diff --git a/causy/graph.html b/causy/graph.html index cd48329..5500623 100644 --- a/causy/graph.html +++ b/causy/graph.html @@ -2247,7 +2247,7 @@
Extensible JSON https://json.org encoder for Python data structures.
\n\nSupports the following objects and types by default:
\n\n+-------------------+---------------+\n| Python | JSON |\n+===================+===============+\n| dict | object |\n+-------------------+---------------+\n| list, tuple | array |\n+-------------------+---------------+\n| str | string |\n+-------------------+---------------+\n| int, float | number |\n+-------------------+---------------+\n| True | true |\n+-------------------+---------------+\n| False | false |\n+-------------------+---------------+\n| None | null |\n+-------------------+---------------+
\n\nTo extend this to recognize other objects, subclass and implement a\n.default()
method with another method that returns a serializable\nobject for o
if possible, otherwise it should call the superclass\nimplementation (to raise TypeError
).
Implement this method in a subclass such that it returns\na serializable object for o
, or calls the base implementation\n(to raise a TypeError
).
For example, to support arbitrary iterators, you could\nimplement default like this::
\n\ndef default(self, o):\n try:\n iterable = iter(o)\n except TypeError:\n pass\n else:\n return list(iterable)\n # Let the base class default method raise the TypeError\n return JSONEncoder.default(self, o)\n
\n", "signature": "(self, obj):", "funcdef": "def"}, "causy.cli.eject": {"fullname": "causy.cli.eject", "modulename": "causy.cli", "qualname": "eject", "kind": "function", "doc": "\n", "signature": "(algorithm: str, output_file: str):", "funcdef": "def"}, "causy.cli.execute": {"fullname": "causy.cli.execute", "modulename": "causy.cli", "qualname": "execute", "kind": "function", "doc": "\n", "signature": "(\tdata_file: str,\tpipeline: str = None,\talgorithm: str = None,\toutput_file: str = None,\trender_save_file: str = None,\tlog_level: str = 'ERROR'):", "funcdef": "def"}, "causy.cli.visualize": {"fullname": "causy.cli.visualize", "modulename": "causy.cli", "qualname": "visualize", "kind": "function", "doc": "\n", "signature": "(output: str):", "funcdef": "def"}, "causy.exit_conditions": {"fullname": "causy.exit_conditions", "modulename": "causy.exit_conditions", "kind": "module", "doc": "\n"}, "causy.exit_conditions.ExitOnNoActions": {"fullname": "causy.exit_conditions.ExitOnNoActions", "modulename": "causy.exit_conditions", "qualname": "ExitOnNoActions", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.ExitConditionInterface"}, "causy.exit_conditions.ExitOnNoActions.check": {"fullname": "causy.exit_conditions.ExitOnNoActions.check", "modulename": "causy.exit_conditions", "qualname": "ExitOnNoActions.check", "kind": "function", "doc": "Check if there are no actions taken in the last iteration and if so, break the loop\nIf it is the first iteration, do not break the loop (we need to execute the first step)
\n\n\n\n", "signature": "(self, graph, graph_model_instance_, actions_taken, iteration):", "funcdef": "def"}, "causy.generators": {"fullname": "causy.generators", "modulename": "causy.generators", "kind": "module", "doc": "\n"}, "causy.generators.logger": {"fullname": "causy.generators.logger", "modulename": "causy.generators", "qualname": "logger", "kind": "variable", "doc": "\n", "default_value": "<Logger causy.generators (WARNING)>"}, "causy.generators.AllCombinationsGenerator": {"fullname": "causy.generators.AllCombinationsGenerator", "modulename": "causy.generators", "qualname": "AllCombinationsGenerator", "kind": "class", "doc": "True if you want to break an iteration, False otherwise
