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Add vignette on benchmarking model options #695

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a3021b4
Initial mockup of speedups vignette
jamesmbaazam Jun 13, 2024
85e3595
reconstruct difftime objects
jamesmbaazam Jun 13, 2024
83188fc
Uncomment all the rstan models
jamesmbaazam Jun 13, 2024
c90550d
Run all the rstan models
jamesmbaazam Jun 13, 2024
85e56e5
Improve wording
jamesmbaazam Jul 12, 2024
2d2bd6a
Improve wording
jamesmbaazam Jul 12, 2024
4f2f6a3
Improve wording
jamesmbaazam Jul 12, 2024
5fe1ef6
Apply suggestions from code review
jamesmbaazam Jul 12, 2024
430bb7e
Improve various sections
jamesmbaazam Jul 13, 2024
54afa0c
First successful run of full vignette with exact models
jamesmbaazam Jul 15, 2024
eb80a88
Add vb models for rstan and cmdstanr
jamesmbaazam Jul 23, 2024
f93e1c6
Load posterior package
jamesmbaazam Jul 23, 2024
a9f10a8
Rename models_configs to model_configs
jamesmbaazam Jul 23, 2024
4a9c8ae
Run epinow() with purrr safely
jamesmbaazam Jul 23, 2024
2e62a80
If the model run into errors, return NA for run time
jamesmbaazam Jul 23, 2024
31e20b3
Break long line of code into new lines
jamesmbaazam Jul 23, 2024
e9aca7a
Improve Rt and infection extraction functions to return NA if model r…
jamesmbaazam Jul 23, 2024
ed7487a
successful run of all exact models
jamesmbaazam Jul 25, 2024
efe777d
hide chunk results
jamesmbaazam Jul 26, 2024
ae6c95d
if the simulation failed, make the timing an NA of class duration
jamesmbaazam Jul 26, 2024
1501654
Fix Rt typesetting
jamesmbaazam Jul 26, 2024
0fc2b83
Add safeguards to return NA if samples don't exist
jamesmbaazam Jul 26, 2024
6212c78
Calculate total and real-time CRPS
jamesmbaazam Jul 26, 2024
7a24953
add new plots
jamesmbaazam Jul 30, 2024
1cae55e
Revise title
jamesmbaazam Aug 1, 2024
7aef464
Update settings
jamesmbaazam Aug 1, 2024
da96bea
Add chunk options to hide logs
jamesmbaazam Aug 1, 2024
8cbd7e2
Return NA duration if simulation failed
jamesmbaazam Aug 1, 2024
0ece6c0
Remove recommendation of non-mechanistic model
jamesmbaazam Aug 1, 2024
30be57f
Add text about CRPS versus run time
jamesmbaazam Aug 1, 2024
fc310f5
Styling
jamesmbaazam Aug 1, 2024
36fbc91
Return NA score of simulation returned NA
jamesmbaazam Aug 1, 2024
4cb0977
Styling
jamesmbaazam Aug 1, 2024
64e2422
Remove pathfinder and Laplace
jamesmbaazam Aug 1, 2024
5605761
Add table of total and real time CRPS
jamesmbaazam Aug 1, 2024
18af0db
Improve test (wording and formatting)
jamesmbaazam Aug 1, 2024
d99fa68
Improve vignette
jamesmbaazam Aug 1, 2024
5925739
Expand on results
jamesmbaazam Aug 1, 2024
8b86f23
Re-render vignette
jamesmbaazam Aug 1, 2024
50fe2c9
Add pkgdown field
jamesmbaazam Aug 1, 2024
680db44
Add scoringutils and bookdown to Suggests
jamesmbaazam Aug 1, 2024
cb5abc2
Switch to Rmarkdown html output
jamesmbaazam Aug 2, 2024
56cdd0f
Improve some sections
jamesmbaazam Aug 2, 2024
35dd9ee
Add caveat about bias from R trajectory
jamesmbaazam Aug 2, 2024
f262b36
Define rt prior once and use everywhere
jamesmbaazam Aug 2, 2024
47a467f
Improve considerations section
jamesmbaazam Aug 2, 2024
10a3c62
Change forecast horizon to 7 days
