pyABC’s interface to external simulators¶
Currently, the R language is supported.
Note
The rpy2 package needs to be installed to interface with the R language. Installation of rpy2 is optional if R support is not required. See also installation of optional dependencies.

class
pyabc.external.
R
(source_file: str)¶ Interface to R.
Parameters: source_file (str) – Path to the file which contains the definitions for the model, the summary statistics and the distance function as well as the observed data. 
display_source_ipython
()¶ Convenience method to print the loaded source file as syntax highlighted HTML within IPython.

distance
(function_name: str)¶ The Rdistance function.
Parameters: function_name (str) – Name of the function in the R script which defines the distance function. Returns: distance – The distance function. Return type: callable

model
(function_name: str)¶ The Rmodel.
Parameters: function_name (str) – Name of the function in the R script which defines the model. Returns: model – The model. Return type: callable

observation
(name: str)¶ The summary statistics of the observed data as defined in R.
Parameters: name (str) – Name of the named list defined in the R script which holds the observed data. Returns: observation – A dictionary like object which holds the summary statistics of the observed data. Return type: r named list

summary_statistics
(function_name: str)¶ The Rsummary statistics.
Parameters: function_name (str) – Name of the function in the R script which defines the summary statistics function. Returns: summary_statistics – The summary statistics function. Return type: callable