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.GeneratorInterface"}, "causy.generators.AllCombinationsGenerator.generate": {"fullname": "causy.generators.AllCombinationsGenerator.generate", "modulename": "causy.generators", "qualname": "AllCombinationsGenerator.generate", "kind": "function", "doc": "\n", "signature": "(\tself,\tgraph: causy.interfaces.BaseGraphInterface,\tgraph_model_instance_: causy.interfaces.GraphModelInterface):", "funcdef": "def"}, "causy.generators.PairsWithNeighboursGenerator": {"fullname": "causy.generators.PairsWithNeighboursGenerator", "modulename": "causy.generators", "qualname": "PairsWithNeighboursGenerator", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.GeneratorInterface"}, "causy.generators.PairsWithNeighboursGenerator.__init__": {"fullname": "causy.generators.PairsWithNeighboursGenerator.__init__", "modulename": "causy.generators", "qualname": "PairsWithNeighboursGenerator.__init__", "kind": "function", "doc": "\n", "signature": "(\tcomparison_settings: causy.interfaces.ComparisonSettings,\tchunked: bool = None,\tshuffle_combinations: bool = None)"}, "causy.generators.PairsWithNeighboursGenerator.shuffle_combinations": {"fullname": "causy.generators.PairsWithNeighboursGenerator.shuffle_combinations", "modulename": "causy.generators", "qualname": "PairsWithNeighboursGenerator.shuffle_combinations", "kind": "variable", "doc": "\n", "default_value": "True"}, "causy.generators.PairsWithNeighboursGenerator.chunked": {"fullname": "causy.generators.PairsWithNeighboursGenerator.chunked", "modulename": "causy.generators", "qualname": "PairsWithNeighboursGenerator.chunked", "kind": "variable", "doc": "\n", "default_value": "True"}, "causy.generators.PairsWithNeighboursGenerator.to_dict": {"fullname": "causy.generators.PairsWithNeighboursGenerator.to_dict", "modulename": "causy.generators", "qualname": "PairsWithNeighboursGenerator.to_dict", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "causy.generators.PairsWithNeighboursGenerator.generate": {"fullname": "causy.generators.PairsWithNeighboursGenerator.generate", "modulename": "causy.generators", "qualname": "PairsWithNeighboursGenerator.generate", "kind": "function", "doc": "\n", "signature": "(\tself,\tgraph: causy.interfaces.BaseGraphInterface,\tgraph_model_instance_: causy.interfaces.GraphModelInterface):", "funcdef": "def"}, "causy.graph": {"fullname": "causy.graph", "modulename": "causy.graph", "kind": "module", "doc": "\n"}, "causy.graph.logger": {"fullname": "causy.graph.logger", "modulename": "causy.graph", "qualname": "logger", "kind": "variable", "doc": "\n", "default_value": "<Logger causy.graph (WARNING)>"}, "causy.graph.Node": {"fullname": "causy.graph.Node", "modulename": "causy.graph", "qualname": "Node", "kind": "class", "doc": "\n", "bases": "causy.interfaces.NodeInterface"}, "causy.graph.Node.__init__": {"fullname": "causy.graph.Node.__init__", "modulename": "causy.graph", "qualname": "Node.__init__", "kind": "function", "doc": "\n", "signature": "(name: str, id: str, values: torch.Tensor)"}, "causy.graph.Node.name": {"fullname": "causy.graph.Node.name", "modulename": "causy.graph", "qualname": "Node.name", "kind": "variable", "doc": "\n", "annotation": ": str"}, "causy.graph.Node.id": {"fullname": "causy.graph.Node.id", "modulename": "causy.graph", "qualname": "Node.id", "kind": "variable", "doc": "\n", "annotation": ": str"}, "causy.graph.Node.values": {"fullname": "causy.graph.Node.values", "modulename": "causy.graph", "qualname": "Node.values", "kind": "variable", "doc": "\n", "annotation": ": torch.Tensor"}, "causy.graph.UndirectedGraphError": {"fullname": "causy.graph.UndirectedGraphError", "modulename": "causy.graph", "qualname": "UndirectedGraphError", "kind": "class", "doc": "Common base class for all non-exit exceptions.
