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install-r-mkl.sh: On the FAS cluster, the default linear algebra libraries used by R are very slow. By following the commands in this file we can compile R from source and link it with Intel MKL, which is an extremely fast linear algebra library. Might not be super necessary but could speed up things. -
scratch.sh: Bunch of bash snippets to run various things on the cluster.
analysis0_cleandata.R: Glen's data cleaning script.subset_testwindow.R: Subset the data to within a window around the test date. For individuals who were tested, we restrict their responses to the time two weeks before and after their first test date. For individuals who ever tested positive, the first test date is the first date positive test. Otherwise, the first test date is the earliest test date. For individuals who were not tested, we use the date one week before their last response as the pseudo test date. We take data two weeks before the pseudo test date and one week after the pseudo test date.household-transmission.R: Study household transmission.testing-behavior.Rmd: Study behavior in response to testing.