Plan the 4th hackathon

[janaobsteter]

This would now be the 4th hackathon (1st@KIS, 2nd@KIS, 3rd@Roslin, 4th@KIS)!

The outcome of the hackathon will be a new stable version of SIMplyBee - we should fix lots of little things, including GitHub actions, vignette on CRAN, test spatial stuff, etc.

• Papers/Projects

  • Revise Laura's paper
  • Plan the spatial paper
  • Work on the paper for setting individual worker and queen variances
  • Test run and discuss Slovenian honeybee breeding programme

• Speed up the package

  • Check profiling from @janaobsteter what should we speed up Profile the package to identify any computational bottlenecks #378
  • Parallelise MultiColony functions  #513 --> we won't be able to parallelise due to the global SP object :(
  • We need to speed up setMisc and getMisc gaynorr/AlphaSimR#107?

• Testing

  • Figure how Chris is implementing his tests so that they run as part of R CMD check
  • Do we need to pass simParamBee to every AlphaSimR function? #120
  • Implement the above on our side (this will address testthat failing due to SP on R CMD check #86)
  • Add tests for spatial stuff
  • Build tests for getCaste #100
  • Check that the new use of SP$caste and the x@ind == 0 test works as intended #209
  • break and fix vignettes (problem with the .ignore F2*)

• Website

  • Update website and document this process How do we use pkgdown to build a website  #497
  • Ensure all vignettes are on the website and on CRAN (for example see quan gen vignette is missing on cran #506)
  • Move logo to another folder #446

• Polish the package

  • Fix failing cross example #540
  • Consolidate parameter default in functions #170
  • Recurrent: Update NEWS file to summarise key changes between versions  #522
  • Check the beekepers positions in the spatial vignette #529

• GitHub actions

  • Add GitHub actions #514
  • R CMD check on push Implement R CMD check after every commit with GitHub actions #83
  • Publish/Redo website?
  • Code formatting Implement automatic code formatting  #129 Make use of lintr and/or styler automatic (for every commit) #309

• Minor bits

  • Revise last_event slot in the Colony - do we need it? #10
  • Change vignette A to "Introduction to honeybee biology" #511
  • setMisc() is not working on Colony-class and is not present for a MultiColony-class #512
  • Do we need beePedigreeCross()? #515
  • myMapCasteToColonyGv takes checkProduction argument, but it shouldn't #516
  • Do we need species = "GENERIC" in genome simulation? #524
  • getCastePop (getDrones) should not have an argument "removeFathers" #504
  • Remove warning from getCastePop() #496
  • Figure out what is the issue with MultiColony-class.Rd #494
  • Why don't sampling functions use SP$ values as defaults? #462
  • Manage edge cases in value functions  #450
  • Make drone quantitative values truly haploid? #519

[gregorgorjanc]

Closing this - some issues will be addressed in #588