Got infectives and susceptibles indices working in class Population.  Now to implement occults and tidy the interface.

Built infective and susceptible indices in Population<> template.  Messy!  Added Mcmc class to get the interface requirements to Population<> a bit clearer.

Added STLIndex.hpp template to Framework.  This might well prove *very* useful!

At the stage of testing a likelihood calculation

Added code to calculate integrated infectious pressure

Added code to calculate integrated infectious pressure

Converted SpatPointPop to make use of Boost::multi_index_container.  This is a pretty awesome bit of software!!

Added random number generation class.  This is basically a wrapper round GSL, but will use (eventually) SPRNG.

Irrelevant commit squash

Got basic inference on tx parameters working.  Now to implement the infection times!

Commit squash

Implemented distance limiting in the beta functions.  Swapped exp for ACML fastexp function.

Moved product calculation in likelihood to its own private method in Mcmc

Moved integral calculation to its own private method in Mcmc.  Small performance trade off, but only slight.

Debugging stage in the code.  Currently, -nans are cropping up in the adaptive covariance matrix.  Requires to be sorted!

Fixed bug in product caching

Now have a working MCMC algorithm capable of infering tx params and infection times.  Still require to implement the RJ for occults

First steps to implementation of MPI parallelisation for the MCMC.  Got the build system sorted.  Parallelised just the tx parameters so far.  Still need to sort out the parallel implementations in the parameter writer system before I can test the code

Almost perfected the tx parameter update.  Looks awesomely fast!

Now have working code for the MPI parallel version

Got first attempt at parallelising the infection time update.  This is hard, since keeping the distributed product cache consistent is proving challenging.  This version, therefore, does away with the product cache, and therefore calculates the product from scratch.  The major rate limiting step appears to be the serialised update of the movee's integrated infection pressure.  This could be inlined to improve performance, though.

Working 3rd generation MPI code.  Scalability still leaves a lot to be desired, though it should be possible to concatenate the infection time (id,time) proposal tuple to reduce messaging time.

Packaged Infection time proposal into a struct.  Makes very little difference to the runtime and scalability.

Reduced message passing to just an all_reduce for the loglikelihood.  This improves scalability somewhat, though we are still limited by the fact that the message passing takes as long as the infection time update step.

Code for adding and removing occults added, but not yet tested or debugged

Corrected bug in the Framework Makefile.am.  Removed linking to the ACML libraries.  This should be added as a configure option IMHO

Replaced sequenced index with random access index in SpatPointPop.  Implemented timed dynamic load balancing function in Mcmc class.  This times the average time that a processor takes to calculate an element of the integral sum, and redistributes the elements of the sum according to processor speed.  *However*, on the Warwick HPC, we are sometimes getting lame nodes which appear to not be timing themselves correctly.  Not sure why.  Therefore, chunk-based dynamic load balancing may be a better option,despite the increase in message passing.

Removed faulty load balancing code, needs further work, but currently getting the model mixing right is more important.

Found bug in the adaptive empirical covariance matrix class.  Fixed.  FMD model extended to include species, etc.  Trialing on francesca.

Messing about with the algorithm to improve the lousy mixing.  This is the final commit before implementing parameter groups

Have redesigned the MCMC class, separating the tx parameter update step into a separate class.  Polymorphism needs tidying up, and more work to do on separating out the likelihood.  This code is untested!!

Commit squash

Implemented modularised multi-site updater module.  Appears to work well.

3 stage updating for FMD model.  Implemented DIC, but as yet very untested!

Commit squash

Messing about with the model parameterisation to improve mixing. About to centre covariates around their means

Played around with model.  Fixed a small bug in the Adaptive Updater.  Added powers to the model.

Added middleware to do random walks on functions of parameters.  Still needs a little tuning, however.  Also added a single site logMRW updater.

Made changes for basic (non removal time imputed) Australia Equine Influenza model.

Updated configure.ac, updated auseiMcmc.cpp to reflect new file paths, etc

Working code for simulated SIR model.  No great shakes here!

Working ausei code for simple SINR model, no imputation of recovery times.  The mixing problem appears to stem from the fact that the data are quantized into integer days which doesn't fit all that easily into the continuous time framework.  Need to discuss this.

Added code to impute recovery times, as well as a hyperparameter on the prior.  Now have dependency issues, so probably will end up implementing the non-centered parameterisation.  Ug!

Model working for square root of area and number of horses

Added SirDeterministic.cpp class to simulate a deterministic homogeneous SIR epidemic

Interim commit

First attempt at building in within yard SIR epidemic.  Rough around the edges: MCMC tuning needs looking at, as does the transmission model -- part of it is not actually used for the SI epidemic.  Also need to decide on where to take the model -- do we still need to impute any times?

Took gamma_2 updater out of the system. Did not need it!

Add src/sim/Makefile.am

Got within property SIR epidemic working, together with estimation of within property transmission rate.  Seems rather high, though, so will need to recheck the model.

Added density independent disease transmission - divide beta by N in the SIRDeterministic simulation

First steps towards full EI model.  Need to implement the within property epidemic in terms of proportions of individuals in the population

Working towards full Ausei model

Fixed project environment

Interim commit

Removed Eclipse .project file

Removed release directory from tree

Added Eclipse project files

Model with vaccination status, within property SEIR, and fixed 2 day property level infection to onset time.

Removed Eclipse files, and obsolete test data

Got rid of .settings folder.  Added eclipse files to .gitignore

Changed location of StochasticNode class.  Updated file version.

Fixed a bug in the build system.

Added .gitignore

Commit squash

Added GPLv3 licence

Release version 1.0