Gregor Gorjanc

Website: point to Owen's "mechanistic model" simulation

1

Owen used AlphaSimR for "mechanistic" simulations. It would be neat to point to that simulation work in the forthcoming website.

**Is your feature request related to a problem? Please describe.** Some users are confused with SimParam errors, because error messages are not clear. **Describe the solution you'd like** Can we...

Implement tree sequence

4

This is a big one and a project on its own, but here are some initial ideas * use tskit C library to store tree sequence? * import tree sequence,...

Write vignette on recombination

3

**Is your feature request related to a problem? Please describe.** There is no documentation how recombinations are simulated. **Describe the solution you'd like** A short vignette describing the implemented recombination...

* plant breeding: wheat, maize, clonal, forage, ... (Jon & Philip) see code at https://github.com/HighlanderLab/jbancic_alphasimr_plants * animal breeding: beef, dairy, layer, ... (WHO!?) * pkg-down like slendr.net

Follow `newEmptyPop()` and add function to create empty MultiPop - this is mostly for programming use and edge cases.

Write vignette on how to modify runMacs() and how to use other simulators for founders

3

Essentially turn this script into https://github.com/gaynorr/AlphaSimR_Examples/blob/master/misc/ManualMaCS.R https://github.com/gaynorr/AlphaSimR_Examples/blob/master/misc/msprime.R and show how to bring in stdpopsim results and SlendR results too

Write vignette on how to import data

1

Turn https://github.com/gaynorr/AlphaSimR/discussions/118 into Rmd and maybe add more text

Expand the MultiPop functionality

7

Work with Philip on * renaming MegaPop to MultiPop * looking into S4 method dispatch * expanding other/some AlphaSimR functions so they all work with MultiPop (what are the design...

Expand getPed() with a recursive argument

1

**Describe the solution you'd like** We would like to call `getPed()` and get deep pedigree **Additional context** Currently we get 1 generation, so maybe that could stay as default, but...