From 2a72a9688203efe1dfa70e4ad5e4b0b4798bd49d Mon Sep 17 00:00:00 2001 From: Florencia D'Andrea Date: Wed, 3 Jul 2024 10:52:55 -0700 Subject: [PATCH] Update slides - First version --- custom.scss | 68 ++-- slides.html | 283 ++++++++++++-- slides.qmd | 349 +++++++++++++++++- .../libs/revealjs/dist/theme/quarto.css | 4 +- 4 files changed, 631 insertions(+), 73 deletions(-) diff --git a/custom.scss b/custom.scss index eab5bd4..6977e92 100644 --- a/custom.scss +++ b/custom.scss @@ -1,20 +1,21 @@ /*-- scss:defaults --*/ +@font-face { + font-family: "Khula"; + src: url("https://fonts.googleapis.com/css2?family=Khula:wght@300;400;600;700;800&display=swap"); +} // fonts -$font-family-sans-serif: 'EB Garamond', serif !default; +$font-family-sans-serif: 'Khula', sans-serif !default; $font-family-monospace: "Fira Mono", monospace !default; $presentation-title-slide-text-align: "left"; $code-block-font-size: 0.5em; $code-color: #5f5f5f; -$presentation-heading-font-weight: 700 !default; -$presentation-h1-font-size: 1.5em !default; -$presentation-h2-font-size: 1.4em !default; -$presentation-h3-font-size: 1.2em !default; -$presentation-h4-font-size: 1em !default; -$presentation-font-smaller: 0.85em !default; -$presentation-line-height: 1.7em !default; +$presentation-font-smaller: 10px !default; +$presentation-line-height: 1.5em !default; +$font-size-root: 10px !default; + // colors @@ -25,18 +26,16 @@ $link-color: #68737A !default; $selection-bg: #FAA381 !default; // headings -$presentation-heading-font: 'Albert Sans', sans-serif !default; +$presentation-heading-font: 'Work Sans', sans-serif !default; $presentation-heading-color: #399E5A !default; +$presentation-heading-font-weight: 300 !default; +$presentation-h1-font-size: 0.5em !default; +$presentation-h2-font-size: 1.3em !default; +$presentation-h3-font-size: 1.2em !default; +$presentation-h4-font-size: 1.1em !default; /*-- scss:rules --*/ -@import url(https://fonts.googleapis.com/css?family=Fira+Mono:400,700); -@import url('https://fonts.googleapis.com/css2?family=EB+Garamond:ital,wght@0,400;0,500;0,600;0,700;0,800;1,400;1,500;1,600;1,700&display=swap'); -@import url('https://fonts.googleapis.com/css2?family=Albert+Sans:ital,wght@0,100;0,200;0,300;0,400;0,500;0,600;0,700;0,800;0,900;1,100;1,200;1,300;1,400;1,500;1,600;1,700;1,800;1,900&display=swap'); - - - - .reveal a { line-height: 1.5em; } @@ -76,18 +75,39 @@ $presentation-heading-color: #399E5A !default; #title-slide { text-align: left; +} - .quarto-title-authors { - justify-content: left; - - .quarto-title-author { - padding-left: 350px; +#title-slide .title { + font-size: 1.6em; + position: relative; + left: 300px; + } + + +#title-slide .quarto-title-author { + padding-left: 300px; padding-right: 0; width: 100%; - } } -} + +.quarto-title-author-name { + font-size: 0.85em !important; + } + + .quarto-title-affiliation { + font-size: 0.65em !important; + } + .text-c { text-align: center; -} \ No newline at end of file +} + + .title { + width: 850px; +} + +.p{ + font-weight: 200 !important; +} + diff --git a/slides.html b/slides.html index af24afc..89f1083 100644 --- a/slides.html +++ b/slides.html @@ -12,8 +12,8 @@ - - GeoCovid Buenos Aires + + Projecting Human Mobility and Disease Data to Support Decision-Making @@ -329,19 +329,19 @@
-
-

GeoCovid Buenos Aires

+
+

Projecting Human Mobility and Disease Data to Support Decision-Making

-Florencia D’Andrea, Ph.D. +Eco-epidemiology of Zoonotic Diseases Lab

- Research Software Developer / Data Analyst + Paul Allen School of Medicine | Washington State University

- Dr. Fernandez Lab - Washington State University + Presented by Dr. Florencia D’Andrea

@@ -349,42 +349,271 @@

GeoCovid Buenos Aires

Welcome!

