ArtPoon/kamphir

Issues

• Use sequential Monte Carlo instead of MCMC

  #52 opened 9 years ago by ArtPoon
  0

• Reimplement tree shape kernel as C shared library

  #51 opened 9 years ago by ArtPoon
  3

• Subtree kernel may not be positive definite

  #50 opened 9 years ago by rmcclosk
  0

• delimiter + tipdate doesn't work as expected

  #49 opened 9 years ago by rmcclosk
  0

• Rcolgem non-fatal error

  #48 opened 9 years ago by rmcclosk
  0

• Priors don't work

  #47 opened 9 years ago by rmcclosk
  0

• Error in approx()

  #46 opened 9 years ago by ArtPoon
  5

• Maximum recursion depth crash

  #45 opened 9 years ago by ArtPoon
  4

• Repeating serialization error

  #33 opened 9 years ago by rmcclosk
  7

• Don't create an R cluster when ncores = 1

  #34 opened 9 years ago by rmcclosk
  0

• Possible rcolgem off-by-one error

  #35 opened 9 years ago by rmcclosk
  0

• Stop if a non-ultrametric tree is passed without delimiter+position

  #41 opened 9 years ago by rmcclosk
  0

• Zero division error

  #40 opened 9 years ago by rmcclosk
  4

• Getting negative values for coalescent dot-product kernel

  #44 opened 9 years ago by ArtPoon
  3

• Run hangs on OS-X

  #43 opened 9 years ago by ArtPoon
  0

• Missing factor of 2 in kernal computation

  #30 opened 9 years ago by rmcclosk
  1

• Kamphir won't run on cluster

  #39 opened 9 years ago by rmcclosk
  0

• Implement coalescent times kernel

  #36 opened 9 years ago by ArtPoon
  0

• Implement adaptive MCMC for automatically tuning proposal variances

  #37 opened 9 years ago by ArtPoon
  0

• using mclapply within rcolgem locking up Kamphir

  #29 opened 9 years ago by ArtPoon
  11

• rcolgem: Generate sampleStates at respective tip heights

  #25 opened 10 years ago by ArtPoon
  0

• dill crash on cluster

  #28 opened 9 years ago by ArtPoon
  2

• R parallel appears to be only spawning 2 processes in mclapply()

  #10 opened 9 years ago by ArtPoon
  1

• Allow user to set multiple trees as target

  #1 opened 9 years ago by ArtPoon
  2

• rcolgem crash

  #27 opened 9 years ago by ArtPoon
  0

• Bug in simulate.binary.dated.tree.0 [known issue for rcolgem]

  #6 opened 9 years ago by ArtPoon
  1

• Use prior distributions in calculating kernel score

  #4 opened 9 years ago by ArtPoon
  2

• crash in Rcolgem, no trees

  #26 opened 10 years ago by ArtPoon
  1

• IndexError in multiprocessing async_results

  #12 opened 10 years ago by ArtPoon
  1

• pthread_cond_wait: Resource busy

  #11 opened 10 years ago by ArtPoon
  1

• rcolgem: ODE error

  #21 opened 10 years ago by ArtPoon
  2

• Implement change point in ODE for rcolgem

  #23 opened 10 years ago by ArtPoon
  1

• Control-C does not exit kamphir because of multithreading

  #24 opened 10 years ago by ArtPoon
  0

• Method validation

  #14 opened 10 years ago by ArtPoon
  7

• Processing large trees is unusually slow

  #22 opened 10 years ago by ArtPoon
  0

• rcolgem: Object 'v' not found

  #20 opened 10 years ago by ArtPoon
  0

• Seg fault in rcolgem, memory not mapped

  #19 opened 10 years ago by ArtPoon
  1

• Pickle crash

  #18 opened 10 years ago by ArtPoon
  2

• Allow user to set arbitrary Rscript driver

  #3 opened 10 years ago by ArtPoon
  1

• Time-out tree simulation if MASTER takes too long to simulate trees.

  #17 opened 10 years ago by ArtPoon
  2

• MASTER is extremely slow if requesting exact number of tips

  #16 opened 10 years ago by ArtPoon
  1

• Python not waiting for MASTER to complete

  #15 opened 10 years ago by ArtPoon
  0

• Auto-optimization of proposal distribution

  #13 opened 10 years ago by ArtPoon
  0

• NewickIO bug

  #8 opened 10 years ago by ArtPoon
  3

• Restore chain from logfile

  #9 opened 10 years ago by ArtPoon
  0

• Parallelize kernel computation

  #7 opened 10 years ago by ArtPoon
  1

• Error in computing make.fgy() in rcolgem

  #5 opened 10 years ago by ArtPoon
  5

• Parse tip states (labels) from Newick input

  #2 opened 10 years ago by ArtPoon
  0