harrispopgen/mushi issues and pull requests

#79 - Errors when using `pip3` to install `mushi`

Issue - State: open - Opened by YuchuanXie about 2 months ago

#78 - jax config import

Pull Request - State: open - Opened by theandyb about 2 months ago

#77 - Use forked prox-tv sdist

Pull Request - State: closed - Opened by WSDeWitt almost 3 years ago

#76 - Python upgrade, and other tidying

Pull Request - State: closed - Opened by WSDeWitt almost 3 years ago

#75 - Question on Ksfs

Issue - State: closed - Opened by RenzoTale88 over 3 years ago - 2 comments

#74 - trend penalty piece of cost functions using incorrect difference order

Issue - State: closed - Opened by WSDeWitt over 3 years ago

#73 - Step-by-step guide from mutyper

Issue - State: open - Opened by RenzoTale88 over 3 years ago - 2 comments

#72 - Docs additions

Pull Request - State: closed - Opened by WSDeWitt almost 4 years ago

#71 - Docstrings and doctests

Pull Request - State: closed - Opened by WSDeWitt almost 4 years ago

#70 - Accommodate non-uniform time grid in trend filter

Issue - State: open - Opened by WSDeWitt almost 4 years ago

#69 - spin out `mushi.optimization` module into an independent package

Issue - State: open - Opened by WSDeWitt almost 4 years ago
Labels: enhancement

#68 - version 1 release candidate

Pull Request - State: closed - Opened by WSDeWitt almost 4 years ago - 6 comments

#67 - update docs after pipeline overhaul

Issue - State: closed - Opened by WSDeWitt almost 4 years ago - 1 comment

#66 - pipeline overhaul

Pull Request - State: closed - Opened by WSDeWitt almost 4 years ago - 1 comment

#65 - 63 true divide

Pull Request - State: closed - Opened by WSDeWitt almost 4 years ago

#64 - int division, closes #63

Pull Request - State: closed - Opened by WSDeWitt almost 4 years ago

#63 - `true_divide` error in folded SFS inference with integer SFS data

Issue - State: closed - Opened by WSDeWitt almost 4 years ago - 1 comment

#62 - Inference of eta using folded SFS

Pull Request - State: closed - Opened by apragsdale about 4 years ago - 1 comment

#61 - Tiny bug in pipeline

Issue - State: closed - Opened by terhorst over 4 years ago - 1 comment
Labels: bug

#60 - Folded SFS

Issue - State: closed - Opened by WSDeWitt over 4 years ago - 1 comment
Labels: enhancement

#59 - alternatives to prox-tv dependency

Issue - State: closed - Opened by WSDeWitt over 4 years ago - 4 comments

#58 - duplicate exponent in ridge term

Issue - State: closed - Opened by WSDeWitt over 4 years ago - 1 comment
Labels: bug

#57 - replace total variation / fused lasso with trend filtering

Issue - State: closed - Opened by WSDeWitt over 4 years ago - 2 comments
Labels: enhancement

#56 - docsdev

Pull Request - State: closed - Opened by WSDeWitt over 4 years ago

#55 - Packagify

Pull Request - State: closed - Opened by WSDeWitt over 4 years ago

#54 - mutyper

Issue - State: closed - Opened by WSDeWitt over 4 years ago

#53 - Baseline

Pull Request - State: closed - Opened by WSDeWitt over 4 years ago

#52 - Retool 1 kg pipeline

Pull Request - State: closed - Opened by WSDeWitt over 4 years ago

#51 - data-dependent Gram-Schmidt orthogonalization

Issue - State: closed - Opened by WSDeWitt over 4 years ago - 15 comments

#50 - basic sim notebook gone

Issue - State: closed - Opened by kamdh over 4 years ago

#49 - Add dvipng to dependencies

Issue - State: closed - Opened by kamdh almost 5 years ago

#48 - Ancestral eta fusion

Pull Request - State: closed - Opened by WSDeWitt almost 5 years ago

#46 - Aitchison geometry

Pull Request - State: closed - Opened by WSDeWitt almost 5 years ago - 4 comments