\n", "bases": "builtins.Exception"}, "causy.graph.UndirectedGraph": {"fullname": "causy.graph.UndirectedGraph", "modulename": "causy.graph", "qualname": "UndirectedGraph", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.BaseGraphInterface"}, "causy.graph.UndirectedGraph.nodes": {"fullname": "causy.graph.UndirectedGraph.nodes", "modulename": "causy.graph", "qualname": "UndirectedGraph.nodes", "kind": "variable", "doc": "\n", "annotation": ": Dict[str, causy.graph.Node]"}, "causy.graph.UndirectedGraph.edges": {"fullname": "causy.graph.UndirectedGraph.edges", "modulename": "causy.graph", "qualname": "UndirectedGraph.edges", "kind": "variable", "doc": "\n", "annotation": ": Dict[str, Dict[str, Dict]]"}, "causy.graph.UndirectedGraph.edge_history": {"fullname": "causy.graph.UndirectedGraph.edge_history", "modulename": "causy.graph", "qualname": "UndirectedGraph.edge_history", "kind": "variable", "doc": "\n", "annotation": ": Dict[Tuple[str, str], List[causy.interfaces.TestResult]]"}, "causy.graph.UndirectedGraph.action_history": {"fullname": "causy.graph.UndirectedGraph.action_history", "modulename": "causy.graph", "qualname": "UndirectedGraph.action_history", "kind": "variable", "doc": "\n", "annotation": ": List[Dict[str, List[causy.interfaces.TestResult]]]"}, "causy.graph.UndirectedGraph.add_edge": {"fullname": "causy.graph.UndirectedGraph.add_edge", "modulename": "causy.graph", "qualname": "UndirectedGraph.add_edge", "kind": "function", "doc": "Add an edge to the graph
\n\nRetrieve the edge history
\n\nRemove an edge from the graph
\n\nRemove an edge from the graph
\n\nUpdate an edge in the graph
\n\nUpdate an edge in the graph
\n\nCheck if any edge exists between u and v. Cases: u -> v, u <-> v, u <- v
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.directed_edge_exists": {"fullname": "causy.graph.UndirectedGraph.directed_edge_exists", "modulename": "causy.graph", "qualname": "UndirectedGraph.directed_edge_exists", "kind": "function", "doc": "True if any edge exists, False otherwise
\n
Check if a directed edge exists between u and v. Cases: u -> v, u <-> v
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.only_directed_edge_exists": {"fullname": "causy.graph.UndirectedGraph.only_directed_edge_exists", "modulename": "causy.graph", "qualname": "UndirectedGraph.only_directed_edge_exists", "kind": "function", "doc": "True if a directed edge exists, False otherwise
\n
Check if a directed edge exists between u and v, but no directed edge exists between v and u. Case: u -> v
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.undirected_edge_exists": {"fullname": "causy.graph.UndirectedGraph.undirected_edge_exists", "modulename": "causy.graph", "qualname": "UndirectedGraph.undirected_edge_exists", "kind": "function", "doc": "True if only directed edge exists, False otherwise
\n
Check if an undirected edge exists between u and v. Note: currently, an undirected edges is implemented just as\na directed edge. However, they are two functions as they mean different things in different algorithms.\nCurrently, this function is used in the PC algorithm, where an undirected edge is an edge which could not be\noriented in any direction by orientation rules.\nLater, a cohersive naming scheme should be implemented.
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.bidirected_edge_exists": {"fullname": "causy.graph.UndirectedGraph.bidirected_edge_exists", "modulename": "causy.graph", "qualname": "UndirectedGraph.bidirected_edge_exists", "kind": "function", "doc": "True if an undirected edge exists, False otherwise
\n
Check if a bidirected edge exists between u and v. Note: currently, a bidirected edges is implemented just as\nan undirected edge. However, they are two functions as they mean different things in different algorithms.\nThis function will be used for the FCI algorithm for now, where a bidirected edge is an edge between two nodes\nthat have been identified to have a common cause by orientation rules.\nLater, a cohersive naming scheme should be implemented.
