This page describes the key performance indicators (KPIs) for the Coronavirus infection used in this study. Daily results can be seen for Sonoma County and for Marin County.
Everything on these pages is based on the actual data about the number of infections, recoveries, and deaths reported on the website of the county. None of it is based on models of the epidemic growth and decline. I am working on these but this data is strictly for measuring actual state of the disease in the county.
Graph of Infections and Recoveries (upper graph)
The upper graph on the page shows the actual trend in the number of Infections (red) and the sum of Infections and Recovered (green). Vertical lines indicate the days when social isolation rules started (SIP), when testing was available to everyone (Test), the day when social isolation was paused (Pause) and the last day. Labels on the graphs show the numbers on that day. Rates of infection per day estimated by regressions for different time periods are shown below the straight line forecasts for two periods. The yellow band shows the confidence interval on the prediction of the number of infections using linear regression.
Table of KPIs
- Doubling rate (doubling.rate), measured in days, is the number of days it takes to double the number of cases. It’s a good measure of how fast the virus is spreading. A low number is bad, or fast-spreading; a high number means we are slowing the growth. The numbers (start.day) and (end.day) are the day numbers, since the start of the virus, of the period used to measure the rate. The start.date is now the day that social distancing was paused.
- R is the reproduction rate of the virus, and measures the number of persons each infected person is likely to pass on to. The mean value or R (Mean.R) is calculated over the latest seven-day period.
- The number of infections per day (Infections.per.day) is the rate at which new infections appear in the data. It is measured as the slope of a linear regression of the Infections curve from the pause in social lockdown to the current day.
- The ratio of recoveries to Infections (Recoveries/Infections) is the calculated ratio as of the current day. One expects that as the virus measures improve and the virus starts receding the recoveries will exceed the infections, a sign the population is getting “better”.
Sample KPI Table
| County | doubling.rate | start.day | end.day | Mean.R | Infections.per.day | Recoveries/Infections |
|---|---|---|---|---|---|---|
| Sonoma | 24.01 | 8 | 96 | 1.2 | 6.04 | 1.27 |
Graph of Estimated R and Daily Infections (left graph)
- The top graph shows the cases per day, as a bar graph.
- The lower graph shows the seven-day moving average estimate of the reproduction number at that time (R), with a horizontal dotted line at the average. The shaded area around the line is the 95% confidence interval for the estimate. Less data means less confidence, of course.
The lower graph below shows how R, the reproduction number, was estimated from the actual Infections data. Reproduction number (R) is the number of new cases an infected individual passed it on to. R greater than 1 means the virus is growing exponentially, less than one means the virus is no longer exploding. The R statistics package EpiEstim was used, assuming an uncertain serial interval (si), the time between contact with an infected person and detection of the disease. This information could be estimated from contact tracing data for individual cases, but counties do not publish it. An average of 4 days was specified, based on studies showing about that for this virus. Standard deviations are just guesses. The package simulates the si distribution as a form of Gamma function, common for this sort of situation.
