Add vignette on benchmarking model options#695

Draft

jamesmbaazam wants to merge 66 commits intomainfrom vig-speedup-options

+991

Commits on Dec 11, 2024

Initial mockup of speedups vignette
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reconstruct difftime objects
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Uncomment all the rstan models
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Run all the rstan models
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Improve wording
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Improve wording
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Improve wording
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Apply suggestions from code review
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Improve various sections
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First successful run of full vignette with exact models
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Add vb models for rstan and cmdstanr
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Load posterior package
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Rename models_configs to model_configs
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Run epinow() with purrr safely
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If the model run into errors, return NA for run time
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Break long line of code into new lines
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Improve Rt and infection extraction functions to return NA if model run was an error
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successful run of all exact models
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hide chunk results
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if the simulation failed, make the timing an NA of class duration
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Fix Rt typesetting
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Add safeguards to return NA if samples don't exist
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Calculate total and real-time CRPS
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add new plots
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Revise title
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Update settings
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Add chunk options to hide logs
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Return NA duration if simulation failed
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Remove recommendation of non-mechanistic model
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Add text about CRPS versus run time
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Styling
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Return NA score of simulation returned NA
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Styling
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Remove pathfinder and Laplace
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Add table of total and real time CRPS
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Improve test (wording and formatting)
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Improve vignette
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Expand on results
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Re-render vignette
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Add pkgdown field
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Add scoringutils and bookdown to Suggests
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Switch to Rmarkdown html output
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Improve some sections
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Add caveat about bias from R trajectory
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Define rt prior once and use everywhere
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Improve considerations section
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Change forecast horizon to 7 days
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Change forecast horizon of estimates to 0 days
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extensive rewrite and successful compilation
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rewrite introduction
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define new models and improve various sections
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rewrite whole vignette
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Fix duplicate chunk names
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Rename Rmd to benchmarks
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Update pkgdown entry for benchmarks vignette
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remove plots and vignettes with old old
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Add mc.cores option
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Add axis labels
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Add model basename to model descriptions
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Rename rt_model_gp column to rt_gp_prior
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Plot timing as points
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Plot stationary and non-stationary model results separately
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Improve the plots
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Use new column name
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Fixes to plots
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Append the model descriptions to the plot data
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