PoonLab / Kaphi

Kernel-embedded ABC-SMC for phylodynamic inference
GNU Affero General Public License v3.0
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Allow user to set model parameters for simulating trees #56

Closed ArtPoon closed 7 years ago

ArtPoon commented 7 years ago

@MathiasRenaud noted a use case where a user may want to simulate trees under specific parameter settings of a model. We discussed adding an "initial parameter values" setting to the Kaphi configuration object, but instead I think the appropriate method would be to specify Dirac delta functions as the prior distributions for the respective parameters.

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MathiasRenaud commented 7 years ago

The current method to be used as an alternative to delta functions for setting specific parameters is to set the priors in the config file as a uniform distribution with hyperparameters 'max' and 'min' both set to the desired value.

priors:
  lambda0:
    dist: 'unif'
    hyperparameters:
    - min: 0.1
    - max: 0.1
  lambda1:
    dist: 'unif'
    hyperparameters:
    - min: 0.2
    - max: 0.2
  mu0:
    dist: 'unif'
    hyperparameters:
    - min: 0.03
    - max: 0.03
  mu1:
    dist: 'unif'
    hyperparameters:
    - min: 0.03
    - max: 0.03
  q01:
    dist: 'unif'
    hyperparameters:
    - min: 0.01
    - max: 0.01
  q10:
    dist: 'unif'
    hyperparameters:
    - min: 0.01
    - max: 0.01