Stan¶
Model export to Stan.
API¶
The standard exporting API is provided:
-
myokit.formats.stan.
exporters
()¶ Returns a dict of all exporters available in this module.
-
class
myokit.formats.stan.
StanExporter
¶ This:class:Exporter <myokit.formats.Exporter> generates a Stan implementation of a Myokit model.
Only the model definition is exported. An interpolating pacing input method is added. No post-processing is included.
The following inputs are provided:
time
- The current simulation time
pace
- The current value of the pacing system, implemented using a very simple pacing mechanism.
-
runnable
(path, model, protocol=None, parameters=None, output=None)¶ Exports a:class:myokit.Model to a Stan model with a parameter estimation file.
Arguments:
path
- A string representing the directory to store the output in.
model
- A Myokit model to export
protocol
- Not implemented!
parameters
- A list of variables or variable names, specifying the model variables to be estimated by stan.
output
- A single variable to be used as the model output (for example an ion current).
-
myokit.formats.stan.
ewriters
()¶ Returns a dict of all expression writers available in this module.
-
class
myokit.formats.stan.
StanExpressionWriter
¶ This:class:ExpressionWriter <myokit.formats.ExpressionWriter> translates Myokit:class:expressions <myokit.Expression> to a Stan syntax.
-
eq
(q)¶ Converts an equation to a string
-
ex
(e)¶ Converts an Expression to a string.
-
set_condition_function
(func=None)¶ Sets a function name to use for if statements
- By setting func to None you can revert back to the default behavior
- (the ternary operator). Any other value will be interpreted as the name of a function taking arguments (condition, value_if_true, value_if_false).
-
set_lhs_function
(f)¶ - Sets a naming function, will be called to get the variable name from a
myokit.LhsExpression
object.
The argument
f
should be a function that takes anLhsExpression
as input and returns a string.
-