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v1.1.9

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@wshlavacek wshlavacek released this 21 Sep 18:17
· 162 commits to master since this release
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In PyBNF version 1.1.9, am was added as a new option for fit_type. When am is selected (fit_type=am in a CONF file), PyBNF executes an adaptive Markov chain Monte Carlo (MCMC) sampling algorithm. The am method has several method-specific options: stablizingCov, adaptive, output_noise_trajectory, output_trajectory, continue_run, calculate_covari, and starting_params. We recommend that am should be used instead of mh. Version 1.1.9 also adds support for new settings for objfunc. When objfunc=neg_bin in a CONF file, PyBNF uses a negative binomial likelihood function in optimization or MCMC sampling. When objfunc=neg_bin_dynamic, PyBNF uses a negative binomial likelihood function in optimization or MCMC sampling and infers the hyperparameter r (dispersion) jointly with model parameters. When objfunc=kl, PyBNF uses the Kullback-Leibler divergence as an objective function in optimization. When objfunc=chi_sq_dynamic, PyBNF uses a Gaussian likelihood function in optimization or MCMC sampling and jointly infers the hyperparameter sigma (standard deviation) jointly with model parameters. The online manual has been updated to explain new features. Please note that versions 1.1.3 through 1.1.8 are prereleases of 1.1.9 and should NOT be used.