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Merged
merged 24 commits into from
Feb 20, 2024
Merged

Simulate infections #557

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3a8a3c7
simulate infections function
sbfnk Feb 13, 2024
db62ef3
add test
sbfnk Feb 18, 2024
fd43468
we always need initial infections
sbfnk Feb 13, 2024
a32036f
add missing truncation
sbfnk Feb 13, 2024
4eef015
swap check for seeding time
sbfnk Feb 14, 2024
dfc611e
update extract function to work with simulations
sbfnk Feb 18, 2024
6bdca31
add news item
sbfnk Feb 18, 2024
1b34849
fix typo
sbfnk Feb 20, 2024
81d0423
add more tests
sbfnk Feb 19, 2024
b3533eb
correctly index infections when no delay
sbfnk Feb 19, 2024
c85dbe6
generation times are now zero-indexed
sbfnk Feb 19, 2024
dbeb911
ensure overdispersion is fixed
sbfnk Feb 19, 2024
b0b1e42
improve checks in simulate_infections
sbfnk Feb 19, 2024
7ae6e1a
expand simulate_infections documentation
sbfnk Feb 19, 2024
1da5b24
add simulate_infections snapshot test
sbfnk Feb 19, 2024
af90765
add backend argument
sbfnk Feb 19, 2024
506b7bb
use simpler Poisson for example
sbfnk Feb 19, 2024
f30f13a
single comment hash for package style
sbfnk Feb 19, 2024
bdd5042
re-render documentation
sbfnk Feb 20, 2024
f0bb605
add reviewer
sbfnk Feb 20, 2024
f159f40
only extract `frac_obs` if `obs_scale_sd` exists
sbfnk Feb 20, 2024
c158a94
Apply suggestions from code review
sbfnk Feb 20, 2024
8e2e2d8
add deprecation context and re-render doc
sbfnk Feb 20, 2024
9bf0212
improve documentation
sbfnk Feb 20, 2024
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expand simulate_infections documentation
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@sbfnk
sbfnk committed Feb 20, 2024
commit 7ae6e1a0f05ca9ce950b629f1aee6ce833d16d21
7 changes: 7 additions & 0 deletions R/simulate_infections.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,13 @@
##' Simulations are done from given initial infections and, potentially
##' time-varying, reproduction numbers. Delays and parameters of the observation
##' model can be specified using the same options as in [estimate_infections()].
##'
##' In order to simulate, all parameters that are specified such as the mean and
##' standard deviatoin of delays or observation scaling, must be fixed.
##' Uncertain parameters are not allowed.
##'
##' A previous function called [simulate_infections()] that simulates from a
##' given model fit has been renamed [forecast_infections()].
##' @param R a data frame of reproduction numbers (column `R`) by date (column
##' `date`). R must be numeric and date must be in date format. If any dates
##' are missing, it will be assumed that R stays the same
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8 changes: 8 additions & 0 deletions man/simulate_infections.Rd
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