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Command line workflow

Deconvolving the data

Covvfit takes as an input a data frame containing deconvolved values.

If you use:

  • LolliPop, follow these instructions on how to run LolliPop. (Note that the smoothing can bias the results, so you may need to deconvolve the data again, if you used smoothing.)
  • Freyja, follow these instructions to assemble the outputs into a data frame.

However, in this tutorial we will work with example data, which have already been deconvolved and assembled into a suitable data frame.

Estimating growth advantages

Tutorial to be added in February 2025.