Samuel Jenness

Default of nwstats.formula in multi-layer networks

2

This is currently an issue in extension packages (HIV, COVID) only, but probably should be handled here. With multi-layer networks, it is necessary to explicitly define the `nwstats.formula` for each...

Standardization of nwstats initialization and updating code

4

As detailed here (https://github.com/EpiModel/EpiModelHIV-p/pull/147), there has been some discrepancy in how the lists of nwstats are initialized and saved across core EpiModel and extension packages. There are different methods used...

trackers module should always run at end of time step

2

Because `trackers.FUN` is implicitly defined, it could run in some unintended order in case there are several extension modules passed. We should always execute this module at the end of...

**Periodically (not every release)** 📆 - [ ] Run code coverage analysis using `covr::report(package_coverage())` - [x] Delint package with `lintr::lint_package`. **Before publishing on CRAN** 🔨 - [x] Do a global...

Remove nolint tags when next version of lintr is published

5

@AdrienLeGuillou : I bet you know the answer to this one. `lintr` picks up a "no visible binding" issue, like below: in all cases in EpiModel with we use the...

get_partners option to return positional IDs of index and partner if only.active = TRUE

7

In `get_partners`, can we add an argument, `unique.ids`, with default of `TRUE` that may be set to `FALSE` if `only.active = TRUE`. If only active partners are subset, then the...

Two different options for phylo plots: ```r plot(as.plot.trasmat(tm)) plot(tm, "phylo") ``` with different base options. Also this ```r plot(tm, style = "phylo") ``` generates errors but the positional argument specification...

add set_network helper fx, matching get_network

4

then use in the modules set_network should have at the least an argument `network` for network position

Would follow general approach as sensitivity parameters. For example, sensitivity parameters are passed as vectors like this: ```r param

Explore moving initialization module outside of netsim function

3

This would make the core model consistent with EvoNet, and probably makes excellent sense overall for model building/extensions.