bayesian-inference - Project Hosting on Google Code

Last 7 days Dec 11, 2009 Revision 90669ea6a5 (updated docs) pushed by fccoelho - updated docs updated docs Dec 11, 2009 Revision b88523be48 (bumped up version on setup.py) pushed by fccoelho - bumped up version on setup.py bumped up version on setup.py Dec 11, 2009 3 new revisions pushed by fccoelho - 8d53750ddd:improved lhs to stop returning infs in samples added some tests for lhs ab1f5a2b4d:Added MCMC module stub fc1bb280e1:implemented fitting based on MCMC for the Melding module. A combination of Metropolis-hastings proposals and importance sampling has shown better performance than the previous SIR approach. A method for self calibrating the variance of the prior distribution to avoid local minima, was also implemented. A new MCMC module was started to collect generic MCMC sampler classes. Unfinished. 8d53750ddd:improved lhs to stop returning infs in samples added some tests for lhs ab1f5a2b4d:Added MCMC module stub fc1bb280e1:implemented fitting based on MCMC for the Melding module. A combination of Metropolis-hastings proposals and importance sampling has shown better performance than the previous SIR approach. A method for self calibrating the variance of the prior distribution to avoid local minima, was also implemented. A new MCMC module was started to collect generic MCMC sampler classes. Unfinished. Last 30 days Dec 03, 2009 Revision 14f119aaac (bug fix) pushed by fccoelho - bug fix bug fix Dec 03, 2009 2 new revisions pushed by fccoelho - 10fda6e004:extended lhs to support multivariate sampling with correlation structure. 4f53bca24c:fixed bug in lhs and tested 10fda6e004:extended lhs to support multivariate sampling with correlation structure. 4f53bca24c:fixed bug in lhs and tested Dec 01, 2009 Revision 4582f34649 (started implementation of the conjugate prior module) pushed by fccoelho - started implementation of the conjugate prior module started implementation of the conjugate prior module Nov 30, 2009 Revision 349ce24da9 (bugfix) pushed by fccoelho - bugfix bugfix Nov 30, 2009 Revision 48df0063fd (fixed bug in gillespie.py) pushed by fccoelho - fixed bug in gillespie.py fixed bug in gillespie.py Nov 27, 2009 Revision d1f384cfa9 (improved uniform likelihood methods improved testing by adop...) pushed by fccoelho - improved uniform likelihood methods improved testing by adopting numpy.testing cool asserts improved uniform likelihood methods improved testing by adopting numpy.testing cool asserts Nov 25, 2009 Revision a0261f0933 (added Uniform log-likelihood function in like.py improved Ba...) pushed by fccoelho - added Uniform log-likelihood function in like.py improved BayesVar, but is still broken added Uniform log-likelihood function in like.py improved BayesVar, but is still broken Nov 24, 2009 Revision dbe51ac97c (improved documentation and minor refactoring in bvariables m...) pushed by fccoelho - improved documentation and minor refactoring in bvariables module. improved documentation and minor refactoring in bvariables module. Earlier this year Nov 02, 2009 Revision 73765928bf (improved cgillespie performance) pushed by fccoelho - improved cgillespie performance improved cgillespie performance Oct 30, 2009 Revision 17d96bef40 (update cython version of gillespie) pushed by fccoelho - update cython version of gillespie update cython version of gillespie Oct 30, 2009 2 new revisions pushed by fccoelho - bae8bf9201:added example files 3ac2336378:minor updates on examples bae8bf9201:added example files 3ac2336378:minor updates on examples Oct 30, 2009 Revision 1f11c73faa (updated docs) pushed by fccoelho - updated docs updated docs Oct 30, 2009 3 new revisions pushed by fccoelho - 1336071c65:changed parameter name in the sir method of Meld class from tau to variance. 64ba0fd48d:bug fixes cb71305695:update docs 1336071c65:changed parameter name in the sir method of Meld class from tau to variance. 