petrelharp/context

Issues

• compare full likelihood for TASEP to analytic equation

  #42 opened 3 years ago by petrelharp
  0

• prove something about approximation for full likelihood?

  #41 opened 3 years ago by petrelharp
  0

• remove (or, fixup?) `nestly/`?

  #40 opened 3 years ago by petrelharp
  0

• write fitted() method for contextTree models

  #39 opened 8 years ago by petrelharp
  1

• translate examples to new style and clean up unused code

  #14 opened 8 years ago by petrelharp
  4

• write predictcounts and projectcounts for tree counts

  #37 opened 8 years ago by petrelharp
  1

• add selection to writeup/docs

  #38 opened 8 years ago by petrelharp
  1

• make an R package

  #29 opened 8 years ago by petrelharp
  2

• put all testing scripts in testing-code

  #34 opened 8 years ago by petrelharp
  1

• test json-tree-cpg

  #36 opened 10 years ago by matsen
  2

• investigate multiple peaks in likelihood surface

  #35 opened 10 years ago by matsen
  1

• make sure peel-transmat gets columns in same order as counts file

  #33 opened 10 years ago by petrelharp
  1

• object 'mutrates' not found

  #32 opened 10 years ago by matsen
  3

• with small data, adhoc guess at rate parameters may be NaN

  #8 opened 10 years ago by petrelharp
  1

• write script to get cheap estimates of initial values and scaling for parameters

  #31 opened 10 years ago by petrelharp
  0

• write down curvature of likelihood surface

  #30 opened 10 years ago by petrelharp
  0

• get better guessing or input of tuning parameters

  #24 opened 10 years ago by petrelharp
  1

• Rscript-callable script that parses output and gives summaries

  #23 opened 10 years ago by matsen
  14

• systematic checking of model inference with simulated counts

  #27 opened 10 years ago by matsen
  1

• Add flag for setting random seed in `sim-seq.R` from the command line.

  #28 opened 10 years ago by matsen
  2

• Error: Must specify a long clade name.

  #26 opened 10 years ago by matsen
  0

• Set up Travis for testing our R code

  #25 opened 10 years ago by matsen
  3

• add in tree information to `context` class

  #10 opened 10 years ago by matsen
  0

• script to run mcmc

  #13 opened 10 years ago by petrelharp
  0

• add more stuff to json

  #20 opened 10 years ago by petrelharp
  0

• script to obtain/view residuals

  #12 opened 10 years ago by petrelharp
  2

• make `boundary` flag in JSON to use meangenmatrix

  #22 opened 10 years ago by matsen
  1

• make unit test for Rscript interface

  #21 opened 10 years ago by petrelharp
  0

• We would like the likfun function to automatically have access to the stuff in the context object

  #19 opened 10 years ago by matsen
  2

• make easier way to setup a model

  #7 opened 10 years ago by petrelharp
  2

• remove -g options

  #6 opened 10 years ago by petrelharp
  0

• add a 'context.mcmc' or somesuch object carrying around relevant Bayesian whatnot

  #11 opened 10 years ago by matsen
  1

• count-seq.R expects counttrans to return a matrix

  #17 opened 10 years ago by matsen
  2

• How to avoid parameter sprawl?

  #2 opened 11 years ago by matsen
  6

• Strictify terminology

  #18 opened 10 years ago by matsen
  1

• switch sign so that 'likfun' is actually log likelihood

  #9 opened 10 years ago by matsen
  1

• `getmutpats` errors out

  #15 opened 10 years ago by matsen
  1

• unable to do inference under TASEP

  #16 opened 10 years ago by matsen
  3

• specialize to the case of an observed X(0)

  #4 opened 10 years ago by matsen
  0

• padding, wings, fringe?

  #3 opened 10 years ago by matsen
  2

• Writeup: do we mind a collision of ell's?

  #1 opened 11 years ago by matsen
  0