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Make epidemic functions directly available #86

Merged
merged 42 commits into from
Aug 11, 2023
Merged

Make epidemic functions directly available #86

merged 42 commits into from
Aug 11, 2023

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pratikunterwegs
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@pratikunterwegs pratikunterwegs commented Aug 8, 2023 •
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This PR is intended to restructure epidemics so as to make the different model functions directly available to users. This replaces the current functionality which hides these functions behind epidemic(model_name = ...). This change fixes #81. @TimTaylor could you check whether this resolves your suggestions in #75?

This PR also:

  1. Cleans up some C++ code so that deterministic ODE models now run about 2x faster (see Benchmarking R-only and Rcpp implementations #62),
  2. Cleans up some documentation around model argument checking and preparation functions, as a WIP on Compress documentation #87.

@pratikunterwegs
Simplify default ODE struct members
848f7af
@pratikunterwegs
Deafult ODE struct operations on temp members
1a24328
@pratikunterwegs
.epidemic_default_cpp takes simpler arguments
1266c0f
@pratikunterwegs
Deafault model args prep returns simplified args
1d85048
@pratikunterwegs
Document .check_args_epidemic_default
e0d4de5
@pratikunterwegs
Add fn epidemic_default_cpp()
cdcb17f
@pratikunterwegs
Rename test-default and use epidemic_default_cpp()
17e5e70
@pratikunterwegs
ODE struct Vacamole: simplify members, use temp members in calcs
7645dc7
@pratikunterwegs
.epidemic_vacamole_cpp() takes simplified arguments
dd987f2
@pratikunterwegs
.prepare_args_epidemic_vacamole returns simplified args
531cfc6
@pratikunterwegs
Add limit checking to infection params for Vacamole
06bed5b
@pratikunterwegs
Minor rearrangement of .epidemic_ebola_cpp()
54ed736
@pratikunterwegs
Reorder parameters and function call in .epidemic_ebola_cpp()
d7db36b
@pratikunterwegs
Simplify ebola model args prep
70f909b
@pratikunterwegs
Rename seir_erlang to epidemic_ebola_r, add epidemic_ebola_cpp
e44d223
@pratikunterwegs
Add epidemic_vacamole_cpp as exposed Rcpp fn
22c8571
@pratikunterwegs
Fn output_to_df takes population as argument
aefb10e
@pratikunterwegs
Correct fn output_to_df() operation on Rcpp matrix output
8485a4e
@pratikunterwegs
Correct for contact reduction > 1.0 in header fn
9cc974c
@pratikunterwegs
Update interventions header for simpler args in ODE structs
0d52ad9
@pratikunterwegs
Update vaccination header for simpler args in ODE structs
405ed28
@pratikunterwegs
Remove fn epidemic()
26eaaee
@pratikunterwegs
Update examples and docs for references to epidemic()
8a34811
@pratikunterwegs
Update RcppExports
003c0e5
@pratikunterwegs
Update vignette with newly exposed fns
837faaf
@pratikunterwegs
Update tests with newly exposed fns
1fffa6f
@pratikunterwegs
Update R documentation files
4337156
@pratikunterwegs
Update WORDLIST
62bae04
@pratikunterwegs
Add newly exposed fns to NAMESPACE
9ad87d3
@pratikunterwegs
Update Readme with new function
5488264
@pratikunterwegs pratikunterwegs mentioned this pull request Aug 9, 2023
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@pratikunterwegs pratikunterwegs merged commit a02fd7c into main Aug 11, 2023
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@pratikunterwegs pratikunterwegs deleted the dev/direct-funs branch August 11, 2023 09:08
@pratikunterwegs pratikunterwegs mentioned this pull request Aug 15, 2023
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Rename and expose C++ model functions directly
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