Bertozzi_PNAS2020: update to match Table 1 of paper

[dilpath]

Some details in #99

I also changed the problem to be a simple SIR model, instead of the reparameterized SIR, but the reparameterization parameters are used in the parameters table, s.t. users can compare their parameter estimates to Table 1 of the original publication. The reparameterization is implemented as an SBML initial assignment rule $\beta = \frac{R_0 \gamma}{N}$.

I also removed some features like lockdown events, since they are irrelevant for reproducing the figure in Table 1 but complicate the simulation.

The scripts were updated to use petab.v1 and support output from petab.Problem.to_files_generic.

Checklist for the submission of new PEtab problems

• [X] The PEtab problem is based on a model that is peer-reviewed and published
• [X] The problem ID is in the format {LAST_NAME_OF_FIRST_AUTHOR}_{ABBREVIATED_JOURNAL_NAME}{YEAR_OF_PUBLICATION}
• [X] The problem ID is in the pull request title
• [X] There is a GitHub issue for this problem
  • [X] The problem ID is in the issue title
  • [X] A brief model description (one or two sentences)
  • [X] A brief data description (one or two sentences)
  • [X] The issue and PR are linked to each other (#99)
  • [X] Differences between the implementation and the original publication are described
  • [X] Experience of fitting / uncertainty analysis (e.g. optimizer used, hyperparameters, reproducibility of best fit)
  • [X] Source of nominal parameters (e.g.: taken from the original publication, or from your own fitting)
• [X] The SBML file
  • [X] Annotation with reference to the original publication (example)
  • [X] The model ID and model name attributes in the SBML model file match the problem name (example)
• [X] PEtab files
  • [X] A "simulated data" measurement table is included, using the nominal parameters
  • [X] A visualization table is included, that can be used with the simulate data to reproduce figures from the original publication
  • [X] The PEtab problem is valid (check with e.g. petablint -vy problem.yaml)
• [X] The PEtab problem author(s) are assigned to the GitHub issue
• [X] The README has been updated with python scripts/overview.py --update
  • [X] The new PEtab problem row in the generated table has the correct reference (and other entries)

[dilpath]

This PR passes CI (see #228, which is branched off this).