petrelharp context issues

petrelharp / context

Context-dependent mutation rate inference machinery.

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compare full likelihood for TASEP to analytic equation

#42 petrelharp opened 2 years ago
0
prove something about approximation for full likelihood?

#41 petrelharp opened 2 years ago
0
remove (or, fixup?) `nestly/`?

#40 petrelharp opened 2 years ago
0
write fitted() method for contextTree models

#39 petrelharp closed 7 years ago
1
add selection to writeup/docs

#38 petrelharp closed 7 years ago
1
write predictcounts and projectcounts for tree counts

#37 petrelharp closed 7 years ago
1
test json-tree-cpg

#36 matsen opened 9 years ago
2
investigate multiple peaks in likelihood surface

#35 matsen opened 9 years ago
1
put all testing scripts in testing-code

#34 petrelharp closed 7 years ago
1
make sure peel-transmat gets columns in same order as counts file

#33 petrelharp closed 9 years ago
1
object 'mutrates' not found

#32 matsen closed 9 years ago
3
write script to get cheap estimates of initial values and scaling for parameters

#31 petrelharp opened 9 years ago
0
write down curvature of likelihood surface

#30 petrelharp opened 9 years ago
0
make an R package

#29 petrelharp closed 7 years ago
2
Add flag for setting random seed in `sim-seq.R` from the command line.

#28 matsen closed 9 years ago
2
systematic checking of model inference with simulated counts

#27 matsen closed 9 years ago
1
Error: Must specify a long clade name.

#26 matsen closed 9 years ago
0
Set up Travis for testing our R code

#25 matsen opened 10 years ago
3
get better guessing or input of tuning parameters

#24 petrelharp closed 9 years ago
1
Rscript-callable script that parses output and gives summaries

#23 matsen closed 9 years ago
14
make `boundary` flag in JSON to use meangenmatrix

#22 matsen closed 10 years ago
1
make unit test for Rscript interface

#21 petrelharp opened 10 years ago
0
add more stuff to json

#20 petrelharp closed 10 years ago
0
We would like the likfun function to automatically have access to the stuff in the context object

#19 matsen closed 10 years ago
2
Strictify terminology

#18 matsen opened 10 years ago
1
count-seq.R expects counttrans to return a matrix

#17 matsen closed 10 years ago
2
unable to do inference under TASEP

#16 matsen closed 10 years ago
3
`getmutpats` errors out

#15 matsen closed 10 years ago
1
translate examples to new style and clean up unused code

#14 petrelharp closed 7 years ago
4
script to run mcmc

#13 petrelharp closed 10 years ago
0
script to obtain/view residuals

#12 petrelharp closed 10 years ago
2
add a 'context.mcmc' or somesuch object carrying around relevant Bayesian whatnot

#11 matsen closed 10 years ago
1
add in tree information to `context` class

#10 matsen opened 10 years ago
0
switch sign so that 'likfun' is actually log likelihood

#9 matsen closed 10 years ago
1
with small data, adhoc guess at rate parameters may be NaN

#8 petrelharp closed 9 years ago
1
make easier way to setup a model

#7 petrelharp closed 10 years ago
2
remove -g options

#6 petrelharp closed 10 years ago
0
Em pass

#5 matsen closed 10 years ago
1
specialize to the case of an observed X(0)

#4 matsen closed 10 years ago
0
padding, wings, fringe?

#3 matsen closed 10 years ago
2
How to avoid parameter sprawl?

#2 matsen opened 10 years ago
6
Writeup: do we mind a collision of ell's?

#1 matsen closed 10 years ago
0