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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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a7477a0
Initial mockup of speedups vignette
jamesmbaazam Jun 13, 2024
0374e06
reconstruct difftime objects
jamesmbaazam Jun 13, 2024
86b7b74
Uncomment all the rstan models
jamesmbaazam Jun 13, 2024
750fac7
Run all the rstan models
jamesmbaazam Jun 13, 2024
0d3ee1b
Improve wording
jamesmbaazam Jul 12, 2024
cd06eeb
Improve wording
jamesmbaazam Jul 12, 2024
e0333a2
Improve wording
jamesmbaazam Jul 12, 2024
61b7a44
Apply suggestions from code review
jamesmbaazam Jul 12, 2024
3f5b6cc
Improve various sections
jamesmbaazam Jul 13, 2024
7078883
First successful run of full vignette with exact models
jamesmbaazam Jul 15, 2024
0872c77
Add vb models for rstan and cmdstanr
jamesmbaazam Jul 23, 2024
349a28b
Load posterior package
jamesmbaazam Jul 23, 2024
01e9107
Rename models_configs to model_configs
jamesmbaazam Jul 23, 2024
264c0e1
Run epinow() with purrr safely
jamesmbaazam Jul 23, 2024
ace3421
If the model run into errors, return NA for run time
jamesmbaazam Jul 23, 2024
e5204f1
Break long line of code into new lines
jamesmbaazam Jul 23, 2024
b5940a8
Improve Rt and infection extraction functions to return NA if model r…
jamesmbaazam Jul 23, 2024
928c91c
successful run of all exact models
jamesmbaazam Jul 25, 2024
3bcaa0d
hide chunk results
jamesmbaazam Jul 26, 2024
f42bd3e
if the simulation failed, make the timing an NA of class duration
jamesmbaazam Jul 26, 2024
715857e
Fix Rt typesetting
jamesmbaazam Jul 26, 2024
c7c023e
Add safeguards to return NA if samples don't exist
jamesmbaazam Jul 26, 2024
252151c
Calculate total and real-time CRPS
jamesmbaazam Jul 26, 2024
8950323
add new plots
jamesmbaazam Jul 30, 2024
71a3de4
Revise title
jamesmbaazam Aug 1, 2024
bf06382
Update settings
jamesmbaazam Aug 1, 2024
97a6951
Add chunk options to hide logs
jamesmbaazam Aug 1, 2024
9d9e782
Return NA duration if simulation failed
jamesmbaazam Aug 1, 2024
b77ed09
Remove recommendation of non-mechanistic model
jamesmbaazam Aug 1, 2024
c2f7720
Add text about CRPS versus run time
jamesmbaazam Aug 1, 2024
b0e1d25
Styling
jamesmbaazam Aug 1, 2024
145663e
Return NA score of simulation returned NA
jamesmbaazam Aug 1, 2024
e4ce389
Styling
jamesmbaazam Aug 1, 2024
0e46513
Remove pathfinder and Laplace
jamesmbaazam Aug 1, 2024
0fa6509
Add table of total and real time CRPS
jamesmbaazam Aug 1, 2024
da2094c
Improve test (wording and formatting)
jamesmbaazam Aug 1, 2024
10b6918
Improve vignette
jamesmbaazam Aug 1, 2024
e9bb475
Expand on results
jamesmbaazam Aug 1, 2024
7f2edd5
Re-render vignette
jamesmbaazam Aug 1, 2024
3b30bdb
Add pkgdown field
jamesmbaazam Aug 1, 2024
502f352
Add scoringutils and bookdown to Suggests
jamesmbaazam Aug 1, 2024
be5152d
Switch to Rmarkdown html output
jamesmbaazam Aug 2, 2024
5732121
Improve some sections
jamesmbaazam Aug 2, 2024
3103ec1
Add caveat about bias from R trajectory
jamesmbaazam Aug 2, 2024
239137e
Define rt prior once and use everywhere
jamesmbaazam Aug 2, 2024
937eb91
Improve considerations section
jamesmbaazam Aug 2, 2024
df25187
Change forecast horizon to 7 days
jamesmbaazam Aug 2, 2024
f240725
Change forecast horizon of estimates to 0 days
jamesmbaazam Aug 2, 2024
6f095bb
extensive rewrite and successful compilation
jamesmbaazam Aug 7, 2024
0bd1205
rewrite introduction
jamesmbaazam Sep 18, 2024
826aad9
define new models and improve various sections
jamesmbaazam Oct 17, 2024
c7d30f4
rewrite whole vignette
jamesmbaazam Oct 31, 2024
efe0977
Fix duplicate chunk names
jamesmbaazam Oct 31, 2024
20ea043
Rename Rmd to benchmarks
jamesmbaazam Nov 1, 2024
fc18330
Update pkgdown entry for benchmarks vignette
jamesmbaazam Nov 1, 2024
9a40769
remove plots and vignettes with old old
jamesmbaazam Nov 1, 2024
168d03c
Add mc.cores option
jamesmbaazam Nov 8, 2024
c4ec51b
Add axis labels
jamesmbaazam Nov 8, 2024
48d6d74
Add model basename to model descriptions
jamesmbaazam Nov 8, 2024
9f2bb02
Rename rt_model_gp column to rt_gp_prior
jamesmbaazam Nov 8, 2024
b9abd38
Plot timing as points
jamesmbaazam Nov 8, 2024
45381e4
Plot stationary and non-stationary model results separately
jamesmbaazam Nov 8, 2024
560bab2
Improve the plots
jamesmbaazam Nov 8, 2024
b06c201
Use new column name
jamesmbaazam Nov 8, 2024
db4bf80
Fixes to plots
jamesmbaazam Nov 19, 2024
8f3c566
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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