Mr. Swallow has requested we move the "MAJCOM Summary" tab to be the first tab that displays when you open CHAD. Right now it displays the "National Summary" tab, recommend simply switching the locations of the tabs. Mr. Swallow's intent is to have the most useful/unique to CHAD chart be displayed up front. Thank you!

The projections currently show low uncertainty far into the future where the models generally predict low hospitalizations and deaths. However, we know that the two models we have are a subset of possible futures and that there are credible models with a much larger range of uncertainty out into the future. Even the multi-peak and trigger-based mitigation models understate uncertainty far in the future because of unknowns about policy and disease progression.

Given that this tool will be used by non-analysts it's important that we avoid showing users projections that look highly certain when they are not.

Given that analytical reasoning, and also at direction of Mr. Swallow and Dr. Giddings, there is a request to limit all projections to no more than 30 days (both in the projection plots and the MAJCOM summary).

I know that the team had reservations about doing this earlier so I'm happy to discuss the reasoning in more detail.

All,
My latest PR (#27) updates the global.R file to account for changes in the CSV file location in the IHME zip file.
Previous versions of global.R are "hard coded" to assume the target CSV file is the first item in the IHME zip file list.
The PR version of global.R searches the IHME zip file list and assigns the target CSV file name to the list item that includes the strings "Hospitalization" and "csv".

Integrate AMC SIR Infection model into overlay plots. Parse out cumulative deaths, cumulative infections, and daily infections. Estimate hospitalization burden from infection number and hospitalization rates

Describe the bug
Data being pulled in for cases is cumulative. Therefore if the number ever decreases or shows up zero AFTER a reported case number then that is an error. There are counties with recent dates having zeros in the reported case section. This is most likely due to inconsistent reporting from the state health offices and tends to happen over weekends. It typically gets cleared up in the data after a couple days but gives negative daily case numbers in the meantime.

Expected behavior
Cumulative cases should never decrease or have a zero after having reported cases

Screenshots

For this example, row 1 and row 5 have zeros in the recent dates when their has already been cumulative cases on record.

Proposed Solution
When importing the data in, look through the last (maybe 5?) recent dates and check if the case number is lower than the previous date. If so replace with case number with the previous day's number.

I attempted to do this but came up with a nested for loop that takes a while to run. I am sure there are faster ways to do this upfront with some r or dplyr functions.

Urgent need to include Overseas locations ASAP

Mr. Swallow requested we add a legend that explains the size of the dot in addition to the color (which currently displays only when there are red & green dots together). Can we make the legend display unconditionally and add the description of what the size of the dot represents?

Request adding a column in the Download for the Full Data Set to include the Total Reported Case Count as well as an indication somewhere on the MAJCOM summary as to the Radius from the base the data is displaying

Find a new source for SEIAR Model parameters ASAP.

Currently adding in Columbia University Model and Los Alamos National Laboratory Models. Should be ready to push very soon.

Local plots show new cases, new estimated hospitalizations, and new deaths (along with totals). Estimated numbers shouldn't be on the same plot as confirmed data. Therefore confirmed cases and confirmed deaths will stay on the two local plots. Estimated hospitalizations should be removed.

Example
Today is 22 April The data pull for the current cases current column is 21 April
but the output displayed Total, and New, and the graph for Daily Reports is for 20 April.
Other possibility is the data labels are wrong

Shaw AFB 30 mile radius

Need additional filter label for Majcom summary for 16AF. This might be an issue since bases will have a dual label between traditional majcom and 16AF. Might need a separate column label in the dataframe stating 16AF or not. This is necessary for the overseas basis

Items 1-3 are immediate items, 4 is additional when there is time

1. Add in 1, 3, 5, 7 and 14 day case increase rates.
   Rationale/Intent: provides better picture of the trend (trending up or trending down)

2. Add in weekly rate of change in case count (graph of how the growth in cases is changing over time).
   Rationale/Intent: Would like to see if the speed of the case increase is slowing down over time

3. Add in current number of recovered cases on current local health tab.

4. Consider a projection of the number recovered based on the average recovery time

•   A case is "active" on average of 14-days ... so then add daily new case counts for 14 days and subtract from cumulative and deaths
  