-

https://fernandez-lab-wsu.github.io/geocovid-slides/slides.html

+

Slides: https://fernandez-lab-wsu.github.io/geocovid-slides/slides.html




Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.

-

Title slide illustration: The Turing Way Community, & Scriberia. (2020, March 3). Illustrations from the Turing Way book dashes. Zenodo. http://doi.org/10.5281/zenodo.3695300

+
+
+

Roadmap

+

Why are we doing this? Introduction

+

Can you see how people move in the city? R package quadkey

+

Can COVID-19 be related with movement in the city? - GeoCovid app

+

What is important when developing research software? - WebPage

+

Reflection Next steps

+
+
+

Eco-epidemiology of Zoonotic Diseases Lab

+

Washington State University

+
+
+

System thinking approach to integrate the human and ecological components that determines the emergence and persistence of zoonotic diseases.

+
+

+
+
+
+
+

Eco-epidemiology of Zoonotic Diseases Lab

+

Washington State University

+

🐦 GitHub

+

https://github.com/Fernandez-Lab-WSU

+

🌐 Web

+

https://labs.wsu.edu/eco-epi-lab/

+
+
+

COVID-19

+

Human behavioral component starts being recognized

+
    +

  • Map how human mobility changes in space depending on the decisions that were made and how that correlated with the cases.

    • +

  • Project with researchers from Argentina -> Stricter quarantine

    • +
+
+
+

COVID-19

+

Human behavioral component starts being recognized

+

Social, Preventive, and Obligatory isolation established by the Argentine government

+
    +
  • Phase 1: Strict isolation.
    • +
  • Phase 2: Managed isolation.
    • +
  • Phase 3: Isolation by geographic segmentation.
    • +
  • Phase 4: Isolation with progressive reopening.
    • +
  • Phase 5: Last phase search to re-establish new normality.
    • +
-

Click here! I can be a link!

+

Ramírez ML, Martinez SM, Bessone CV, Allemandi DA, Quinteros DA. COVID-19: Epidemiological situation of Argentina and its neighbor countries after three months of pandemic. Disaster Med Public Health Prep.

+
+
+
+

Meta - Data4Good

+
+
+
    +

  • Location of Meta/Facebook users

    +
      +
    • Mobile devices with the Facebook app installed
      • +
    • Lat and Long at a given time.
      • +
    • +

  • Measures applied to the data to ensure privacy and anonymity.

    • +

  • The data is available to researchers by application to the Facebook Data for Good Partner Program

    • +
+
+

+
+
+

Bing Maps Tile System

+
+
+
+

Meta - Data4Good

+
+
+
    +

  • Daily data - 8hs time period Buenos Aires province (UTC-3)

    +
      +
    • 0hs - 8hs.
      • +
    • 8hs - 16hs.
      • +
    • 16hs - 0hs.
      • +
    • +

  • Mapped using a Bing tile architecture

    +
      +
    • Assigning users to individual tiles
      • +
    • +
+
+

+
+
+
+

data4Good WebPage

+
+
+
+

Goal

+

Particular interest in the spatial dynamics of data

+
    +

  • Fundamental tool to map risk and monitor how decision making affects the distribution of cases in a community or city.

    • +

  • Quick overview to monitor decisions quasi-real time

    • +
+
+
+

Step 1

+
+
+

From QuadKeys to raster images

+

QuadKeys represent a location on a map by encoding its hierarchical spatial position as a sequence of characters.

+

🔎📄

+ +
+
+

Step 1

-
-

Dr. Fernandez lab

+
+

From QuadKeys to raster images

+

The tiles can have different sizes, producing maps with more or less level of detail.

+ +
+
+

Step 1

+
+
+

From QuadKeys to raster images

+

The conversion from QuadKey to raster involve several steps

+

:::footer Image source: quadkeyr documentation :::

-
-

Project overview

-

When you click the Render button a document will be generated that includes:

+
+

Why to create an R package

+

When is a good idea to create a software package as part of a research?