64ba0fd48d:bug fixes cb71305695:update docs Oct 22, 2009 Revision 5a1d796e27 (minor fixes) pushed by fccoelho - minor fixes minor fixes Oct 22, 2009 7 new revisions pushed by fccoelho - 3140785e4b:removed build directory from mercurial control 1dc8f2a191:new minor release 7e61be7362:rename 48fc03f9b2:bug fix 9b708aba14:m 115118fe26:mXs 1f6bbb51df:m 3140785e4b:removed build directory from mercurial control 1dc8f2a191:new minor release 7e61be7362:rename 48fc03f9b2:bug fix 9b708aba14:m 115118fe26:mXs 1f6bbb51df:m Oct 12, 2009 Revision 6b784d9860 (fixed some bugs in the __str__ of _BayesVar) pushed by fccoelho - fixed some bugs in the __str__ of _BayesVar fixed some bugs in the __str__ of _BayesVar Oct 12, 2009 2 new revisions pushed by fccoelho - a16954b875:added ascii histogram generator 5927ed654a:started to implement the ascii histogram as the __str__ of _bayesvar a16954b875:added ascii histogram generator 5927ed654a:started to implement the ascii histogram as the __str__ of _bayesvar Oct 12, 2009 Revision 8176e5c96e (removed 2.6 only syntax to make it compatible with python 2....) pushed by fccoelho - removed 2.6 only syntax to make it compatible with python 2.5 removed 2.6 only syntax to make it compatible with python 2.5 Oct 06, 2009 Revision 07249c66a3 (improved documentatio of SDE example.py) pushed by fccoelho - improved documentatio of SDE example.py improved documentatio of SDE example.py Sep 29, 2009 Revision 9df56f9028 (m) pushed by fccoelho - m m Sep 29, 2009 Revision 3b9b5e50cf (bug fix) pushed by fccoelho - bug fix bug fix Sep 29, 2009 Revision 09f1a0bf42 (Rolled back migration to Distribute due to lack of support i...) pushed by fccoelho - Rolled back migration to Distribute due to lack of support in Sage. Rolled back migration to Distribute due to lack of support in Sage. Sep 29, 2009 Revision b3cfeec1db (moved from setuptools to distribute added try/except around ...) pushed by fccoelho - moved from setuptools to distribute added try/except around psyco import moved from setuptools to distribute added try/except around psyco import Sep 23, 2009 Revision ca2ff82a0b (bumped up minor version) pushed by fccoelho - bumped up minor version bumped up minor version Sep 23, 2009 Revision ef520be751 (added import check for gnuplot in gillespie.py) pushed by fccoelho - added import check for gnuplot in gillespie.py added import check for gnuplot in gillespie.py Sep 11, 2009 Revision 3556f77a1d (fixed bug in setThetafromData which gave an error after rece...) pushed by fccoelho - fixed bug in setThetafromData which gave an error after receiving a constant vector as sample. fixed bug in setThetafromData which gave an error after receiving a constant vector as sample. Sep 01, 2009 Revision a5cf8b4221 (improved ABCrun tested it with both deterministic and stocha...) pushed by fccoelho - improved ABCrun tested it with both deterministic and stochastic models. improved ABCrun tested it with both deterministic and stochastic models. Aug 27, 2009 Revision 116efdfb8c (minor bug fixes) pushed by fccoelho - minor bug fixes minor bug fixes Aug 24, 2009 Revision 3c3bc9e4f6 (fixed import bug) pushed by fccoelho - fixed import bug fixed import bug Aug 24, 2009 Revision 50a5c577b9 (removed strict dependency on Gnuplot) pushed by fccoelho - removed strict dependency on Gnuplot removed strict dependency on Gnuplot Jul 28, 2009 2 new revisions pushed by fccoelho - Revision 2698e00242:update docs fixed bug in realtime.py Revision 8c2f44ec3d:added tests with pythoscope to the root of the BIP package Revision 2698e00242:update docs fixed bug in realtime.py Revision 8c2f44ec3d:added tests with pythoscope to the root of the BIP package Jul 27, 2009 Revision d5eb945fe8 (added realtime visualization capabilities to Meld Class. Unt...) pushed by fccoelho - added realtime visualization capabilities to Meld Class. Untested added realtime visualization capabilities to Meld Class. Untested Jul 27, 2009 3 new revisions pushed by fccoelho - Revision b01be54fea:cleaned melding.py to get rid of old implementation. Revision a3205047e4:update docs Revision 58bd94c985:fixed bug in SDE Revision b01be54fea:cleaned melding.py to get rid of old implementation. Revision a3205047e4:update docs Revision 58bd94c985:fixed bug in SDE Jul 15, 2009 Revision 7bee9530da (added psyco check) pushed by fccoelho - added psyco check added psyco check Jul 15, 2009 Revision 04be7339db (cleaned imports) pushed by fccoelho - cleaned imports cleaned imports Jun 22, 2009 81 new revisions pushed by fccoelho - Revision cc9cb40178:Initial directory structure. Revision b066b9aa52:new project started Revision 940b4941b2:Added factory functions to Bayes.py