:25%;">
]

.right-column[
<img src="index_files/figure-html/Nightly_SleepPhase-1.png" width="864" style="display: block; margin: auto;" />
]
]

.panel[.panel-name[HRV]

.left-column[
Using **Oura Ring**<br>
<img src="img/devices/Oura.png" width="100px">
<br>
<img src="img/apps/Oura.png" width="100px"; style="padding:10px; border-radius:25%;">
]

.right-column[
<img src="index_files/figure-html/oura_HRV-1.png" width="864" style="display: block; margin: auto;" />
]

]

.panel[.panel-name[Heart Rate]

.left-column[
Using **Oura Ring**<br>
<img src="img/devices/Oura.png" width="100px">
<br>
<img src="img/apps/Oura.png" width="100px"; style="padding:10px; border-radius:25%;">
]

.right-column[
<img src="index_files/figure-html/oura_HR-1.png" width="864" style="display: block; margin: auto;" />
]

]

---
name: Biological Clock
class: center

## .left[Daily Rhythms and the .darkpurple[Biological Clock]]

.panelset.sideways[

.panel[.panel-name[Sleep]
<img src ="img/apps/dreem.png" height="50px" style="float:right;margin-bottom:-50px;border-radius:10px">
<img src="index_files/figure-html/ggridge_sleep-1.png" width="864" style="display: block; margin: auto;" />

]

.panel[.panel-name[Meals]
<img src ="img/apps/cronometer.png" height="50px" style="float:right;margin-bottom:-50px">
<img src="index_files/figure-html/ggridge_meal-1.png" width="864" style="display: block; margin: auto;" />

]

.panel[.panel-name[Excercise]
<img src ="img/apps/Strava.png" height="50px" style="float:right;margin-bottom:-50px;border-radius:10px">
<img src="index_files/figure-html/ggridge_exercise-1.png" width="864" />

]

---
name: Productivity
class: center

## .left[Tracking .darkpurple[Productivity] and .darkpurple[Screen Time]]

.left-column[
Using **RescueTime**<br>
<img src="img/apps/RescueTime.png" width="100px"; style="padding:10px; border-radius:25%;">
]

.right-column[
<img src="img/PCTimes.png">
]

---
name: Female Cycle
class: left

## .darkpurple[Montly Rhythms] and Hormonal Influences

.panelset.sideways[

.panel[.panel-name[Body Temperature]
<img src ="img/apps/Oura.png" height="50px" style="float:right; margin-bottom:-50px; border-radius:25%">
<img src="index_files/figure-html/bodyTemp_cycle-1.png" width="936" style="display: block; margin: auto;" />
]

.panel[.panel-name[Breathing]
<img src ="img/apps/Oura.png" height="50px" style="float:right;margin-bottom:-50px; border-radius: 25%">
<img src="index_files/figure-html/breathing_cycle-1.png" width="936" style="display: block; margin: auto;" />
]

.panel[.panel-name[Headaches]
<img src ="img/apps/tracknshare.png" height="50px" style="float:right; margin-bottom:-50px; border-radius:25%">
<img src="index_files/figure-html/Headache_cycle-1.png" width="936" style="display: block; margin: auto;" />

] 
]

---
name: Conclusion
class: left

## In Conclusion...You R What You Measure!

.Footnote[Future (R-) Goals:
- **Automate** and **Share** data upload, analysis and visualization 
- Work together on **Digital Health** Data (Viz) Projects ([*Get in touch!*](mailto:irenevandenbroek@gmail.com))]

---
name: Resources
class: left

## Resources

**Blood Sugar Monitoring** for personalized nutrition:<br>
[The Personalized Nutrition Project](http://personalnutrition.org/Home)

<hr>

**Heart Rate Variability:** <br>
📦 {[RHRV](https://rhrv.r-forge.r-project.org/index.html)} <br>
[EliteHRV](https://elitehrv.com) blog <br>
[HRV4Training](https://www.hrv4training.com/blog) blog

<hr>

**Data Visualization** R packages: <br>
📦 {[echarts4r](https://echarts4r.john-coene.com)} <br>
📦 {[ggridges](https://cran.r-project.org/web/packages/ggridges/vignettes/introduction.html)} <br>
📦 {[ggplot2](https://ggplot2.tidyverse.org)}

---
name: Bonus slides
class: inverse, center, middle

background-image: url(img/logo_transparent.png)
background-position: 5% 10%
background-size: 10%, cover

<br>
#Bonus slides <br>
(Slides that did not fit in the 10 min talk)

---
name: HRV Recommendations
class: center

## .left[Be aware *how* Heart Rate Variability is .darkpurple[Measured]...]

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    </tr>
    
  </thead>
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  </thead>
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<td class="gt_row gt_left">Electric (chest strap)</td>
<td class="gt_row gt_left">Optic (wrist, arm, finger, ear)</td></tr>
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<td class="gt_row gt_left gt_striped">First thing upon awakening</td>
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<td class="gt_row gt_left">5 min</td>
<td class="gt_row gt_left">> 1 min</td></tr>
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<td class="gt_row gt_left gt_striped">Sitting</td></tr>
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<td class="gt_row gt_left">Paced</td></tr>
    <tr><td class="gt_row gt_left gt_stub gt_striped" style="font-weight: bold;">Frequency</td>
<td class="gt_row gt_left gt_striped">Every day</td>
<td class="gt_row gt_left gt_striped">At least 3x per week</td></tr>
  </tbody>
  
