diff --git a/vignettes/design-principles.Rmd b/vignettes/design-principles.Rmd index 3e5bd0ba..2269375f 100644 --- a/vignettes/design-principles.Rmd +++ b/vignettes/design-principles.Rmd @@ -41,11 +41,14 @@ This document is primarily intended to be read by those interested in understand ## Overview -### Transmission chains and branching processes +## Dependencies -Branching processes are stochastic models that provide a simple way -to model the early phase of an outbreak. They only require data on -cases and are useful for drawing inferences on $R_0$ [@farrington2003]. +* Input validation: + - [checkmate](https://github.com/mllg/checkmate/): exports many `test_*()`, + `check_*()` and `assert_*()` functions and is available on CRAN. +* Fast data manipulation: + - [data.table](https://rdatatable.gitlab.io/data.table/): provides a + high-performance version of base R’s ``. Branching processes have some limitations. For instance, they do not not take into account the depletion of susceptibles in the population. Additionally, @@ -320,28 +323,3 @@ tagged columns using [linelist](https://github.com/reconhub/linelist) package. * functions for decomposing case count time series into linelists with tagged columns (not aware of packages for achieving this). - -### Dependencies - -This new architecture might require the following dependencies: - -* For handling simulations: - - - [epicontacts](https://github.com/reconhub/epicontacts/): for -shared s3 methods??? (TBC) - - [projections](https://github.com/reconhub/projections/): for -shared summary, print, and visualization methods?? (TBC) - - [simulacr](https://github.com/reconhub/simulacr/): for -shared summary, print, and visualization methods?? (TBC) - - [linelist](https://github.com/reconhub/linelist/): for tagging - linelists as raw inputs into `epichains`?? (TBC) - -* Visual outlook: - - - [cli](https://github.com/r-lib/cli/) for printing -messages, errors, warnings, progress bar, and other user-facing features. - -* Input validation: - - - [checkmate](https://github.com/mllg/checkmate/) for input validation. -