Revision 9ef8e7da70:fixed project files Revision e0417f334a:changed attribute range to rang to avoid collision with reserver keyword Revision 55cbebeab1:translated some docstrings Revision a03b509719:updated figure. fixed bug in demo code. Revision 8804d0edc2:improved docstrings; added test suite with pythoscope. No tests implemented yet Revision 4731cdf181:[No log message] Revision 32674e61a8:[No log message] Revision 845f73281a:update Revision 0c848c74dd:Implementation of the simple SMC Condensation algorithm done not fully tested yet Revision 9982dd6b5b:Added visualization to the Condensation module. Filter not working correctly Revision 40e6ac805d:Condensation algorithm working correctly. After some bugfixes Revision 31cac68c41:Added package to solve Stochastic differential equations Revision aa5c5de9dd:added tests to like module Revision 7ed2084674:added tests to like module Revision 3d57f359b2:expanded tests Revision 567d9b3bcb:Added Melding and lhs module these will be part of a basic inference modules to be collected in the Bayes package Revision c063c965b4:Began refactoring of the Melding module Revision 643bf990b1:added more tests Revision 7d04901d65:added more tests Revision a22851b0f3:Extended tests on the like module Revision 82217921be:started the setup.py Revision 455bcb3863:added more tests Revision db63ed208b:added more tests Revision 9357585f37:added more tests to the like.py functions. Still missing tests for weibull and Categorical Likelihood. Revision 46600aab24:added master package BIP Revision 33bde73344:refactoring Revision 11d80a6865:fix Revision b18b57d01a:fix Revision c795402cef:fix Revision 2345d5632f:[No log message] Revision f3231486a1:Added initial epydoc documentation Revision 78fb300082:added help files Revision 23de57238c:[No log message] Revision cac7bd9689:added documentation Revision 947481560c:improved doc formatting Revision a7356cbcec:fix Revision 5c2b0ef454:Refactoring of the Melding module complete, Meld class tested with single compartment model. Revision 51eacf97be:improved documentation Revision e8b02f46de:renames Bayes module to bvariables Revision 90f637ea68:renames Bayes module to bvariables Revision f9b127c9f5:Improved Melding module to allow sequential inferences Revision 21efc4e696:fixed bugs in Meld class Revision e081726bad:Added support for parallel processing on SMP machine to the melding module Revision 9218ff93e3:First implementation of Approximate Bayesian Computation versio of bayesian Melding done! Untested. Revision 259b9b86d2:fixed some bugs on the ABC method of Melding Revision 3989f072da:Still testing and improving ABC implementation. Changed basic fitness function to a normalized RMS deviation measure, in order to b able to compare any curves or single points Revision 2652b702ff:fixed bug in LHS Revision fc0aee71c0:Started tests for the melding module Revision e47e1641fe:bug fixes Revision a8a7b3dd00:lhs sampling function modified to accept sample size as a shape tuple or an integer. some improvements to Meld class Revision 16a8d76bdf:improved documentation Revision 3bc6ecf564:Fixed bugs in Meld Class Revision 40d3e01e65:fixed bugs on Melding added lhs from sample on lhs module Revision 3621ffc331:Implemented lhsFromDensity on lhs module. added tests for it but they are still empty Revision 28dc4ff7ca:updated documentation for the package Revision a40b78bfbe:fixed bugs in setup.py Revision 80cbb024b9:fixed basic fit method on Meld class Revision 4b3fd6e21a:fixed bugs in Melding.py Revision f15d26411d:bugs fixed. new sir with likelihoods for timeseries working. Revision 6eee5e5eb2:improved performance or the parallel runs Revision 026a1abefe:paralelized likelihood calculations Revision 37d60eaf1e:paralelized get posteriors Revision f2dec7ae5b:Now sir method returns 0 when it is does not complete successfully allowing for retries. Revision 6d9c9c2d5d:minor changes Revision 77dd461688:Added real-time vizualization module based on Gnuplot Revision 1a7f41ecfa:SIR returns 1 if successful 0 if not; allowing for retries in the case of zero weights. Revision d42c4ead15:some fixes Revision bc143d5943:removed import of visualization module from Melding.py Revision 712693e7f9:Added limit enforcing in setPhiFrom Data and setThetaFromData in melding.py Revision da858ef252:updated