  
</table>
</div>

---
name: HRV Analysis 
class: center

## .left[...and *how* Heart Rate Variability is .darkpurple[Analysed]...]

<div style="vertical-align:top; display:inline-block; text-align:center; width:33%;">
   <img src="img/RR.png">
    <span style="display:block;">Time Domain</span>
</div>

<div style="vertical-align:top; display:inline-block; text-align:center; width:33%;">
   <img src="img/psd.png">
    <span style="display:block;">Frequency Domain</span>
</div>

<div style="vertical-align:top; display:inline-block; text-align:center; width:33%;">
   <img src="img/Poincare.png">
    <span style="display:block;">Non-Linear Analysis</span>
</div>

---
name: HRV Long-term
class: top left

## .left[Another application of HRV: .darkpurple[Long-term] measurements]

.left-column[.center[HRV for **Biofeedback** or **Sport Performance** <br><br> <img src="img/devices/polarH10.png" width = "40%">  <br> Polar H10 <br><br> <img src="img/apps/HRVlogger.png" width = "40%" style="padding:10px; border-radius:30%"> <br> HRV Logger app
]]

.right-column[
<img src="index_files/figure-html/HRV_longterm-1.png" width="864" style="display: block; margin: auto;" />
]

---
name: api
class: center

## .left[How to get the Data? All Ways lead to R...!]

.panelset[

.panel[.panel-name[Manual vs Magical]

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<br>

.xlarge[MANUAL] <br> Export + Import Files <br>]

.pull-right[<svg aria-hidden="true" role="img" viewBox="0 0 640 512" style="height:5em;width:6.25em;vertical-align:-0.125em;margin-left:1em;margin-right:1em;font-size:inherit;fill:#586CC4;overflow:visible;position:relative;"><path d="M537.6 226.6c4.1-10.7 6.4-22.4 6.4-34.6 0-53-43-96-96-96-19.7 0-38.1 6-53.3 16.2C367 64.2 315.3 32 256 32c-88.4 0-160 71.6-160 160 0 2.7.1 5.4.2 8.1C40.2 219.8 0 273.2 0 336c0 79.5 64.5 144 144 144h368c70.7 0 128-57.3 128-128 0-61.9-44-113.6-102.4-125.4zm-132.9 88.7L299.3 420.7c-6.2 6.2-16.4 6.2-22.6 0L171.3 315.3c-10.1-10.1-2.9-27.3 11.3-27.3H248V176c0-8.8 7.2-16 16-16h48c8.8 0 16 7.2 16 16v112h65.4c14.2 0 21.4 17.2 11.3 27.3z"/></svg><svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:5em;width:5em;vertical-align:-0.125em;margin-left:1em;margin-right:1em;font-size:inherit;fill:#586CC4;overflow:visible;position:relative;"><path d="M224 96l16-32 32-16-32-16-16-32-16 32-32 16 32 16 16 32zM80 160l26.66-53.33L160 80l-53.34-26.67L80 0 53.34 53.33 0 80l53.34 26.67L80 160zm352 128l-26.66 53.33L352 368l53.34 26.67L432 448l26.66-53.33L512 368l-53.34-26.67L432 288zm70.62-193.77L417.77 9.38C411.53 3.12 403.34 0 395.15 0c-8.19 0-16.38 3.12-22.63 9.38L9.38 372.52c-12.5 12.5-12.5 32.76 0 45.25l84.85 84.85c6.25 6.25 14.44 9.37 22.62 9.37 8.19 0 16.38-3.12 22.63-9.37l363.14-363.15c12.5-12.48 12.5-32.75 0-45.24zM359.45 203.46l-50.91-50.91 86.6-86.6 50.91 50.91-86.6 86.6z"/></svg>
<br>

.xlarge[MAGICAL] <br> Cloud + API <br>

]

]

.panel[.panel-name[Example Oura API]

```r
connect.api <- function(startdate, token, username, password, data_type){
    url <- paste0("https://api.ouraring.com/v1/", data_type, "?start=",
                  startdate, "&access_token=", token)
    get_data <- GET(url, authenticate(username, password, type = "basic"))
    content <- content(get_data, "text")
    json <- fromJSON(content, flatten = TRUE)
    df <- as.data.frame(json)
}
```

```r
oura <- map(c("sleep", "activity", "readiness"), connect.api, startdate = "2020-01-29",
            token = key_get("Token", keyring= "oura"),
            username = key_get("Username", keyring="oura"),
            password = key_get("Password", keyring= "oura"))
```
<hr>
.left[📦 {httr} : Connect <br>
📦 {keyring}: Store credentials <br>
Or look for dedicated packages: e.g., 📦 {rStrava}]
]

]

---
name: Daily patterns
class: center

## .left[Insights from Time Series: .darkpurple[Daily Patterns]]

.panelset[

.panel[.panel-name[Blood Sugar]

.left-column[
Using **Free Style Libre** Sensor <br>
<img src="img/devices/FreeStyleLibre.png" width="100px">
<br>
<img src="img/apps/FSL.png" width="100px"; style="padding:10px; border-radius:25%;">
]

.right-column[
<img src="index_files/figure-html/FSL_glucose-1.png" width="864" style="display: block; margin: auto;" />
]
]

.panel[.panel-name[Activity]

.left-column[
Using **Oura Ring**<br>
<img src="img/devices/Oura.png" width="100px">
<br>
<img src="img/apps/Oura.png" width="100px"; style="padding:10px; border-radius:25%;">
]

.right-column[
<img src="index_files/figure-html/Daily_Activity-1.png" width="864" style="display: block; margin: auto;" />
]

]