#45 - 40 time calibration

Pull Request - State: closed - Opened by WSDeWitt almost 5 years ago

#44 - remove stdpopsim submodule

Issue - State: closed - Opened by WSDeWitt almost 5 years ago

#43 - Notation standardization & improvement

Issue - State: closed - Opened by kamdh almost 5 years ago - 6 comments

#42 - Three op splitting

Pull Request - State: closed - Opened by WSDeWitt about 5 years ago

#41 - generalize 3-operator splitting to 4 operators

Issue - State: closed - Opened by WSDeWitt about 5 years ago - 1 comment

#40 - time calibration

Issue - State: closed - Opened by WSDeWitt about 5 years ago - 30 comments

#37 - three operator splitting allows negativity

Issue - State: closed - Opened by WSDeWitt about 5 years ago - 23 comments
Labels: bug

#36 - write more tests

Issue - State: closed - Opened by WSDeWitt about 5 years ago

#35 - Update docs to reflect newest requirements

Issue - State: closed - Opened by kamdh about 5 years ago

#34 - Get rid of logy, logZ transformation

Issue - State: closed - Opened by kamdh about 5 years ago - 2 comments

#33 - Autodiff2

Pull Request - State: closed - Opened by WSDeWitt about 5 years ago

#32 - Eta fit

Pull Request - State: closed - Opened by WSDeWitt about 5 years ago

#31 - Optimization

Pull Request - State: closed - Opened by kamdh about 5 years ago - 1 comment

#30 - test-msprime.ipynb broken

Issue - State: closed - Opened by kamdh about 5 years ago

#29 - test.ipynb broken

Issue - State: closed - Opened by kamdh about 5 years ago - 5 comments

#28 - stdpopsim directory empty

Issue - State: closed - Opened by kamdh about 5 years ago - 5 comments

#27 - Optimization

Pull Request - State: closed - Opened by kamdh about 5 years ago

#26 - 1kg

Pull Request - State: closed - Opened by WSDeWitt about 5 years ago

#25 - Hard sv thresh

Pull Request - State: closed - Opened by WSDeWitt about 5 years ago - 1 comment

#24 - heatmaps for matrix vizualization

Pull Request - State: closed - Opened by WSDeWitt about 5 years ago - 2 comments

#23 - Rank regularize

Pull Request - State: closed - Opened by WSDeWitt about 5 years ago

#22 - k-SFS, mutation history matrix, and frequency binning---oh my!

Pull Request - State: closed - Opened by WSDeWitt about 5 years ago

#21 - 11 msprime

Pull Request - State: closed - Opened by WSDeWitt about 5 years ago

#20 - placing msprime mutations according to mushi \mu(t)

Pull Request - State: closed - Opened by WSDeWitt about 5 years ago

#19 - simulation with msprime

Pull Request - State: closed - Opened by WSDeWitt about 5 years ago

#18 - No weight ramp

Pull Request - State: closed - Opened by WSDeWitt about 5 years ago

#17 - Markov random field priors

Issue - State: closed - Opened by WSDeWitt about 5 years ago - 6 comments

#16 - ramping regularization with TMRCA CDF

Issue - State: closed - Opened by WSDeWitt about 5 years ago - 1 comment

#14 - dimension reduction for mutational signatures

Issue - State: closed - Opened by WSDeWitt about 5 years ago

#13 - fused lasso

Issue - State: closed - Opened by WSDeWitt over 5 years ago - 5 comments

#11 - Use "real" coalescent simulation, instead of just the forward model

Issue - State: closed - Opened by WSDeWitt over 5 years ago - 9 comments

#10 - SFS noise model

Issue - State: closed - Opened by WSDeWitt over 5 years ago - 1 comment

#9 - Get rid of shitty xkcd plots

Issue - State: closed - Opened by kamdh over 5 years ago

#8 - Enforcing flatness beyond the coalescent horizon

Issue - State: closed - Opened by WSDeWitt over 5 years ago - 14 comments

#7 - Convergence theory for large n

Issue - State: closed - Opened by WSDeWitt over 5 years ago - 5 comments

#6 - enforcing eta(T) = eta(infty)

Issue - State: closed - Opened by kamdh over 5 years ago - 1 comment

#5 - indexing errors in formulae

Issue - State: closed - Opened by kamdh over 5 years ago - 4 comments

#4 - Gaussian measure to handle asymptotic boundary condition

Issue - State: closed - Opened by WSDeWitt over 5 years ago - 1 comment

#3 - Derive gradient instead of relying on numerical differentiation

Issue - State: closed - Opened by WSDeWitt over 5 years ago - 10 comments

#2 - trapezoidal instead of box quadrature for expected coalescent times

Issue - State: closed - Opened by WSDeWitt over 5 years ago - 1 comment

#1 - push code commit

Issue - State: closed - Opened by kamdh over 5 years ago

GitHub / harrispopgen/mushi issues and pull requests