rmcclosk/thesis

Issues

• Grid search experiments: fix or remove

  #54 opened 8 years ago by rmcclosk
  0

• Reference for sampling corresponding to removal

  #53 opened 8 years ago by rmcclosk
  0

• Particles with infinite weights for random networks

  #52 opened 9 years ago by rmcclosk
  0

• Better gamma-alpha correspondence

  #51 opened 9 years ago by rmcclosk
  1

• Find the original reference for transmission trees

  #50 opened 9 years ago by rmcclosk
  0

• Use mixtures to screen for intra-patient samples

  #49 opened 9 years ago by rmcclosk
  2

• Package igraph

  #46 opened 9 years ago by rmcclosk
  1

• Write more documentation

  #41 opened 9 years ago by rmcclosk
  1

• Allow more prior distributions

  #48 opened 9 years ago by rmcclosk
  1

• Subsample Novitsky data

  #47 opened 9 years ago by rmcclosk
  0

• Get data from UK

  #43 opened 9 years ago by rmcclosk
  1

• More detailed logging in ABC

  #20 opened 9 years ago by rmcclosk
  6

• Plot gamma instead of alpha

  #31 opened 9 years ago by rmcclosk
  1

• Implement peer-driven sampling

  #40 opened 9 years ago by rmcclosk
  2

• Clip out HVR from published data

  #44 opened 9 years ago by rmcclosk
  1

• A new name for everything

  #32 opened 9 years ago by rmcclosk
  1

• Initial sampling needs to respect joint priors

  #45 opened 9 years ago by rmcclosk
  0

• Rework species trees / transmission trees section of thesis

  #26 opened 9 years ago by rmcclosk
  0

• Expand uniform priors

  #36 opened 9 years ago by rmcclosk
  1

• Redo ABC experiments with free "m" parameter

  #35 opened 9 years ago by rmcclosk
  1

• Find more real data sets

  #34 opened 9 years ago by rmcclosk
  4

• Unit tests for the main netabc code

  #42 opened 9 years ago by rmcclosk
  0

• Find realistic values of alpha

  #39 opened 9 years ago by rmcclosk
  2

• Make a bimodal distribution on alpha

  #38 opened 9 years ago by rmcclosk
  1

• Compiler error

  #37 opened 9 years ago by rmcclosk
  1

• Test nLTT by itself

  #33 opened 9 years ago by rmcclosk
  1

• Make Sackin's index-based classifiers

  #24 opened 9 years ago by rmcclosk
  1

• Expand priors for China experiments

  #29 opened 9 years ago by rmcclosk
  0

• Update schematics

  #28 opened 9 years ago by rmcclosk
  0

• Restore from saved state

  #30 opened 9 years ago by rmcclosk
  0

• Experiments take too long

  #27 opened 9 years ago by rmcclosk
  0

• Compress intermediate files

  #23 opened 9 years ago by rmcclosk
  0

• Run ABC with different "truth" than was used to tune tree kernel

  #22 opened 9 years ago by rmcclosk
  1

• Figure out guidelines for tree kernel parameters

  #21 opened 9 years ago by rmcclosk
  1

• Speed up expt.py

  #25 opened 9 years ago by rmcclosk
  0

• treekernel segfaults when rbf_variance is too high

  #6 opened 9 years ago by rmcclosk
  1

• netabc setting random seed doesn't work

  #18 opened 9 years ago by rmcclosk
  3

• Some of the ABC simulations are failing

  #17 opened 9 years ago by rmcclosk
  2

• Increase realism for ABC simulations

  #16 opened 9 years ago by rmcclosk
  4

• ladderize was broken

  #19 opened 9 years ago by rmcclosk
  1

• Redo some of the kernel classification experiments with coalescence times

  #12 opened 9 years ago by rmcclosk
  1

• Figure for application note

  #7 opened 9 years ago by rmcclosk
  4

• Rewrite expt.py to use MPI

  #14 opened 9 years ago by rmcclosk
  2

• Implement multiple sampling times

  #11 opened 9 years ago by rmcclosk
  2

• Tree kernel is being computed wrong within ABC-SMC

  #15 opened 9 years ago by rmcclosk
  1

• How to use kernel as distance metric

  #13 opened 9 years ago by rmcclosk
  1

• ABC-SMC is buggy

  #10 opened 9 years ago by rmcclosk
  1

• Remove libR dependency

  #9 opened 9 years ago by rmcclosk
  0

• Try grid search for 1-2 parameter models

  #5 opened 9 years ago by rmcclosk
  1

• Use existing network clusters for phylo clustering validation

  #8 opened 9 years ago by rmcclosk
  1