imma spaghetti coder
235 lines of code changed in 1 file:
more comments
11 lines of code changed in 1 file:
simplified the logic
54 lines of code changed in 1 file:
correcting for some other situations
109 lines of code changed in 1 file:
sequential code
84 lines of code changed in 1 file:
working on more then two matrices case
102 lines of code changed in 1 file:
I cleaned up some things and moved to a proportional framework. S, I and R are now 0 to 1 and sum to 1. There is an additional host population size parameter that scales each of these proportions. I use a delta exchange operator on the proportions.
Also, I fixed most of the mixing issues in a (stupidly) trivial fashion. I had assumed that smaller scaleFactors result in smaller operations. Starting scaleFactors off at 0.99 for recoveryRate and reproductiveNumber fixes most everything.
53 lines of code changed in 3 files:
Reverting accidental change
1 lines of code changed in 1 file:
Keeping source Java 1.5 compatible.
263 lines of code changed in 2 files:
Some cleanup of time keeping.
66 lines of code changed in 3 files:
Streamlining Timeseries Statistics.
27 lines of code changed in 1 file:
ugly but works, just like me
57 lines of code changed in 1 file:
updating Likelihood
20 lines of code changed in 1 file:
Rather than a custom logger, I've switched to statistics that describe time series. Have separate statistics for susceptibles, infecteds, recovereds and effective population size through time. Need to implement user-defined ranges and step sizes in the XML.
107 lines of code changed in 3 files:
commented out a parser
1 lines of code changed in 1 file:
fixed small bug
3 lines of code changed in 1 file:
Starting to implement a time series logger.
284 lines of code changed in 3 files:
Reparameterized transmission rate to R0. This allows me to put a lower limit of 1.0 on R0. Appears to working with simulated data. Need to assume a value on recovery rate for identifiability. Still getting poor acceptance probabilites. However, have had success with an operator that scales S, I and R simultaneously.
scale(sir.reproductiveNumber) 0.0036
scale(sir.susceptibles) 0.0099
scale(sir.infecteds) 0.1221
scale(sir.recovereds) 0.0106
up:sir.susceptibles sir.infecteds sir.recovereds down: 0.3145
35 lines of code changed in 4 files:
I had moved this to forward time. It didn't work very well at all. Too difficult to choose good initial parameter values. Switch back to backward time. Now working on multivariate operators.
70 lines of code changed in 5 files:
Improved MCMC moves for allopolyploid model (diploid root, moves of legs).
234 lines of code changed in 4 files:
updating
24 lines of code changed in 1 file:
Commented changes - still revising
124 lines of code changed in 2 files:
Rolling back SIRModel likelihood.
1 lines of code changed in 1 file:
Convergence issues had been an identifiability problem. Was going to an initial state with non-zero recovereds. I fixed this here by adding a likelihood to the model that prefers zero recovereds. However, this is causing massively slow mixing, because changing any one of the epidemiological parameters pushes the initial recovereds off their mark. Will attempt to move to a forward-simulation approach.
99 lines of code changed in 1 file:
minor changes
63 lines of code changed in 1 file:
sort epoch times
38 lines of code changed in 1 file:
Fixed issue with initial state. However, now there seems to be convergence issues.
44 lines of code changed in 3 files:
Identified bug in DynamicalVariable reset. Everything looks more-or-less in order. Testing now.
16 lines of code changed in 3 files:
I've implemented store/restore in DynamicalSystem and called this from SIRModel. No longer having errors, but something is still wrong.
117 lines of code changed in 4 files:
Streamlined Variable and Force constructors in DynamicalSystem. Interfaced SIRModel with DynamicalSystem. Doing just-in-time extension of timeseries when getValue is called. Compiles and runs, but gives a state-not-restored-correctly error.
164 lines of code changed in 3 files:
new buffer helper
1 lines of code changed in 1 file:
recompiled beagle.jar
0 lines of code changed in 1 file:
Beagle epoch model parser
5 lines of code changed in 1 file:
pass BufferIndexHelper to updateTransitionMatrices
47 lines of code changed in 2 files:
the meat of Beagle epoch model
507 lines of code changed in 1 file:
pass BufferIndexHelper to updateTransitionMatrices
37 lines of code changed in 1 file:
new buffer helper
76 lines of code changed in 1 file:
getBranchIndex signature
2 lines of code changed in 1 file:
helper that knows everything
59 lines of code changed in 1 file:
parser for Beagle epoch model
89 lines of code changed in 1 file:
Implemented linear interpolation for getValue and trapezoidal rule for getIntegral.
71 lines of code changed in 2 files:
Implemented helper classes for dynamical systems. This is designed to simulate partial differential system via the simple Euler method. After forward calculation, can ask for the value at any point in time via fast binary search.
236 lines of code changed in 6 files:
MJTL and ASTL now only take a substitution model as an option (they will extract it from the site model if not given).
9 lines of code changed in 2 files:
Updated skeleton of SIRModel. Includes S, I and R parameters and doesn't crash. Returns dummy likelihood.
93 lines of code changed in 3 files:
Adding interface for epoch models using BEAGLE
318 lines of code changed in 7 files:
Updated BeastMC3 copyright message (uses BeastVersion now).
5 lines of code changed in 1 file:
Adding a CnCs counting class
856 lines of code changed in 8 files:
Adding multiply-labelled tree model. MulSpeciesTreeModel, MulMSCoalescent, MulSpeciesBindings, MulSpeciesTreePrior. Operators MulTreeNodeSlide, MulTreeSequenceReassignment. Plus parsers.
Minor updates to AlloppSpeciesBindings, AlloppSpeciesNetworkModel, the latter dues to changes in logging behaviour.
3530 lines of code changed in 15 files:
Modified EB Poisson smoother for sampling distribution
52 lines of code changed in 1 file:
Implemented saving and loading of 'BEAUti' files using Java Serialization. Seems to work but complex models are not yet tested.
176 lines of code changed in 35 files:
Cleaned up the interface for selecting starting trees.
1 lines of code changed in 1 file:
Cleaned up the interface for selecting starting trees.
123 lines of code changed in 2 files: