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Add vignette on benchmarking model options #695

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Add vignette on benchmarking model options #695

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8ecd9d7
Initial mockup of speedups vignette
jamesmbaazam Jun 13, 2024
5c8a9fe
reconstruct difftime objects
jamesmbaazam Jun 13, 2024
4fc58de
Uncomment all the rstan models
jamesmbaazam Jun 13, 2024
a932c6a
Run all the rstan models
jamesmbaazam Jun 13, 2024
e0009e8
Improve wording
jamesmbaazam Jul 12, 2024
bdefe0e
Improve wording
jamesmbaazam Jul 12, 2024
b98626d
Improve wording
jamesmbaazam Jul 12, 2024
97a3b63
Apply suggestions from code review
jamesmbaazam Jul 12, 2024
b21a255
Improve various sections
jamesmbaazam Jul 13, 2024
7053ebd
First successful run of full vignette with exact models
jamesmbaazam Jul 15, 2024
ed7db16
Add vb models for rstan and cmdstanr
jamesmbaazam Jul 23, 2024
a687e31
Load posterior package
jamesmbaazam Jul 23, 2024
dcc5df4
Rename models_configs to model_configs
jamesmbaazam Jul 23, 2024
fb5e820
Run epinow() with purrr safely
jamesmbaazam Jul 23, 2024
9a42ee9
If the model run into errors, return NA for run time
jamesmbaazam Jul 23, 2024
2792e5f
Break long line of code into new lines
jamesmbaazam Jul 23, 2024
f1049a6
Improve Rt and infection extraction functions to return NA if model r…
jamesmbaazam Jul 23, 2024
9417242
successful run of all exact models
jamesmbaazam Jul 25, 2024
3d384bc
hide chunk results
jamesmbaazam Jul 26, 2024
4845690
if the simulation failed, make the timing an NA of class duration
jamesmbaazam Jul 26, 2024
8c0a9c1
Fix Rt typesetting
jamesmbaazam Jul 26, 2024
7a35492
Add safeguards to return NA if samples don't exist
jamesmbaazam Jul 26, 2024
bbf968d
Calculate total and real-time CRPS
jamesmbaazam Jul 26, 2024
3cbdb43
add new plots
jamesmbaazam Jul 30, 2024
776ce63
Revise title
jamesmbaazam Aug 1, 2024
fde6c52
Update settings
jamesmbaazam Aug 1, 2024
8b308e5
Add chunk options to hide logs
jamesmbaazam Aug 1, 2024
e2a2289
Return NA duration if simulation failed
jamesmbaazam Aug 1, 2024
c750058
Remove recommendation of non-mechanistic model
jamesmbaazam Aug 1, 2024
c94dc49
Add text about CRPS versus run time
jamesmbaazam Aug 1, 2024
10ae6bc
Styling
jamesmbaazam Aug 1, 2024
9d38485
Return NA score of simulation returned NA
jamesmbaazam Aug 1, 2024
65be9ff
Styling
jamesmbaazam Aug 1, 2024
f0ddb43
Remove pathfinder and Laplace
jamesmbaazam Aug 1, 2024
7f551fc
Add table of total and real time CRPS
jamesmbaazam Aug 1, 2024
2cc3f78
Improve test (wording and formatting)
jamesmbaazam Aug 1, 2024
1ea9a1d
Improve vignette
jamesmbaazam Aug 1, 2024
68cd3fc
Expand on results
jamesmbaazam Aug 1, 2024
a9dc4cb
Re-render vignette
jamesmbaazam Aug 1, 2024
a9bdb6d
Add pkgdown field
jamesmbaazam Aug 1, 2024
52ac1a7
Add scoringutils and bookdown to Suggests
jamesmbaazam Aug 1, 2024
722d1aa
Switch to Rmarkdown html output
jamesmbaazam Aug 2, 2024
e548d2b
Improve some sections
jamesmbaazam Aug 2, 2024
47cfe00
Add caveat about bias from R trajectory
jamesmbaazam Aug 2, 2024
bde3a89
Define rt prior once and use everywhere
jamesmbaazam Aug 2, 2024
7d131bf
Improve considerations section
jamesmbaazam Aug 2, 2024
beb3354
Change forecast horizon to 7 days
jamesmbaazam Aug 2, 2024
9ebc829
Change forecast horizon of estimates to 0 days
jamesmbaazam Aug 2, 2024
cddb783
extensive rewrite and successful compilation
jamesmbaazam Aug 7, 2024
55bc34c
rewrite introduction
jamesmbaazam Sep 18, 2024
ea27544
define new models and improve various sections
jamesmbaazam Oct 17, 2024
fd71d35
rewrite whole vignette
jamesmbaazam Oct 31, 2024
ca939ca
Fix duplicate chunk names
jamesmbaazam Oct 31, 2024
afb9950
Rename Rmd to benchmarks
jamesmbaazam Nov 1, 2024
8a2a32e
Update pkgdown entry for benchmarks vignette
jamesmbaazam Nov 1, 2024
180a39a
remove plots and vignettes with old old
jamesmbaazam Nov 1, 2024
f246391
Add mc.cores option
jamesmbaazam Nov 8, 2024
3571cc3
Add axis labels
jamesmbaazam Nov 8, 2024
12bb72f
Add model basename to model descriptions
jamesmbaazam Nov 8, 2024
e44394f
Rename rt_model_gp column to rt_gp_prior
jamesmbaazam Nov 8, 2024
68ad9a4
Plot timing as points
jamesmbaazam Nov 8, 2024
9f3be5f
Plot stationary and non-stationary model results separately
jamesmbaazam Nov 8, 2024
c09d5ea
Improve the plots
jamesmbaazam Nov 8, 2024
cb9ba77
Use new column name
jamesmbaazam Nov 8, 2024
19a462f
Fixes to plots
jamesmbaazam Nov 19, 2024
d156d22
Append the model descriptions to the plot data
jamesmbaazam Nov 19, 2024
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1 change: 1 addition & 0 deletions DESCRIPTION
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Expand Up @@ -135,6 +135,7 @@ Suggests:
precommit,
progressr,
rmarkdown,
scoringutils,
spelling,
testthat,
usethis,
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2 changes: 2 additions & 0 deletions _pkgdown.yml
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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:
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