epydoc documentation Revision 20bb0ca805:bug fixes Revision 926391757f:improved information output during runtime Revision d4b090e92c:minor bugfixes Revision 321ee3718c:Made it compatible with multiprocessing in 2.6 and new versions of python Revision f2d2044e89:fixed bug in melding.py Revision 02fbaef1ca:Parallelized GilespieSSA Stochatic diferential equation solver Revision 6a5bdaa95e:removed builtin names 'vars' and 'round' from gillespie.py Revision f15566b679:added some type enforcing for sage compatibility Revision cc9cb40178:Initial directory structure. Revision b066b9aa52:new project started Revision 940b4941b2:Added factory functions to Bayes.py Revision 9ef8e7da70:fixed project files Revision e0417f334a:changed attribute range to rang to avoid collision with reserver keyword Revision 55cbebeab1:translated some docstrings Revision a03b509719:updated figure. fixed bug in demo code. Revision 8804d0edc2:improved docstrings; added test suite with pythoscope. No tests implemented yet Revision 4731cdf181:[No log message] Revision 32674e61a8:[No log message] Revision 845f73281a:update Revision 0c848c74dd:Implementation of the simple SMC Condensation algorithm done not fully tested yet Revision 9982dd6b5b:Added visualization to the Condensation module. Filter not working correctly Revision 40e6ac805d:Condensation algorithm working correctly. After some bugfixes Revision 31cac68c41:Added package to solve Stochastic differential equations Revision aa5c5de9dd:added tests to like module Revision 7ed2084674:added tests to like module Revision 3d57f359b2:expanded tests Revision 567d9b3bcb:Added Melding and lhs module these will be part of a basic inference modules to be collected in the Bayes package Revision c063c965b4:Began refactoring of the Melding module Revision 643bf990b1:added more tests Revision 7d04901d65:added more tests Revision a22851b0f3:Extended tests on the like module Revision 82217921be:started the setup.py Revision 455bcb3863:added more tests Revision db63ed208b:added more tests Revision 9357585f37:added more tests to the like.py functions. Still missing tests for weibull and Categorical Likelihood. Revision 46600aab24:added master package BIP Revision 33bde73344:refactoring Revision 11d80a6865:fix Revision b18b57d01a:fix Revision c795402cef:fix Revision 2345d5632f:[No log message] Revision f3231486a1:Added initial epydoc documentation Revision 78fb300082:added help files Revision 23de57238c:[No log message] Revision cac7bd9689:added documentation Revision 947481560c:improved doc formatting Revision a7356cbcec:fix Revision 5c2b0ef454:Refactoring of the Melding module complete, Meld class tested with single compartment model. Revision 51eacf97be:improved documentation Revision e8b02f46de:renames Bayes module to bvariables Revision 90f637ea68:renames Bayes module to bvariables Revision f9b127c9f5:Improved Melding module to allow sequential inferences Revision 21efc4e696:fixed bugs in Meld class Revision e081726bad:Added support for parallel processing on SMP machine to the melding module Revision 9218ff93e3:First implementation of Approximate Bayesian Computation versio of bayesian Melding done! Untested. Revision 259b9b86d2:fixed some bugs on the ABC method of Melding Revision 3989f072da:Still testing and improving ABC implementation. Changed basic fitness function to a normalized RMS deviation measure, in order to b able to compare any curves or single points Revision 2652b702ff:fixed bug in LHS Revision fc0aee71c0:Started tests for the melding module Revision e47e1641fe:bug fixes Revision a8a7b3dd00:lhs sampling function modified to accept sample size as a shape tuple or an integer. some improvements to Meld class Revision 16a8d76bdf:improved documentation Revision 3bc6ecf564:Fixed bugs in Meld Class Revision 40d3e01e65:fixed bugs on Melding added lhs from sample on lhs module Revision 3621ffc331:Implemented lhsFromDensity on lhs module. added tests for it but they are still empty Revision 28dc4ff7ca:updated documentation for the package Revision a40b78bfbe:fixed bugs in setup.py Revision 80cbb024b9:fixed basic fit method on Meld class Revision 4b3fd6e21a:fixed bugs in Melding.py Revision f15d26411d:bugs fixed. new sir with likelihoods for timeseries working. Revision 6eee5e5eb2:improved performance or the parallel