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.edge_value": {"fullname": "causy.graph.UndirectedGraph.edge_value", "modulename": "causy.graph", "qualname": "UndirectedGraph.edge_value", "kind": "function", "doc": "\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.add_node": {"fullname": "causy.graph.UndirectedGraph.add_node", "modulename": "causy.graph", "qualname": "UndirectedGraph.add_node", "kind": "function", "doc": "True if a bidirected edge exists, False otherwise
\n
Add a node to the graph
\n\nCheck if a directed path from u to v exists
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.directed_paths": {"fullname": "causy.graph.UndirectedGraph.directed_paths", "modulename": "causy.graph", "qualname": "UndirectedGraph.directed_paths", "kind": "function", "doc": "True if a directed path exists, False otherwise
\n
Return all directed paths from u to v
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.inducing_path_exists": {"fullname": "causy.graph.UndirectedGraph.inducing_path_exists", "modulename": "causy.graph", "qualname": "UndirectedGraph.inducing_path_exists", "kind": "function", "doc": "list of directed paths
\n
Check if an inducing path from u to v exists.\nAn inducing path from u to v is a directed path from u to v on which all mediators are colliders.
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.unpack_run": {"fullname": "causy.graph.unpack_run", "modulename": "causy.graph", "qualname": "unpack_run", "kind": "function", "doc": "\n", "signature": "(args):", "funcdef": "def"}, "causy.graph.AbstractGraphModel": {"fullname": "causy.graph.AbstractGraphModel", "modulename": "causy.graph", "qualname": "AbstractGraphModel", "kind": "class", "doc": "True if an inducing path exists, False otherwise
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.GraphModelInterface, abc.ABC"}, "causy.graph.AbstractGraphModel.__init__": {"fullname": "causy.graph.AbstractGraphModel.__init__", "modulename": "causy.graph", "qualname": "AbstractGraphModel.__init__", "kind": "function", "doc": "\n", "signature": "(\tgraph=None,\tpipeline_steps: Optional[List[causy.interfaces.IndependenceTestInterface]] = None)"}, "causy.graph.AbstractGraphModel.pipeline_steps": {"fullname": "causy.graph.AbstractGraphModel.pipeline_steps", "modulename": "causy.graph", "qualname": "AbstractGraphModel.pipeline_steps", "kind": "variable", "doc": "\n", "annotation": ": List[causy.interfaces.IndependenceTestInterface]"}, "causy.graph.AbstractGraphModel.graph": {"fullname": "causy.graph.AbstractGraphModel.graph", "modulename": "causy.graph", "qualname": "AbstractGraphModel.graph", "kind": "variable", "doc": "\n", "annotation": ": causy.interfaces.BaseGraphInterface"}, "causy.graph.AbstractGraphModel.pool": {"fullname": "causy.graph.AbstractGraphModel.pool", "modulename": "causy.graph", "qualname": "AbstractGraphModel.pool", "kind": "variable", "doc": "\n", "annotation": ": <bound method BaseContext.Pool of <multiprocessing.context.DefaultContext object at 0x1073a5e10>>"}, "causy.graph.AbstractGraphModel.create_graph_from_data": {"fullname": "causy.graph.AbstractGraphModel.create_graph_from_data", "modulename": "causy.graph", "qualname": "AbstractGraphModel.create_graph_from_data", "kind": "function", "doc": "Create a graph from data
\n\nCreate all possible nodes
\n\nExecute all pipeline_steps
\n\n\n\n", "signature": "(self):", "funcdef": "def"}, "causy.graph.AbstractGraphModel.execute_pipeline_step": {"fullname": "causy.graph.AbstractGraphModel.execute_pipeline_step", "modulename": "causy.graph", "qualname": "AbstractGraphModel.execute_pipeline_step", "kind": "function", "doc": "the steps taken during the step execution
\n
Filter the graph
\n\nCreate a graph model
\n\n\n\n", "signature": "(\tpipeline_steps: Optional[List[causy.interfaces.IndependenceTestInterface]] = None) -> type[causy.graph.AbstractGraphModel]:", "funcdef": "def"}, "causy.graph.Loop": {"fullname": "causy.graph.Loop", "modulename": "causy.graph", "qualname": "Loop", "kind": "class", "doc": "the graph model