jamesmbaazam Aug 2, 2024
d7555fc
Change forecast horizon of estimates to 0 days
jamesmbaazam Aug 2, 2024
eabc090
extensive rewrite and successful compilation
jamesmbaazam Aug 7, 2024
963e221
rewrite introduction
jamesmbaazam Sep 18, 2024
6af7368
define new models and improve various sections
jamesmbaazam Oct 17, 2024
22e477c
rewrite whole vignette
jamesmbaazam Oct 31, 2024
e06bfc7
Fix duplicate chunk names
jamesmbaazam Oct 31, 2024
1dbcc04
Rename Rmd to benchmarks
jamesmbaazam Nov 1, 2024
0fd36f2
Update pkgdown entry for benchmarks vignette
jamesmbaazam Nov 1, 2024
7aa3c09
remove plots and vignettes with old old
jamesmbaazam Nov 1, 2024
bee1bbd
Add mc.cores option
jamesmbaazam Nov 8, 2024
acfb32a
Add axis labels
jamesmbaazam Nov 8, 2024
d1a83f8
Add model basename to model descriptions
jamesmbaazam Nov 8, 2024
251fff7
Rename rt_model_gp column to rt_gp_prior
jamesmbaazam Nov 8, 2024
616cd6d
Plot timing as points
jamesmbaazam Nov 8, 2024
ed12ac0
Plot stationary and non-stationary model results separately
jamesmbaazam Nov 8, 2024
82bcb12
Improve the plots
jamesmbaazam Nov 8, 2024
f320b29
Use new column name
jamesmbaazam Nov 8, 2024
01d0132
Fixes to plots
jamesmbaazam Nov 19, 2024
f2ecafd
Append the model descriptions to the plot data
jamesmbaazam Nov 19, 2024
11f9faf
Clarify intro paragraphs
jamesmbaazam Jan 21, 2025
18b70d9
Use new interfaces
jamesmbaazam Jan 21, 2025
2876e26
Move out inline code in plotting code
jamesmbaazam Jan 21, 2025
1ae7f88
Improve text
jamesmbaazam Jan 21, 2025
f97bec6
Modularise extraction steps
jamesmbaazam Jan 21, 2025
56d36b1
Drastic rewrite and restructuring
jamesmbaazam Jan 21, 2025
e740945
More rewriting, combining of chunks, and modularising
jamesmbaazam Jan 22, 2025
923faa4
more updates
jamesmbaazam Jan 23, 2025
097ff33
Use purrr::map_depth to simplify nested lapply
jamesmbaazam Jan 27, 2025
48a2167
update vignette
jamesmbaazam Jan 28, 2025
76e9161
update vignette
jamesmbaazam Jan 28, 2025
b6e89ac
Add captions and update key takeaways
jamesmbaazam Jan 28, 2025
8f82327
update vignette
jamesmbaazam Jan 29, 2025
b362c9c
render vignette
jamesmbaazam Jan 29, 2025
ed9646d
Delete EpiNow2.Rproj
jamesmbaazam Jan 29, 2025
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1 change: 1 addition & 0 deletions DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -135,6 +135,7 @@ Suggests:
precommit,
progressr,
rmarkdown,
scoringutils,
spelling,
testthat,
usethis,
Expand Down
18 changes: 0 additions & 18 deletions EpiNow2.Rproj

This file was deleted.

2 changes: 2 additions & 0 deletions _pkgdown.yml
Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,8 @@ navbar:
href: articles/estimate_infections_options.html
- text: Using epinow() for running in production mode
href: articles/epinow.html
- text: Model benchmarks
href: articles/benchmarks.html
casestudies:
text: Case studies
menu:
Expand Down
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Binary file added vignettes/benchmarks-crps-plotting-rt-total-1.png
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Binary file added vignettes/benchmarks-process-runtimes-1.png
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