Write model run outputs #41
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zsusswein
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zsusswein
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natemcintosh
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Note on this that I don't know that there is an issue describing the plan for this PR (?) so in reviewing I am somewhat unsure what the goals are. |
kgostic
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To fix weirdness with unicode parsing error from.....somewhere?
Co-authored-by: Adam Howes <[email protected]>
for more information, see https://pre-commit.ci
Co-authored-by: Katie Gostic (she/her) <[email protected]>
Co-authored-by: Adam Howes <[email protected]>
Co-authored-by: Katie Gostic (she/her) <[email protected]>
Co-authored-by: Katie Gostic (she/her) <[email protected]>
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The failing check is a known, unrelated issue. It's being handled in #60 |
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* Ignore CI/CD stuff in Rbuildignore * Extract diagnostics from fitted model * Basic output schema * Use `.pre-commit.config.yaml` from main To fix weirdness with unicode parsing error from.....somewhere? * Update output schema * Bump NEWS * Bump NEWS * Expand on readme * Use setequal for column name checks h/t @natemcintosh * Apply suggestions from code review Co-authored-by: Adam Howes <[email protected]> * Update with Adam's review * Update R/write_output.R * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update R/extract_diagnostics.R Co-authored-by: Katie Gostic (she/her) <[email protected]> * Add alert with dates for low case count diagnostic * Apply suggestions from code review Co-authored-by: Adam Howes <[email protected]> * Use new R-universe Stan repository * Update README.md Co-authored-by: Katie Gostic (she/her) <[email protected]> * Update README.md Co-authored-by: Katie Gostic (she/her) <[email protected]> * Condense dir creation * Expose quantiles for summarization * Save the description of the different EpiNow2 params * Add comment explaining why dates work * Clarify comment on EpiNow2 param outputs * Add `reports` to output --------- Co-authored-by: Adam Howes <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Katie Gostic (she/her) <[email protected]>
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At long last, the output schema PR is ready to go. There are a few actions failing; these should be ignored (see #49). I'm sorry about the size here -- it's really much fewer than ~1200 lines of code, but still not awesome of me.
These are the functions and documentation to go from fitted EpiNow2 model to a directory of outputs ready to be uploaded to Azure Blob. I feel good about all the functionality and that the schema includes most of what we want (in particular both pre- and post-nowcast cases).
It would be particularly helpful to get review on: