ACT-covid-resources / data-science-methods-project2

Project #2 Data Visualization

COVID-19 Dashboard for the General Ontario Public

Team Members:

• Elisa Du
• Malikeh Ehghaghi
• Yuanhao Lou
• Jack Ellis

The Dashboard

Page 1: Case status and testing volumes in Ontario

Page 2: Vaccination status in Canada

Overview

Many visualization tools have been built since the start of the COVID-19 pandemic. This particular dashboard aims to provide the Ontario public with an understanding of the current case progression and testing status within Ontario, as well as the vaccination status of Ontario compared to other Canadian provinces and territories. The Ontario public can use this dashboard to determine how effectively current public health measures are in reducing virus spread, as well as to ascertain the safety level of their local communities. The first page of the dashboard provides information on case-related statistics (e.g. total case and death counts, average daily testing volumes, percent positivity rate, and outbreak frequencies) for different PHUs within Ontario. The second page of the dashboard contains visualizations that compare the vaccine distribution and administration of Ontario to other provinces and territories. This may help the public determine how soon they will be vaccinated. The dashboard was created with flexdashboard in R.

Dashboard Summary

The goal of this dashboard is to provide the Ontario general public with up-to-date information on COVID-19 testing, case status, and vaccination.

Data Sources

          Ontario GeoHub

• https://geohub.lio.gov.on.ca/datasets/ministry-of-health-public-health-unit-boundary/geoservice?geometry=-168.377%2C38.920%2C-1.122%2C58.787

Ontario Data Catalogue

• https://data.ontario.ca/dataset/status-of-covid-19-cases-in-ontario-by-public-health-unit-phu
• https://data.ontario.ca/dataset/a2dfa674-a173-45b3-9964-1e3d2130b40f/resource/07bc0e21-26b5-4152-b609-c1958cb7b227/download/testing_metrics_by_phu.csv
• https://data.ontario.ca/dataset/1115d5fe-dd84-4c69-b5ed-05bf0c0a0ff9/resource/d1bfe1ad-6575-4352-8302-09ca81f7ddfc/download/cases_by_status_and_phu.csv
• https://data.ontario.ca/dataset/ontario-covid-19-outbreaks-data/resource/36048cc1-3c47-48ff-a49f-8c7840e32cc2

Statistics Canada:

• https://www12.statcan.gc.ca/census-recensement/2016/dp-pd/prof/details/download-telecharger/comp/GetFile.cfm?Lang=E&FILETYPE=CSV&GEONO=058

Canada Public Health Services:

• https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/covid-19-vaccine-treatment/vaccine-rollout.html

Canada COVID-19 Github Repository:

• https://raw.githubusercontent.com/ccodwg/Covid19Canada/master/timeseries_prov/vaccine_administration_timeseries_prov.csv

Government of Canada:

• https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/covid-19-vaccine-treatment/vaccine-rollout.html

CTV News:

• https://www.ctvnews.ca/health/coronavirus/coronavirus-vaccine-tracker-how-many-people-in-canada-have-received-shots-1.5247509?fbclid=IwAR3HMQewAhl4fmp8SisM6Pdq-xQN-hG9sa0Q9C1ugzqlNa8UZNGblDHGBcA

Carto:

• https://thomson.carto.com/tables/canada_provinces/public/map

Final product

Final dashboard can be viewed in the browser by opening the file STA-2453_P2.html.

To run the dashboard...

Step 1. Clone the repo. If needed, instructions can be found here.

Step 2. Install the package versions and R version specified in requirements.txt.

Step 3. Open STA-2453_P2.Rmd in RStudio and knit the file (should take no more than 5 min for dashboard to show up).

Things to note...

• Please ensure that Firefox browser is installed. This is because the map of Canada on Page 2 of the dashboard uses a Firefox webdriver to scrape vaccine data. Unfortunately the webdriver would not work for any other web browser.
• Please view the dashboard in full screen for optimal display.

File Directory

• Ministry_of_Health_Public_Health_Unit_Boundary.geojson - latitude and longitude coordinates used to specify the map outline of PHUs within Ontario to generate Page 1 map.

• cases_by_status_and_phu.csv - time series data that includes number of active cases, resolved cases, and deaths for all PHUs. Used for Page 1 map.

• socioeconomic_phu.csv- dataset of PHU name and their corresponding median after-tax household income in 2015.

• clean_socioeconomic_income_by_phu.R - cleaning script used to generate socioeconomic_phu.csv from 2016 Canadian Census dataset.

• canada_provinces.geojson- latitude and longitude coordinates used to specify the map outline of Canadian provinces/territories to generate Page 2 map.

• vaccine_administration_total_prov.csvand vaccine_distribution.csv- Vaccine received by each province/territory, categorized by brand name (Pfizer/BioNTech, Moderna). Used to generate bar chart (not actually used in code, since actual URLs were used to fetch most updated data).

• province_populations.csv - Population by Canadian province/territory scraped from Wikipedia. Used to generate per population bar chart.

• vaccine_administration_timeseries_prov_2.csv - time series data of cumulative vaccine administration counts for each province/territory.

• vaccine_province.csv and vaccine_distribution2.csv- dataset containing various vaccine metrics for each province/territory scraped from CTV News. Used to generate Page 2 map.