epidemics v0.3.0 - Githubissues

epiverse-trace / epidemics

A library of published compartmental epidemic models, and classes to represent demographic structure, non-pharmaceutical interventions, and vaccination regimes, to compose epidemic scenarios.

https://epiverse-trace.github.io/epidemics/

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epidemics v0.3.0 #217

Closed pratikunterwegs closed 2 months ago

pratikunterwegs commented 2 months ago

This PR is working towards a v0.3.0 release by checking off items in #216.

pratikunterwegs commented 2 months ago

Some issues thrown up that are worth keeping in mind:

R CMD check requires RcppEigen to be in Imports, but devtools::check(remote = TRUE, manual = TRUE) throws a note that it should "probably only be in LinkingTo", but this addition is IIRC autogenerated by {usethis};
LaTeX issues throw up a warning;
‘epidemics-manual.tex’ is generated at some point which throws a note;
https://opensource.org/license/mit/ connection times out on some networks, throwing a note;
HTML version of the manual on MacOS throws issues which generate a note.

github-actions[bot] commented 2 months ago

This is how benchmark results would change (along with a 95% confidence interval in relative change) if 376cc99d50e1884e0fd90b746a7b39416c64701f is merged into main:

:heavy_check_mark:default_ode: 10.8ms -> 10.7ms [-2.28%, +0.26%]
:heavy_check_mark:default_ode_interventions: 73.8ms -> 73.6ms [-1.27%, +0.88%]
:heavy_check_mark:default_ode_param_vec: 825ms -> 825ms [-0.68%, +0.74%]
:heavy_check_mark:default_ode_paramvec_intervs: 6.27s -> 6.26s [-0.72%, +0.44%]
:heavy_check_mark:ebola: 623ms -> 625ms [-0.63%, +1.1%] Further explanation regarding interpretation and methodology can be found in the documentation.