    -
  • Content authored with markdown
    • -
  • Output from executable code
    • +
  • Easier to reuse the functions.
    • +
  • Better code quality (i.e. tests, documentation)
    • +
  • Ensures computational reproducibility.
-
-

quadkeyr

-

When you click the Render button a presentation will be generated that includes both content and the output of embedded code. You can embed code like this:

-
-
-
[1] 2
+
+

rOpenSci peer-review

+
+
+

Scientific package review process

+ +
+

-
-

Website

+
+

+ +
+

https://github.com/ropensci/quadkeyr https://joss.theoj.org/papers/10.21105/joss.06500

+
+
+
+

Variable

+

percent_change

+
+
+

R package: quadkeyr

+
+
+

D’Andrea F, Fernandez P (2024). quadkeyr: Tools for converting QuadKey-identified datasets (Microsoft’s Bing Maps Tile System) into raster images and analyzing Meta (Facebook) Mobility Data.. R package version 0.1.0, https://github.com/ropensci/quadkeyr, https://docs.ropensci.org/quadkeyr/.

+
+

+
+
+
+

quadkey documentation

+
+
+
+

Example

+

We were not going to see the consequences of decisions immediately. Non-permitted behaviors would be possible to detect

+
+
+

Conclusion

+

We managed to generate the raster to visualize citizen mobility on a map

+
+
+

GeoCovidAR

+

Integrate city mobility information with daily reported covid cases

+
+
+

Tab 1

+

General exploration

-
-

App

+
+

Tab 2

+

Compare departments

+

You can download a report

+
+
+

Tab 3

+

Generalidades

+
+
+

Conclusions

+

An app was generated to view covid19 data

+

Modulos

+

Possible to reuse in other diseases with ease For example DENGUE

+
+
+

Where is the project data?

+

Website: GeoCovid Buenos Aires

+

3 datasets

+

COVID-19 rasters

+
+
+

Overview del proyect

+

R-Shiny app GeocovidApp quadkeyr R package website PostgreSQL database

+
+
+

Who I am?

+
+
+

Contact

+
+
+
+
+
+
+

+
+
+
+
+
+

🐦 Twitter
+@cantoflor_87

+

📢 Mastodon

+

@florencia@techhub.social

+

🌐 Web

+

https://florenciadandrea.com

+
+
+
+
+

Conclusion

+
    +
  • Monitoring system
    • +
  • Integration ecological components (hosts there are distribution and contacts) with the complexity of the human behavior. This determines the spatial distribution of cases and is essential to understand the dynamics of transmission.
    • +
  • Flexible tool daptable to future scenarios
    • +
+
+
+

Funding

+ +

CDC’s Center for Forecasting and Outbreak Analytics. This project was made possible by cooperative agreement CDC-RFA-FT-23-0069 (grant # NU38FT000009-01-00) from the CDC’s Center for Forecasting and Outbreak Analytics. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the Centers for Disease Control and Prevention.

+

MIDAS-NIH COVID-19 urgent grant program.

+

Paul G. Allen School for Global Health, Washington State University.

Thank you!

