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Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2

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parksw3/omicron-generation

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Flow

To make the whole project from source (~17 minutes on a new-ish, nice-ish desktop):

git clone https://github.com/parksw3/omicron-generation.git ##
cd omicron-generation
make Makefile
make pullall
## make use_cache
make omicron-generation.pdf

To make just the figures and the manuscript (using cached versions of the calculation files), uncomment the use_cache command

See the rdacache/README.md for more information about the cache.

Organization

The main tex document is in this directory.

  • R/ has some files with R functions
  • scripts/ has programs which do the main analysis
  • figures/ has programs which make the figures
  • rdaout/ is where scripts outputs go
  • rdacache/ is for saved copies of rdaout/ files. The idea is to avoid re-running slow programs, but we haven't yet carefully distinguished slow programs from others

There is a lot of possibly-confusing linking: many of the directories use symbolic links for each other to avoid "../" calls. This is all supposed to be handled smoothly by make.

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Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2

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