mhinsch/rpathsonpaths

Issues

• document data formats (esp. outputs)

  #51 opened 7 years ago by mhinsch
  0

• analysis+results in vignette

  #52 opened 7 years ago by mhinsch
  0

• visnetwork?

  #53 opened 7 years ago by mhinsch
  1

• export to dibbler

  #50 opened 7 years ago by mhinsch
  0

• 'extending rpathsonpaths' vignette

  #49 opened 7 years ago by mhinsch
  0

• Provide network data in a useful format

  #30 opened 8 years ago by mhinsch
  1

• get rid of *all* R CMD check warnings/errors/notes

  #48 opened 7 years ago by mhinsch
  0

• NEWS file

  #47 opened 7 years ago by mhinsch
  0

• Tests!

  #27 opened 7 years ago by mhinsch
  1

• examples in API docs

  #45 opened 7 years ago by mhinsch
  0

• package help page

  #46 opened 7 years ago by mhinsch
  0

• test coverage

  #44 opened 7 years ago by mhinsch
  0

• update documentation!

  #41 opened 7 years ago by mhinsch
  0

• Follow RECON package guidelines

  #3 opened 7 years ago by thibautjombart
  1

• check that rates make sense in 'external' param of popsnetwork

  #40 opened 7 years ago by mhinsch
  0

• Let PopsNetwork objects survive end of R session

  #18 opened 7 years ago by mhinsch
  2

• Handle string vectors instead of factors?

  #22 opened 7 years ago by mhinsch
  2

• check validity of node ids in 'external' param of popsnetwork

  #39 opened 7 years ago by mhinsch
  0

• properly handle NA (basically everywhere)

  #42 opened 7 years ago by mhinsch
  1

• Remove node objects

  #29 opened 7 years ago by mhinsch
  1

• Specify boost dependency

  #36 opened 7 years ago by thibautjombart
  3

• mortality (?)

  #43 opened 7 years ago by mhinsch
  0

• simple frontend for sims with multiple loci

  #37 opened 7 years ago by mhinsch
  2

• mutations outside of LD range

  #38 opened 7 years ago by mhinsch
  1

• Problems with gcc 4.8

  #35 opened 8 years ago by thibautjombart
  6

• make absolute input rates settable in roots

  #33 opened 8 years ago by mhinsch
  0

• ibm needs to normalize allele frequencies after processing a node

  #32 opened 8 years ago by mhinsch
  0

• add IBM

  #25 opened 8 years ago by mhinsch
  0

• uninitialized sources crash the constructor

  #31 opened 8 years ago by mhinsch
  0

• assertions -> exceptions

  #21 opened 8 years ago by mhinsch
  2

• add backwards simulation

  #26 opened 8 years ago by mhinsch
  0

• Be explicit about the different states of PopsNetwork objects

  #14 opened 8 years ago by mhinsch
  2

• Add function to check for duplicate links in edge list

  #24 opened 8 years ago by mhinsch
  1

• Should setAlleleFreqs be restricted to source nodes?

  #13 opened 8 years ago by mhinsch
  1

• Metadata in plots

  #8 opened 8 years ago by mhinsch
  0

• make sure user input can't crash network lib

  #28 opened 8 years ago by mhinsch
  1

• Be clear (in docs and elsewhere) about the precise meaning of the various rate parameters

  #23 opened 8 years ago by mhinsch
  0

• Add case study (Salmonella outbreak) to vignette

  #4 opened 8 years ago by thibautjombart
  1

• Optionally check integrity of user-supplied data in constructor

  #6 opened 8 years ago by mhinsch
  1

• Integer node ids in examples.

  #20 opened 8 years ago by mhinsch
  0

• Ditch column name requirements in function parameters?

  #11 opened 8 years ago by mhinsch
  2

• Allow for metadata to be associated with nodes/edges

  #10 opened 8 years ago by mhinsch
  1

• Use Rcpp's range checked indexing

  #19 opened 8 years ago by mhinsch
  0

• Check for isolated sub-networks without inputs

  #7 opened 8 years ago by mhinsch
  3

• Properly handle networks with missing node ids

  #12 opened 8 years ago by mhinsch
  1

• Allow for non-numeric node ids

  #9 opened 8 years ago by mhinsch
  1

• Proper generation of README and vignettes

  #17 opened 8 years ago by mhinsch
  0

• Proper dependencies in Makefile

  #16 opened 8 years ago by mhinsch
  0

• R shouldn't crash when accidentally accessing a PopsNetwork object after session reload

  #5 opened 8 years ago by mhinsch
  2

• Naming conventions (camelCase -> underscores)

  #15 opened 8 years ago by mhinsch
  1