diff --git a/slides.qmd b/slides.qmd index d38dee5..6a622f3 100644 --- a/slides.qmd +++ b/slides.qmd @@ -1,13 +1,14 @@ --- -title: 'GeoCovid Buenos Aires' +title: 'Projecting Human Mobility and Disease Data to Support Decision-Making' author: - - name: "Florencia D'Andrea, Ph.D." - affiliation: "Research Software Developer / Data Analyst" -institute: "Dr. Fernandez Lab - Washington State University" + - name: "Eco-epidemiology of Zoonotic Diseases Lab" + affiliation: "Paul Allen School of Medicine | Washington State University" +institute: "Presented by Dr. Florencia D'Andrea" title-slide-attributes: - data-background-image: img/first-slide.png + data-background-image: img/first_slide.png data-background-size: contain - data-background-opacity: "0.5" + data-background-opacity: "0.8" + data-background-position: left filters: - roughnotation format: @@ -23,6 +24,7 @@ format: ## Welcome! +Slides: [https://fernandez-lab-wsu.github.io/geocovid-slides/slides.html](https://fernandez-lab-wsu.github.io/geocovid-slides/slides.html) @@ -31,38 +33,345 @@ format: ::: {.small-text} Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License. +::: + +## Roadmap {background-color="#E5E4E2"} + +Why are we doing this? *Introduction* + +Can you see how people move in the city? *R package `quadkey`* + +Can COVID-19 be related with movement in the city? - *GeoCovid app* -**Title slide illustration**: The Turing Way Community, & Scriberia. (2020, March 3). Illustrations from the Turing Way book dashes. Zenodo. http://doi.org/10.5281/zenodo.3695300 +What is important when developing research software? - WebPage + +Reflection +Next steps + +## Eco-epidemiology of Zoonotic Diseases Lab +#### Washington State University + +:::: {.columns} +:::{.column width="50%" #vcenter} + +System thinking approach to integrate the human and ecological components +that determines the emergence and persistence of zoonotic diseases. ::: +:::{.column width="50%" #vcenter} + +![](img/puzzle.jpg) +::: +:::: + +## Eco-epidemiology of Zoonotic Diseases Lab +#### Washington State University + + +🐦 **GitHub** + +[https://github.com/Fernandez-Lab-WSU](https://github.com/Fernandez-Lab-WSU)
+ + +🌐 **Web** + +[https://labs.wsu.edu/eco-epi-lab/](https://labs.wsu.edu/eco-epi-lab/) + +## COVID-19 +#### Human behavioral component starts being recognized + + +- Map how **human mobility changes in space** depending on +the decisions that were made and how that correlated with the cases. + + +- Project with researchers from Argentina -> Stricter quarantine + +## COVID-19 +#### Human behavioral component starts being recognized + +**Social, Preventive, and Obligatory isolation established by the Argentine government** + +- Phase 1: Strict isolation. +- Phase 2: Managed isolation. +- Phase 3: Isolation by geographic segmentation. +- Phase 4: Isolation with progressive reopening. +- Phase 5: Last phase search to re-establish new normality. :::footer -Click here! I can be a link! +[Ramírez ML, Martinez SM, +Bessone CV, Allemandi DA, Quinteros DA. +COVID-19: Epidemiological situation of +Argentina and its neighbor countries after three +months of pandemic. Disaster Med Public +Health Prep.](https://doi.org/10.1017/ +dmp.2021.90.) ::: -## Dr. Fernandez lab -## Project overview +## Meta - Data4Good + +::::{.columns} + +:::{.column width="70%"} +- Location of Meta/Facebook users + - Mobile devices with the Facebook app installed + - **Lat and Long at a given time**. -When you click the **Render** button a document will be generated that includes: +- Measures applied to the data to ensure privacy and anonymity. + +- The data is available to researchers by application to the Facebook +Data for Good Partner Program + + +::: + +:::{.column width="30%"} + +![](img/metalogo.png) + +::: +::: -- Content authored with markdown -- Output from executable code +:::footer +[Bing Maps Tile System](https://learn.microsoft.com/en-us/bingmaps/articles/bing-maps-tile-system) +::: + +## Meta - Data4Good + +::::{.columns} + +:::{.column width="50%"} + +- Daily data - 8hs time period +Buenos Aires province (UTC-3) + + - 0hs - 8hs. + - 8hs - 16hs. + - 16hs - 0hs. + +- Mapped using a Bing tile architecture + - Assigning users to individual tiles + +::: + +:::{.column width="50%"} + +![](img/tiles.jpg) + +::: +::: + +:::footer +[`data4Good` WebPage](https://dataforgood.facebook.com/) +::: + + + +## Objectives +#### Spatial dynamics of data + + +* Fundamental tool to map risk and monitor how decision making +affects the distribution of cases in a community or city. + +* Quick overview to monitor decisions + + +## Step 1 +#### From QuadKeys to raster images + +**QuadKeys** represent a location on a map by encoding its hierarchical +spatial position as a sequence of characters. + +🔎📄 + +![](img/quadkey_to_raster.png) + +## Step 1 +#### From QuadKeys to raster images + +The tiles can have different sizes, +producing maps with more or less level of