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.LogicStepInterface"}, "causy.graph.Loop.__init__": {"fullname": "causy.graph.Loop.__init__", "modulename": "causy.graph", "qualname": "Loop.__init__", "kind": "function", "doc": "\n", "signature": "(\tpipeline_steps: Optional[List[causy.interfaces.IndependenceTestInterface]] = None,\texit_condition: causy.interfaces.ExitConditionInterface = None)"}, "causy.graph.Loop.execute": {"fullname": "causy.graph.Loop.execute", "modulename": "causy.graph", "qualname": "Loop.execute", "kind": "function", "doc": "\n", "signature": "(\tself,\tgraph: causy.interfaces.BaseGraphInterface,\tgraph_model_instance_: causy.interfaces.GraphModelInterface):", "funcdef": "def"}, "causy.graph.Loop.pipeline_steps": {"fullname": "causy.graph.Loop.pipeline_steps", "modulename": "causy.graph", "qualname": "Loop.pipeline_steps", "kind": "variable", "doc": "\n"}, "causy.graph.Loop.exit_condition": {"fullname": "causy.graph.Loop.exit_condition", "modulename": "causy.graph", "qualname": "Loop.exit_condition", "kind": "variable", "doc": "\n"}, "causy.graph.Loop.serialize": {"fullname": "causy.graph.Loop.serialize", "modulename": "causy.graph", "qualname": "Loop.serialize", "kind": "function", "doc": "\n", "signature": "(self) -> dict:", "funcdef": "def"}, "causy.independence_tests": {"fullname": "causy.independence_tests", "modulename": "causy.independence_tests", "kind": "module", "doc": "\n"}, "causy.independence_tests.logger": {"fullname": "causy.independence_tests.logger", "modulename": "causy.independence_tests", "qualname": "logger", "kind": "variable", "doc": "\n", "default_value": "<Logger causy.independence_tests (WARNING)>"}, "causy.independence_tests.CalculateCorrelations": {"fullname": "causy.independence_tests.CalculateCorrelations", "modulename": "causy.independence_tests", "qualname": "CalculateCorrelations", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.independence_tests.CalculateCorrelations.GENERATOR": {"fullname": "causy.independence_tests.CalculateCorrelations.GENERATOR", "modulename": "causy.independence_tests", "qualname": "CalculateCorrelations.GENERATOR", "kind": "variable", "doc": "\n", "default_value": "<causy.generators.AllCombinationsGenerator object>"}, "causy.independence_tests.CalculateCorrelations.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.independence_tests.CalculateCorrelations.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.independence_tests", "qualname": "CalculateCorrelations.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "1"}, "causy.independence_tests.CalculateCorrelations.PARALLEL": {"fullname": "causy.independence_tests.CalculateCorrelations.PARALLEL", "modulename": "causy.independence_tests", "qualname": "CalculateCorrelations.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "False"}, "causy.independence_tests.CalculateCorrelations.test": {"fullname": "causy.independence_tests.CalculateCorrelations.test", "modulename": "causy.independence_tests", "qualname": "CalculateCorrelations.test", "kind": "function", "doc": "Calculate the correlation between each pair of nodes and store it to the respective edge.
\n\n\n\n", "signature": "(\tself,\tnodes: Tuple[str],\tgraph: causy.interfaces.BaseGraphInterface) -> causy.interfaces.TestResult:", "funcdef": "def"}, "causy.independence_tests.CorrelationCoefficientTest": {"fullname": "causy.independence_tests.CorrelationCoefficientTest", "modulename": "causy.independence_tests", "qualname": "CorrelationCoefficientTest", "kind": "class", "doc": "A TestResult with the action to take
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.independence_tests.CorrelationCoefficientTest.GENERATOR": {"fullname": "causy.independence_tests.CorrelationCoefficientTest.GENERATOR", "modulename": "causy.independence_tests", "qualname": "CorrelationCoefficientTest.GENERATOR", "kind": "variable", "doc": "\n", "default_value": "<causy.generators.AllCombinationsGenerator object>"}, "causy.independence_tests.CorrelationCoefficientTest.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.independence_tests.CorrelationCoefficientTest.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.independence_tests", "qualname": "CorrelationCoefficientTest.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "1"}, "causy.independence_tests.CorrelationCoefficientTest.PARALLEL": {"fullname": "causy.independence_tests.CorrelationCoefficientTest.PARALLEL", "modulename": "causy.independence_tests", "qualname": "CorrelationCoefficientTest.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "False"}, "causy.independence_tests.CorrelationCoefficientTest.test": {"fullname": "causy.independence_tests.CorrelationCoefficientTest.test", "modulename": "causy.independence_tests", "qualname": "CorrelationCoefficientTest.test", "kind": "function", "doc": "Test if x and y are independent and delete edge in graph if they are.
