Change Log

0.4.2 (2016-06-16)

  • Breaking change: replace the observation models added in epifx 0.4.1 with observations models for:
    • Count data where the denominator is known or assumed to be the entire population (epifx.obs.PopnCounts); and
    • Count data where the denominator is reported and may vary, and where the background signal is a fixed proportion (epifx.obs.SampleCounts).

0.4.1 (2016-04-22)

  • Enhancement: provide generic negative binomial observation models for count data and for fractional/percentage data in epifx.obs.

0.4.0 (2016-04-22)

  • This release requires pypfilt >= 0.4.0.

  • Breaking change: models must define default parameter bounds by implementing the param_bounds method.

  • Breaking change: model expectation functions now receive the previous and current state vectors, in addition to the infection probability vector. This means that expectation functions will need to change from:

    expect(params, unit, period, pr_inf)
    

    to:

    expect(params, unit, period, pr_inf, prev, curr)
    
  • Enhancement: epifx.summary.make now passes additional keyword arguments to the pypfilt.summary.HDF5 constructor, allowing users to override default settings, such as first_day=False.

  • Bug fix: ensure that infection probabilities are strictly non-negative.

  • Bug fix: ensure that population invariants are enforced correctly.

  • Bug fix: correctly scale the daily seeding probability.

  • Add instructions for installing epifx in a virtual environment.

0.3.1 (2016-02-25)

  • Bug fix: prevent a runtime error with params['epifx']['one_prng'] = True by correctly retrieving the pypfilt PRNG (params['resample']['rnd']).

0.3.0 (2016-02-23)

  • This release requires pypfilt >= 0.3.0.
  • Provide each summary statistic as a separate class.
  • Inherit from the pypfilt simulation model base class.
  • Host the documentation at Read The Docs.

0.2.0 (2015-11-17)

  • Use an independent PRNG instance for model stochasticity, as distinct from the pypfilt PRNG instance (used for resampling). Note that this breaks backwards compatibility (in terms of producing identical outputs) and can be overridden by setting params['epifx']['one_prng'] = True.
  • This release requires pypfilt >= 0.2.0.

0.1.10 (2015-07-09)

  • Fix a bug where temporal forcing could cause a negative force of infection.

0.1.9 (2015-07-06)

  • Add support for temporal forcing, modulated by the new parameter sigma.

0.1.8 (2015-06-18)

  • Update the model parameter invariants for alpha, based on the priors for R0 and gamma.

0.1.7 (2015-06-18)

  • Sample R0 and calculate alpha, rather than sampling alpha directly.

0.1.6 (2015-06-08)

  • Avoid error messages if no logging handler is configured by the application.
  • Default to comparing only the simulation outputs and ignore the metadata; this can be overridden by the --meta-data (-m) option.
  • Build a universal wheel via python setup.py bdist_wheel, which supports both Python 2 and Python 3.
  • This release requires pypfilt >= 0.1.2.

0.1.5 (2015-06-04)

  • Record credible intervals for state variables (/data/state).

0.1.4 (2015-06-03)

  • Reduce the minimum latent period to half a day.
  • No longer require the simulation period to be included in the simulation parameters dictionary.
  • Hide stderr output from spawned processes when obtaining git metadata, since the error messages have no relevance to the user (they only serve to indicate that the working directory is not part of a git repository).

0.1.3 (2015-06-01)

  • Obtain git metadata from the working directory, if it is contained within a repository. This requires pypfilt >= 0.1.1.

    Note that sensible metadata will only be obtained if the working directory is not manipulated by program code (e.g., os.chdir).

0.1.2 (2015-06-01)

  • Record the enforced limits on model parameters, so that output files include sufficient information to independently produce identical results.

    The default limits on beta and gamma are now identical to the domain of their default priors (1 to 3 days).

  • Added options --verbose and --data-only to the cmp-output script.

  • Ignore the command line (/meta/sim/cmdline) when comparing output files.

0.1.1 (2015-05-29)

  • Added a script (cmp-output) that compares output files for identical simulation outputs and metadata.

0.1.0 (2015-05-29)

  • Initial release.