detail. + +![](img/bing_quadkeys.jpg) + +## Step 1 +#### From QuadKeys to raster images + +The conversion from QuadKey to raster involve several steps + +![](img/workflow_facebook.png) +:::footer -## `quadkeyr` +Image source: `quadkeyr` documentation -When you click the **Render** button a presentation will be generated that includes both content and the output of embedded code. You can embed code like this: +::: -```{r} -1 + 1 +## Why to create an R package +#### When is a good idea to create a software package as part of a research? +- Makes easier to reuse the functions. +- Better code quality (i.e. tests, documentation) +- Ensures computational reproducibility. + +## rOpenSci peer-review + +::::{.columns} + +:::{.column width="70%"} +**Scientific package review process** + +- [rOpenSci webpage](https://ropensci.org/software-review/) + - [rOpenSci Packages: Development, Maintenance, and Peer Review](https://devguide.ropensci.org/preface.html) + +::: + +:::{.column width="30%"} + + +![](img/ropensci.svg) + +::: +:::: + + +## + +![](img/quadkeyr_joss.png) + +::: footer +https://github.com/ropensci/quadkeyr https://joss.theoj.org/papers/10.21105/joss.06500 +::: + +## Variable + +`percent_change` + +## R package: `quadkeyr` + + +::::{.columns} + +:::{.column width="70%"} + +D'Andrea F, Fernandez P (2024). quadkeyr: Tools for converting QuadKey-identified datasets (Microsoft's Bing Maps Tile System) into raster images and analyzing Meta (Facebook) Mobility Data.. R package version 0.1.0, https://github.com/ropensci/quadkeyr, https://docs.ropensci.org/quadkeyr/. + +::: + +:::{.column width="30%"} + +![](img/logo.png) + +::: +::: + +:::footer +[`quadkey` documentation](https://docs.ropensci.org/quadkeyr/index.html) +::: + +## Example + +- We were not going to see the consequences of decisions immediately. +- Non-permitted behaviors would be possible to detect. + +## Conclusion + +We managed to generate the raster to visualize citizen mobility on a map + +## GeoCovidAR + +Integrate city mobility information with daily reported covid cases + +## Tab 1 + +General exploration + +## Tab 2 + +Compare departments + +You can download a report + +## Tab 3 + +Generalidades + +## Conclusions + +- GeoCovidAR App integrates COVID-19 and Facebook Mobility Data + +## Where is the project data? +#### Website: GeoCovid Buenos Aires + +3 datasets + +COVID-19 +rasters + +## Overview del proyect + +R-Shiny app GeocovidApp +`quadkeyr` R package +website +PostgreSQL database + +## Who I am? + +#### Contact + +:::: {.columns} +:::{.column width="40%" #vcenter} + +```{r foto, echo = FALSE, out.width=250, fig.align='center'} +knitr::include_graphics("https://res.cloudinary.com/flor/image/upload/w_1000,ar_1:1,c_fill,g_auto,e_art:hokusai/v1683580772/IMG_20220607_130734112_mu4fpd.jpg") ``` +::: + +:::{.column width="60%" #vcenter} +🐦 **Twitter** +[@cantoflor_87](http://twitter.com/cantoflor_87)
+ +📢 **Mastodon** + +[@florencia@techhub.social](https://techhub.social/@florencia) + +🌐 **LinkedIn** + +[https://www.linkedin.com/in/florenciadandrea/](https://www.linkedin.com/in/florenciadandrea/) + +::: +:::: + +## Conclusion + +- Monitoring system +- Integration ecological components +(hosts there are distribution and contacts) with the complexity of the +human behavior. +This determines the spatial distribution of cases and is essential +to understand the dynamics of transmission. +- Flexible tool daptable to future scenarios + +## Funding + +![](img/foresite.jpg) + +**CDC's Center for Forecasting and Outbreak Analytics.** +This project was made possible by cooperative agreement CDC-RFA-FT-23-0069 +(grant # NU38FT000009-01-00) from the CDC's Center for +Forecasting and Outbreak Analytics. +Its contents are solely the responsibility of the authors +and do not necessarily represent the official views of +the Centers for Disease Control and Prevention. + +**MIDAS-NIH** COVID-19 urgent grant program. + +Paul G. Allen School for Global Health, **Washington State University**. -## Website -## App +## Thank you! -## Thank you! \ No newline at end of file diff --git a/slides_files/libs/revealjs/dist/theme/quarto.css b/slides_files/libs/revealjs/dist/theme/quarto.css index d46387a..da14b28 100644 --- a/slides_files/libs/revealjs/dist/theme/quarto.css +++ b/slides_files/libs/revealjs/dist/theme/quarto.css @@ -1,5 +1,5 @@ -@import"./fonts/source-sans-pro/source-sans-pro.css";@import"https://fonts.googleapis.com/css?family=Fira+Mono:400,700";@import"https://fonts.googleapis.com/css2?family=EB+Garamond:ital,wght@0,400;0,500;0,600;0,700;0,800;1,400;1,500;1,600;1,700&display=swap";@import"https://fonts.googleapis.com/css2?family=Albert+Sans:ital,wght@0,100;0,200;0,300;0,400;0,500;0,600;0,700;0,800;0,900;1,100;1,200;1,300;1,400;1,500;1,600;1,700;1,800;1,900&display=swap";:root{--r-background-color: #FFFFFF;--r-main-font: EB Garamond, serif;--r-main-font-size: 40px;--r-main-color: 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