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ashokkrish / spatialEpisim

spatialEpisim: Spatial Tracking of Infectious Disease Epidemics using Mathematical Models
GNU General Public License v3.0
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Integrate `spatialEpisim.foundation` into the unstable spatialEpisim branch (`leftover-spaghetti-casserole`) #45

Closed bryce-carson closed 1 month ago

bryce-carson commented 1 month ago

The refactoring in #36 is complete, but remains to be integrated because the foundation package is inaccurate due to ambiguities in the algorithm, as read from the old code and literature. Optimizations must follow after accuracy, so ensuring implementation and documentation is correct are my primary focus for the remainder of the project.

This new issue is opened to reflect that the general refactoring is complete, but that there is still work to be done and this issue will track all issues which will be closed and reopened in the appropriate repository (krishnamurthylab/spatialEpisim.foundation#1, for example). Issues represent bugs in documentation, implementation, or performance.

This issue will be closed when leftover-spaghetti-casserole is merged into unstable.

bryce-carson commented 1 month ago

@ashokkrish, I have published the (working, but inaccurate and slightly bugged) early development version of spatialEpisim.foundation to the drat repository. I will now be integrating it into spatialEpisim in the leftover-spaghetti-casserole branch. 😄 Things will be moving more quickly now.

bryce-carson commented 1 month ago

Significant progress has been made on this issue. I am able to start a Shiny session and can provide most arguments to SVEIRD.BayesianDataAssimilation(), but the application will crash because not all arguments are valid (a front-end issue, not a back-end issue); I need to ensure I provide the correct type of argument and that uploaded data is of the right shape (like the examples in the spatialEpisim.foundation package).