runs Revision 026a1abefe:paralelized likelihood calculations Revision 37d60eaf1e:paralelized get posteriors Revision f2dec7ae5b:Now sir method returns 0 when it is does not complete successfully allowing for retries. Revision 6d9c9c2d5d:minor changes Revision 77dd461688:Added real-time vizualization module based on Gnuplot Revision 1a7f41ecfa:SIR returns 1 if successful 0 if not; allowing for retries in the case of zero weights. Revision d42c4ead15:some fixes Revision bc143d5943:removed import of visualization module from Melding.py Revision 712693e7f9:Added limit enforcing in setPhiFrom Data and setThetaFromData in melding.py Revision da858ef252:updated epydoc documentation Revision 20bb0ca805:bug fixes Revision 926391757f:improved information output during runtime Revision d4b090e92c:minor bugfixes Revision 321ee3718c:Made it compatible with multiprocessing in 2.6 and new versions of python Revision f2d2044e89:fixed bug in melding.py Revision 02fbaef1ca:Parallelized GilespieSSA Stochatic diferential equation solver Revision 6a5bdaa95e:removed builtin names 'vars' and 'round' from gillespie.py Revision f15566b679:added some type enforcing for sage compatibility Apr 23, 2009 r90 (added some type enforcing for sage compatibility) committed by fccoelho - added some type enforcing for sage compatibility added some type enforcing for sage compatibility Apr 18, 2009 r89 (removed builtin names 'vars' and 'round' from gillespie.py ) committed by fccoelho - removed builtin names 'vars' and 'round' from gillespie.py removed builtin names 'vars' and 'round' from gillespie.py Apr 17, 2009 StochasticDifferentialEquationsSolvers (Short description of the SDE package) Wiki page edited by fccoelho Apr 17, 2009 StochasticDifferentialEquationsSolvers (Short description of the SDE package) Wiki page edited by fccoelho Apr 17, 2009 StochasticDifferentialEquationsSolvers (Short description of the SDE package) Wiki page added by fccoelho Apr 17, 2009 r85 (Parallelized GilespieSSA Stochatic diferential equation solv...) committed by fccoelho - Parallelized GilespieSSA Stochatic diferential equation solver Parallelized GilespieSSA Stochatic diferential equation solver Apr 07, 2009 r84 (fixed bug in melding.py) committed by fccoelho - fixed bug in melding.py fixed bug in melding.py Mar 30, 2009 r83 (Made it compatible with multiprocessing in 2.6 and new versi...) committed by fccoelho - Made it compatible with multiprocessing in 2.6 and new versions of python Made it compatible with multiprocessing in 2.6 and new versions of python Mar 26, 2009 r82 (minor bugfixes) committed by fccoelho - minor bugfixes minor bugfixes Mar 26, 2009 r81 (improved information output during runtime) committed by fccoelho - improved information output during runtime improved information output during runtime Mar 19, 2009 r80 (bug fixes) committed by fccoelho - bug fixes bug fixes

81 new revisions pushed by fccoelho - Revision cc9cb40178:Initial directory structure. Revision b066b9aa52:new project started Revision 940b4941b2:Added factory functions to Bayes.py Revision 9ef8e7da70:fixed project files Revision e0417f334a:changed attribute range to rang to avoid collision with reserver keyword Revision 55cbebeab1:translated some docstrings Revision a03b509719:updated figure. fixed bug in demo code. Revision 8804d0edc2:improved docstrings; added test suite with pythoscope. No tests implemented yet Revision 4731cdf181:[No log message] Revision 32674e61a8:[No log message] Revision 845f73281a:update Revision 0c848c74dd:Implementation of the simple SMC Condensation algorithm done not fully tested yet Revision 9982dd6b5b:Added visualization to the Condensation module. Filter not working correctly Revision 40e6ac805d:Condensation algorithm working correctly. After some bugfixes Revision 31cac68c41:Added package to solve Stochastic differential equations Revision aa5c5de9dd:added tests to like module Revision 7ed2084674:added tests to like module Revision 3d57f359b2:expanded tests Revision 567d9b3bcb:Added Melding and lhs module these will be part of a basic inference modules to be collected in the Bayes package Revision c063c965b4:Began refactoring of the Melding module Revision 643bf990b1:added more tests Revision 7d04901d65:added more tests Revision a22851b0f3:Extended tests on the