Changed saved prior predictive data #478
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This also splits figure saving from data saving
Try this Pull Request!Open Julia and type: import Pkg
Pkg.activate(temp=true)
Pkg.add(url="https://github.com/CDCgov/Rt-without-renewal", rev="477-change-saved-prior-predictive-data", subdir="EpiAware")
using EpiAware |
seabbs
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Oct 7, 2024
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## 404-upgrade-the-testmode-pipeline-script-to-just-pipeline-script #478 +/- ##
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…ne-script' into 477-change-saved-prior-predictive-data
seabbs
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404-upgrade-the-testmode-pipeline-script-to-just-pipeline-script
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…dictive + full (#445) * remove most compat from pipeline * Update test_pipelinefunctions.jl * Fix the truthdata output to be missing or Int * change to daily increments in latent processes * Change default AD mode to ReverseDiff{true} * Create changelog.md * reformat * change filename * Update simulate.jl * add a testmode to pipelinetypes * tighten typing * fix constructor * fix constructor * pipeline helper functions * unit tests and end-to-end tests * remove old scripts * Fix y_t type * bring inference prefixing into line with truthdata prefixing * reformat * interim commit * rename and collect plot functions * tidy up tests * basic plots to Makie * new plot tests and test reorganisation * Update runtests.jl * reformat * 455 plotting methods of prior predictive (#462) * add priorpredictive method to make_inference * Add pipeline priorpredictive boolean * reformat * remove inference_method kwarg because can be dispatched on * remove specialisation on forecast results add missing handling as well * move inference step into own function and give fail cover with error report * remove passing inference_method * add a latent model name to InferenceConfig * Util for setting up PI levels * prior pred plot * export prior_predictive_plot * remove dead end-to-end test in favour of direct test of prior_predictive_plot * Make pipeline inference tests more focused (#475) * fix tests and capture forecasting failures * delete stale end-to-end test * Full priorpred check pipeline script (#476) * Hotfix: Doc link to main * create xexpy function with x = 1 typestable (#473) * rename data folder * catch bug where objects were getting saved to root dir * fix bug where being saved to root * add priorpredictive mode to the inference config struct * do_truthdata behaviour modifed by prior predictive * send priorpredictive mode in generate_inference * update tests * prior predictive pipeline * reformat --------- Co-authored-by: Sam Abbott <[email protected]> * Add oneexpy to pipeline (#480) * Changed saved prior predictive data (#478) * change to pipeline being part of InferenceConfig This also splits figure saving from data saving * fix passed var * change serialisation target dir * update tests and config usage to pass pipeline object --------- Co-authored-by: Sam Abbott <[email protected]> * Update run_priorpred_pipeline.jl * Only save strings rather than Exception objects --------- Co-authored-by: Sam Abbott <[email protected]>
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This PR changes the serialisation behaviour of the pipeline to reduce unnecessary objects being serialised (less important) and deals with problems in deserialising around reconstructing arbitrary Julia types (more important).
Closes #477 .
NB: While doing this PR, I was passing more pipeline data to
infer... so it became easier to just pass thepipelinestruct instance. This lets us select the inference post-processing based on the pipeline (e.g. testmode, priorpredictive etc). There might be a slicker way to do this which we can revisit in the future.