MN-COVID-19

This r markdown file was setup for my personal use to look at COVID-19 data in Minnesota (not a lot of comments: added later if I have time).

1. Please download all files to the same directory and run "COVID.Rproj"

2. Open "COVID_markdown.Rmd" and knit the pdf. This file will call "mdhCovidWebScrape.R" to grab response data and merge current COVID-19 data (from MDH website) into "MNCovidData.csv", and "COVID.R", which will preprocess "MNCovidData.csv" and generate plots.

3. Outputs a pdf file named "COVID_markdown.pdf".

Brief explanation of the plots

• Left middle: Bars represent daily numbers for new case (green) and death (orange); lines represent 7-day moving average of the new case and death.

  • Left y axis for new case
  • Right y axis for new death

• Left bottom: Bars represent daily positive rate (green) and case fatality rate (orange); lines represent 7-day moving average (purple represents the number of daily tests)

  • Left y axis for daily positive rate and case fatality rate
  • Right y axis for daily tests

• Right top: Bars represent daily numbers of new admitted hospitalizations (red) and new admitted icu hospitalizations (blue); lines represent 7-day moving average (orange represents the number of total deaths)

  • Left y axis for total deaths
  • Right y axis for daily admitted hospitalization cases

• Right 2nd from the top: Bars represent daily numbers of current hospitalizations (red) and current icu hospitalizations (blue); lines represent 7-day moving average (purple represents the number of current active cases)

  • Left y axis for current active cases
  • Right y axis for current hospitalization cases

• Right 3rd from the top: Bars represent current number of people with at least one dose of vaccination (red) and current number of people with completed vaccination (blue)

• Right bottom: Bars represent weekly number of vaccination doses (blue); orange line represents the total number of vaccination doses administered to date

• According to MDH, the gray shaded area for the most recent 7 days indicates "Due to the need to confirm reports and reporting delays, data maybe incomplete".

Note:

• The csv data (current version: 2020-09-01) may not be updated regularly, but you can find the most recent data in the following link. The daily positive case number reported here is using today's total positve cases minus the the total positive cases from the previous day in the MDH Daily Update. So the positive case number may be slightly different from the positive case count by specimen colletced date.

• COVID Data source: https://www.health.state.mn.us/diseases/coronavirus/situation.html

• Response data source: "https://mn.gov/covid19/data/response.jsp"

• Library needed for this R markdown: tidyverse, ggrepel, gridExtra, knitr, kableExtra, rvest, lubridate

• If you are interested in COVID-19 data by county, take a look in CountyDataFromNYTimes.

Minor change: 2021-10-14

Made some updates to html version. Added a table for weekly vaccine breakthrough cases.

• html version: https://htmlpreview.github.io/?https://github.com/coolbaby0208/MN-COVID19/blob/master/COVID_markdown_html.html
• source: https://www.health.state.mn.us/diseases/coronavirus/stats/vbt.html

Minor change: 2021-10-06

Made some updates to html version. Added plots with data for most recent 60 days to better visualize the recent trend.

Minor change: 2021-08-13

Made some updates to clean up the labels in the plots and replaced the daily vaccination doses administered to weekly doses. Also removed the up number in the total accumulated hospitalized and ICU numbers since MDH only updated the number from 2 days before the report date.

Minor change: 2021-08-10

Update the bottom right plot from daily doses administered to weekly doses.

Minor change: 2021-06-23

Fix up 0 issues in total hospitalization due to 2-day reporting delay.

Minor change: 2021-03-18

Remove surge capacity in the pdf version due to limited space and add vaccination data by people in both pdf and html.

Minor change: 2021-01-05

Add html version: https://htmlpreview.github.io/?https://github.com/coolbaby0208/MN-COVID19/blob/master/COVID_markdown_html.html

Minor change: 2020-12-29

Add vaccination data (source: https://mn.gov/covid19/vaccine/data/index.jsp)

Major change: 2020-10-14

Major change due to MDH reports data in new format

Major change: 2020-10-09

Major change due to MDH reports "Current hospitalization" with a differetn dataset Link: https://mn.gov/covid19/assets/HospitalCapacity_HistoricCSV_tcm1148-449110.csv

Add current hospitalization and ICU numbers to the 2nd plot of the right column. Also made changes to the 3rd plot of the right column to reflect change in data structure from MDH.

Table is revised to show current hospitalization and current ICU numbers.

Major change: 2020-09-24

Major change due to MDH changes how they report "Hospitalization"

Top right plot now shows the following 3 curves and two bars: Curves:

• Total hospitalization (cumulative)
• Total ICU (cumulative)
• Total deaths (cumulative)

Bars:

• New hospitalization
• New ICU

Table is revised to show daily new hospitalization and daily new ICU numbers.

Another change in the 2nd plot: 2020-08-18

Add positive percentage by number of people tested daily in addition to number of daily tests. This data was reported starting on 2020-07-30 to account for multiple testings of the same individual.

Major change in the 1st and 2nd plots: 2020-07-15

Data for New cases, Daily tests, Daily positive rate and Case fatality rate are using either specimen collection date (e.g., New cases) or date reported to MDH (e.g., Daily tests from testing data table) if the data is more than a week old.

For data within a week, the variables mentioned above will be calculated using MDH Daily Update.

• New cases = Today's Total positive cases (cumulative) - Yesterday's Total positive cases (cumulative)
• Daily tests = Today's Total approximate number of completed tests - Yesterday's Total approximate number of completed tests

For data older than a week, the variables mentioned above will be calculated as the following.

• New cases from Positive cases by date specimen collected data table
• Daily tests from Testing data table: Total approximate number of completed tests - Total approximate number of completed tests from the previous day

Differences between the 1st and 2nd plots (left column).

Because Positive cases by date specimen collected data table starts on 3/5 and Testing data table starts on 3/28, you only see new cases data from 3/5 to 3/28 and you won't see data before 3/28 in the 2nd plot.

Example output