like module Revision 82217921be:started the setup.py Revision 455bcb3863:added more tests Revision db63ed208b:added more tests Revision 9357585f37:added more tests to the like.py functions. Still missing tests for weibull and Categorical Likelihood. Revision 46600aab24:added master package BIP Revision 33bde73344:refactoring Revision 11d80a6865:fix Revision b18b57d01a:fix Revision c795402cef:fix Revision 2345d5632f:[No log message] Revision f3231486a1:Added initial epydoc documentation Revision 78fb300082:added help files Revision 23de57238c:[No log message] Revision cac7bd9689:added documentation Revision 947481560c:improved doc formatting Revision a7356cbcec:fix Revision 5c2b0ef454:Refactoring of the Melding module complete, Meld class tested with single compartment model. Revision 51eacf97be:improved documentation Revision e8b02f46de:renames Bayes module to bvariables Revision 90f637ea68:renames Bayes module to bvariables Revision f9b127c9f5:Improved Melding module to allow sequential inferences Revision 21efc4e696:fixed bugs in Meld class Revision e081726bad:Added support for parallel processing on SMP machine to the melding module Revision 9218ff93e3:First implementation of Approximate Bayesian Computation versio of bayesian Melding done! Untested. Revision 259b9b86d2:fixed some bugs on the ABC method of Melding Revision 3989f072da:Still testing and improving ABC implementation. Changed basic fitness function to a normalized RMS deviation measure, in order to b able to compare any curves or single points Revision 2652b702ff:fixed bug in LHS Revision fc0aee71c0:Started tests for the melding module Revision e47e1641fe:bug fixes Revision a8a7b3dd00:lhs sampling function modified to accept sample size as a shape tuple or an integer. some improvements to Meld class Revision 16a8d76bdf:improved documentation Revision 3bc6ecf564:Fixed bugs in Meld Class Revision 40d3e01e65:fixed bugs on Melding added lhs from sample on lhs module Revision 3621ffc331:Implemented lhsFromDensity on lhs module. added tests for it but they are still empty Revision 28dc4ff7ca:updated documentation for the package Revision a40b78bfbe:fixed bugs in setup.py Revision 80cbb024b9:fixed basic fit method on Meld class Revision 4b3fd6e21a:fixed bugs in Melding.py Revision f15d26411d:bugs fixed. new sir with likelihoods for timeseries working. Revision 6eee5e5eb2:improved performance or the parallel runs Revision 026a1abefe:paralelized likelihood calculations Revision 37d60eaf1e:paralelized get posteriors Revision f2dec7ae5b:Now sir method returns 0 when it is does not complete successfully allowing for retries. Revision 6d9c9c2d5d:minor changes Revision 77dd461688:Added real-time vizualization module based on Gnuplot Revision 1a7f41ecfa:SIR returns 1 if successful 0 if not; allowing for retries in the case of zero weights. Revision d42c4ead15:some fixes Revision bc143d5943:removed import of visualization module from Melding.py Revision 712693e7f9:Added limit enforcing in setPhiFrom Data and setThetaFromData in melding.py Revision da858ef252:updated epydoc documentation Revision 20bb0ca805:bug fixes Revision 926391757f:improved information output during runtime Revision d4b090e92c:minor bugfixes Revision 321ee3718c:Made it compatible with multiprocessing in 2.6 and new versions of python Revision f2d2044e89:fixed bug in melding.py Revision 02fbaef1ca:Parallelized GilespieSSA Stochatic diferential equation solver Revision 6a5bdaa95e:removed builtin names 'vars' and 'round' from gillespie.py Revision f15566b679:added some type enforcing for sage compatibility

Revision cc9cb40178:Initial directory structure. Revision b066b9aa52:new project started Revision 940b4941b2:Added factory functions to Bayes.py Revision 9ef8e7da70:fixed project files Revision e0417f334a:changed attribute range to rang to avoid collision with reserver keyword Revision 55cbebeab1:translated some docstrings Revision a03b509719:updated figure. fixed bug in demo code. Revision 8804d0edc2:improved docstrings; added test suite with pythoscope. No tests implemented yet Revision 4731cdf181:[No log message] Revision 32674e61a8:[No log message] Revision 845f73281a:update Revision 0c848c74dd:Implementation of the simple SMC Condensation algorithm done not fully tested yet Revision 9982dd6b5b:Added