The Analytic Garden

The omicron variant of concern (VOC) has been circulating world wide for about two months. I thought it would be interesting to look at its growth rate compared to the currently predominate delta strain.  On December 29 2021, I downloaded metadata for 6,553,878 sequences from GISAID . A question arises about whether GISAID sequence data is a representative sample of the world COVID-19 situation.  Here are the top ten countries submitting sequences: Country Count USA 2077490 United Kingdom 1586855 Germany 309670 Denmark 278104 Canada 230413 Japan 185716 France 174125 Sweden 138151 Switzerland 102008 India 99823 temp <- meta_data %>% select(Location) %>% separate(Location, c( "Region" , "Country...

  I really do. I want to like Julia . There is much to like: a great REPL , multiple dispatch ; concurrent, parallel, and distributed computing;  direct calling of C and Fortran libraries; dynamic type system; nice package manager; macros, etc. There are problems with Julia that may be showstoppers for me. My usual workflow with Python, R, Java, or C++ is to write code in small pieces and incrementally test, building the program one routine at a time. For example, I typically write the input routine, test; write the data processing steps, one step at a time and test; write plotting routines and test. Test the whole program and fix any problems. I really should write the tests first like I tell students, but sometimes I cheat.  The process described above is common. Julia makes approaching programming in that manner frustrating. The source of the frustration is compile time latency . Julia's  JIT compiler results in great execution speeds, but you pay a price each ti...

The first step toward change is awareness. The second step is acceptance.  ~ Nathaniel Branden There is nothing permanent except change. ~ Heraclitus I previously looked at the problem of segmenting a time series. Segmenting involves discovering points in the series where there is change. One question arises immediately; when what changes?  In a previous post , we tried to segment the series based on changes to the parameters of a probability distribution or on discovering outliers in the trend discovered by a Kalman filter. Bayesian Change Point Again Here's the data from the previous post. This is  temperature anomaly  data from the   NASA Global Climate Change  site. We could think of this data as a series of linear segments. Each segment has a mean. The data in each segment is scattered around the linear line segments. Within each segment, we assume the mean is constant. The mean is described by an intercept and slope. The data points are scatt...

This disease, called COVID 19, will be over much sooner than you think. Christian people all over this country, praying, have overwhelmed it. ~  Kenneth Copeland With everything going on with COVID, you don't know what's going to happen. ~ Demetrius Andrade Here are the current 7-day moving averages of cases in the five county area in NY's Capital Distract.  The data is from  https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-counties.csv .  It's depressing that despite vaccination we are at approximately at the same case-load as December 2020. In July 202, we were down to essentially no cases. What happened. Delta happened, school started, the weather got colder, more time indoors, people got tired of masks and social distancing, people refused to get vaccinated, vaccine effectiveness declined. Lots happened. It looks like we might reach the January-February 2021 peak in cases in early 2022. Here's the code for producing this plot. #' plot_cou...