\n\n\n\n", "signature": "(\tself,\tnodes: List[str],\tgraph: causy.interfaces.BaseGraphInterface) -> Optional[causy.interfaces.TestResult]:", "funcdef": "def"}, "causy.independence_tests.PartialCorrelationTest": {"fullname": "causy.independence_tests.PartialCorrelationTest", "modulename": "causy.independence_tests", "qualname": "PartialCorrelationTest", "kind": "class", "doc": "A TestResult with the action to take
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.independence_tests.PartialCorrelationTest.GENERATOR": {"fullname": "causy.independence_tests.PartialCorrelationTest.GENERATOR", "modulename": "causy.independence_tests", "qualname": "PartialCorrelationTest.GENERATOR", "kind": "variable", "doc": "\n", "default_value": "<causy.generators.AllCombinationsGenerator object>"}, "causy.independence_tests.PartialCorrelationTest.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.independence_tests.PartialCorrelationTest.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.independence_tests", "qualname": "PartialCorrelationTest.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "1"}, "causy.independence_tests.PartialCorrelationTest.PARALLEL": {"fullname": "causy.independence_tests.PartialCorrelationTest.PARALLEL", "modulename": "causy.independence_tests", "qualname": "PartialCorrelationTest.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "False"}, "causy.independence_tests.PartialCorrelationTest.test": {"fullname": "causy.independence_tests.PartialCorrelationTest.test", "modulename": "causy.independence_tests", "qualname": "PartialCorrelationTest.test", "kind": "function", "doc": "Test if nodes x,y are independent given node z based on a partial correlation test.\nWe use this test for all combinations of 3 nodes because it is faster than the extended test (which supports combinations of n nodes). We can\nuse it to remove edges between nodes which are not independent given another node and so reduce the number of combinations for the extended test.
\n\n\n\n\nA TestResult with the action to take
\n
TODO: we are testing (C and E given B) and (E and C given B), we just need one of these, remove redundant tests.
\n", "signature": "(\tself,\tnodes: Tuple[str],\tgraph: causy.interfaces.BaseGraphInterface) -> Optional[List[causy.interfaces.TestResult]]:", "funcdef": "def"}, "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestLinearRegression", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.GENERATOR": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.GENERATOR", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestLinearRegression.GENERATOR", "kind": "variable", "doc": "\n", "default_value": "<causy.generators.AllCombinationsGenerator object>"}, "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestLinearRegression.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "1000"}, "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.PARALLEL": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.PARALLEL", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestLinearRegression.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "True"}, "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.test": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.test", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestLinearRegression.test", "kind": "function", "doc": "Test if nodes x,y are independent given Z (set of nodes) based on partial correlation using linear regression and a correlation test on the residuals.\nWe use this test for all combinations of more than 3 nodes because it is slower.
\n\n\n\n\nA TestResult with the action to take
\n
TODO: Does not run in reasonable time yet.
\n", "signature": "(\tself,\tnodes: List[str],\tgraph: causy.interfaces.BaseGraphInterface) -> Optional[List[causy.interfaces.TestResult]]:", "funcdef": "def"}, "causy.independence_tests.ExtendedPartialCorrelationTestMatrix": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestMatrix", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestMatrix", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.GENERATOR": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.GENERATOR", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestMatrix.GENERATOR", "kind": "variable", "doc": "\n", "default_value": "<causy.generators.PairsWithNeighboursGenerator object>"}, "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestMatrix.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "1000"}, "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.PARALLEL": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.PARALLEL", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestMatrix.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "False"}, "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.test": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.test", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestMatrix.test", "kind": "function", "doc": "Test if nodes x,y are independent given Z (set of nodes) based on partial correlation using the inverted covariance matrix (precision matrix).\nhttps://en.wikipedia.org/wiki/Partial_correlation#Using_matrix_inversion\nWe use this test for all combinations of more than 3 nodes because it is slower.