visualization to the Condensation module. Filter not working correctly Revision 40e6ac805d:Condensation algorithm working correctly. After some bugfixes Revision 31cac68c41:Added package to solve Stochastic differential equations Revision aa5c5de9dd:added tests to like module Revision 7ed2084674:added tests to like module Revision 3d57f359b2:expanded tests Revision 567d9b3bcb:Added Melding and lhs module these will be part of a basic inference modules to be collected in the Bayes package Revision c063c965b4:Began refactoring of the Melding module Revision 643bf990b1:added more tests Revision 7d04901d65:added more tests Revision a22851b0f3:Extended tests on the like module Revision 82217921be:started the setup.py Revision 455bcb3863:added more tests Revision db63ed208b:added more tests Revision 9357585f37:added more tests to the like.py functions. Still missing tests for weibull and Categorical Likelihood. Revision 46600aab24:added master package BIP Revision 33bde73344:refactoring Revision 11d80a6865:fix Revision b18b57d01a:fix Revision c795402cef:fix Revision 2345d5632f:[No log message] Revision f3231486a1:Added initial epydoc documentation Revision 78fb300082:added help files Revision 23de57238c:[No log message] Revision cac7bd9689:added documentation Revision 947481560c:improved doc formatting Revision a7356cbcec:fix Revision 5c2b0ef454:Refactoring of the Melding module complete, Meld class tested with single compartment model. Revision 51eacf97be:improved documentation Revision e8b02f46de:renames Bayes module to bvariables Revision 90f637ea68:renames Bayes module to bvariables Revision f9b127c9f5:Improved Melding module to allow sequential inferences Revision 21efc4e696:fixed bugs in Meld class Revision e081726bad:Added support for parallel processing on SMP machine to the melding module Revision 9218ff93e3:First implementation of Approximate Bayesian Computation versio of bayesian Melding done! Untested. Revision 259b9b86d2:fixed some bugs on the ABC method of Melding Revision 3989f072da:Still testing and improving ABC implementation. Changed basic fitness function to a normalized RMS deviation measure, in order to b able to compare any curves or single points Revision 2652b702ff:fixed bug in LHS Revision fc0aee71c0:Started tests for the melding module Revision e47e1641fe:bug fixes Revision a8a7b3dd00:lhs sampling function modified to accept sample size as a shape tuple or an integer. some improvements to Meld class Revision 16a8d76bdf:improved documentation Revision 3bc6ecf564:Fixed bugs in Meld Class Revision 40d3e01e65:fixed bugs on Melding added lhs from sample on lhs module Revision 3621ffc331:Implemented lhsFromDensity on lhs module. added tests for it but they are still empty Revision 28dc4ff7ca:updated documentation for the package Revision a40b78bfbe:fixed bugs in setup.py Revision 80cbb024b9:fixed basic fit method on Meld class Revision 4b3fd6e21a:fixed bugs in Melding.py Revision f15d26411d:bugs fixed. new sir with likelihoods for timeseries working. Revision 6eee5e5eb2:improved performance or the parallel runs Revision 026a1abefe:paralelized likelihood calculations Revision 37d60eaf1e:paralelized get posteriors Revision f2dec7ae5b:Now sir method returns 0 when it is does not complete successfully allowing for retries. Revision 6d9c9c2d5d:minor changes Revision 77dd461688:Added real-time vizualization module based on Gnuplot Revision 1a7f41ecfa:SIR returns 1 if successful 0 if not; allowing for retries in the case of zero weights. Revision d42c4ead15:some fixes Revision bc143d5943:removed import of visualization module from Melding.py Revision 712693e7f9:Added limit enforcing in setPhiFrom Data and setThetaFromData in melding.py Revision da858ef252:updated epydoc documentation Revision 20bb0ca805:bug fixes Revision 926391757f:improved information output during runtime Revision d4b090e92c:minor bugfixes Revision 321ee3718c:Made it compatible with multiprocessing in 2.6 and new versions of python Revision f2d2044e89:fixed bug in melding.py Revision 02fbaef1ca:Parallelized GilespieSSA Stochatic diferential equation solver Revision 6a5bdaa95e:removed builtin names 'vars' and 'round' from gillespie.py Revision f15566b679:added some type enforcing for sage compatibility

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