commit

object function and gradient in python

Sillyness w/ negation

Sillyness w/ negation

Sillyness w/ negation

Add stuff
Comments
Use L-BFGS-B
add docs page
Merge branch 'master' into ratematrix
add reference
lag time
False alarm
Add comment to _ratematrix.pyx and tests for the cython DGEMM interfaces
OpenMP parallel
1. Add OpenMP parallelism to gradient calculation. 2. Add code for computing approximate Hessian, central-limit uncertainties. 3. Fix a bug where we were specifying the transition probabilities backward in the theta vector. Not really a bug, but it meant that theta was actually not the equilibrium probabilities, as I had indicated.
py3 integer division
sparse buildK
starting wok on sparse test_dK_dtheta
sparse
sparse working
typefix
Move some utilities into separate files and get the hessian stuff running w/ sparse
flake8
doc