Rationale/intent: this is an estimate but can eventually help us assess the level of immunity in the community

These items are requested additions to the Current Local Area Summary tab:

1. Effective Reproduction Number (Rt) within selected radius of installation
   . Rt = (5 day average new cases) / (14 day average new cases)
   . Example (115 new cases last five days divided by 5 days) / (207 new cases last 14 days divided by 14 days) = 23 / 14.79 = 1.56
2. Show case count info per 1000 to make it more comparable to our installations.
3. Add doubling rate for the specific radius that was selected vs. just by county

From Linda Lee:

I checked out the CHAD tool. Really like it. When I ran the test report utility, I found a flaw in one of the reported numbers.

For instance, in the CHAD panel, when I select the Pentagon, it shows +58 for New Confirmed Fatalities, but the test report shows +1077 for New Fatalities

The national CHIME estimate is delayed much further than the local area CHIME estimates. Do we know why that is? It's possible that the local areas we've chosen happen to be earlier but it seems unlikely.

Describe the bug
When the installation is located in a large county, the standard 50 mile radius does not always include the county in which the installation exists. This leads to inaccurate current local health data/local health projections

To Reproduce
Steps to reproduce the behavior:
See Edwards or DM. Current local health projections are inaccurate/incomplete until the user scales out far enough to "catch" the county center.

Expected behavior
When an installation is selected it should include the county in which it exists regardless of the installations proximity to the county's centroid or the user defined radius.

Screenshots

Additional context

Bug exists when sidebar MAJCOM filter selects any of the below bases, hot spot chart throws an error or displays no bases. This might be due to the way the cases are being counted, or filters placed on the chart.

• AFSOC
• PACAF
• UASFA
• HQ

Is your feature request related to a problem? Please describe.

R_t is the initial reproduction number R₀ over time. When this number falls below 1, it indicates the spread of the virus is decreasing. This number can be very beneficial as an indicator for different regions.

http://systrom.com/blog/the-metric-we-need-to-manage-covid-19/

Describe the solution you'd like

A Solution and excellent visualization exists over at:
https://rt.live/

With the code and documentation at
https://github.com/k-sys/covid-19/blob/master/Realtime%20R0.ipynb

Transitioning this methodology to the county level or selected region would be the goal for CHAD

Alternative Solution

The results by state are provided at
https://d14wlfuexuxgcm.cloudfront.net/covid/rt.csv

This can be a backup plan with full citation given to the creator, if we can't manage to adapt for county level values

Need to change the label for the red line ASAP, "Estimated COVID Patient Bed Capacity"

Need a design mockup/idea for possible construction of a new tab. The new tab would be the first tab seen when the app loads up. The tab could contain overview information, how to get started, and links to further documentation (could be Github write ups).

Hot Spot chart on MAJCOM Summary tab needs fixed axis on the y-scale along with fixed scaling bounds on the bubble size and color. This is so when the filter for MAJCOM is changed, a large red bubble will correspond to the scale among all bases as opposed to just among the filtered bases. Allows for proper visual comparison when filter is changed.

Need new documentation to help show users how to use the features of CHAD and also how one should interpret what the metrics and charts are displaying. This can be documentation shown on a tab, written in markdown and displayed on the Github repo, added to the more information section on the app, etc.

Describe the bug
On the MAJCOM summary plot, tan/brown is displaying when IHME is selected on the map instead of green. Green displays properly when CHIME is selected. This seems to only happen when deployed. When running locally on my computer, everything is green. Once deployed, IHME filter displays brown instead. See screenshots below. Code for color hasn't changed.

Expected behavior
Color of points should be green when IHME filter is selected on MAJCOM Summary map, for cases under 5% population.

Screenshots
On the web:

On my computer:

Looking to change the data source from USAFacts to JHU for US County level cases and deaths. Needs to be done with the least amount of change to the code. Ideally just a change to the data pull line in the global, along with column name changes to match the old data source.

JHU time series cases for counties
https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_US.csv

JHU time series deaths for counties
https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_US.csv