\n\n\n\n", "signature": "(\tself,\tnodes: List[str],\tgraph: causy.interfaces.BaseGraphInterface) -> Optional[causy.interfaces.TestResult]:", "funcdef": "def"}, "causy.independence_tests.PlaceholderTest": {"fullname": "causy.independence_tests.PlaceholderTest", "modulename": "causy.independence_tests", "qualname": "PlaceholderTest", "kind": "class", "doc": "A TestResult with the action to take
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.independence_tests.PlaceholderTest.NUM_OF_COMPARISON_ELEMENTS": {"fullname": "causy.independence_tests.PlaceholderTest.NUM_OF_COMPARISON_ELEMENTS", "modulename": "causy.independence_tests", "qualname": "PlaceholderTest.NUM_OF_COMPARISON_ELEMENTS", "kind": "variable", "doc": "\n", "default_value": "2"}, "causy.independence_tests.PlaceholderTest.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.independence_tests.PlaceholderTest.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.independence_tests", "qualname": "PlaceholderTest.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "10"}, "causy.independence_tests.PlaceholderTest.PARALLEL": {"fullname": "causy.independence_tests.PlaceholderTest.PARALLEL", "modulename": "causy.independence_tests", "qualname": "PlaceholderTest.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "False"}, "causy.independence_tests.PlaceholderTest.test": {"fullname": "causy.independence_tests.PlaceholderTest.test", "modulename": "causy.independence_tests", "qualname": "PlaceholderTest.test", "kind": "function", "doc": "Placeholder test for testing purposes
\n\nEnum where members are also (and must be) strings
\n", "bases": "enum.StrEnum"}, "causy.interfaces.TestResultAction.REMOVE_EDGE_UNDIRECTED": {"fullname": "causy.interfaces.TestResultAction.REMOVE_EDGE_UNDIRECTED", "modulename": "causy.interfaces", "qualname": "TestResultAction.REMOVE_EDGE_UNDIRECTED", "kind": "variable", "doc": "\n", "default_value": "<TestResultAction.REMOVE_EDGE_UNDIRECTED: 'REMOVE_EDGE_UNDIRECTED'>"}, "causy.interfaces.TestResultAction.UPDATE_EDGE": {"fullname": "causy.interfaces.TestResultAction.UPDATE_EDGE", "modulename": "causy.interfaces", "qualname": "TestResultAction.UPDATE_EDGE", "kind": "variable", "doc": "\n", "default_value": "<TestResultAction.UPDATE_EDGE: 'UPDATE_EDGE'>"}, "causy.interfaces.TestResultAction.UPDATE_EDGE_DIRECTED": {"fullname": "causy.interfaces.TestResultAction.UPDATE_EDGE_DIRECTED", "modulename": "causy.interfaces", "qualname": "TestResultAction.UPDATE_EDGE_DIRECTED", "kind": "variable", "doc": "\n", "default_value": "<TestResultAction.UPDATE_EDGE_DIRECTED: 'UPDATE_EDGE_DIRECTED'>"}, "causy.interfaces.TestResultAction.DO_NOTHING": {"fullname": "causy.interfaces.TestResultAction.DO_NOTHING", "modulename": "causy.interfaces", "qualname": "TestResultAction.DO_NOTHING", "kind": "variable", "doc": "\n", "default_value": "<TestResultAction.DO_NOTHING: 'DO_NOTHING'>"}, "causy.interfaces.TestResultAction.REMOVE_EDGE_DIRECTED": {"fullname": "causy.interfaces.TestResultAction.REMOVE_EDGE_DIRECTED", "modulename": "causy.interfaces", "qualname": "TestResultAction.REMOVE_EDGE_DIRECTED", "kind": "variable", "doc": "\n", "default_value": "<TestResultAction.REMOVE_EDGE_DIRECTED: 'REMOVE_EDGE_DIRECTED'>"}, "causy.interfaces.TestResult": {"fullname": "causy.interfaces.TestResult", "modulename": "causy.interfaces", "qualname": "TestResult", "kind": "class", "doc": "\n"}, "causy.interfaces.TestResult.__init__": {"fullname": "causy.interfaces.TestResult.__init__", "modulename": "causy.interfaces", "qualname": "TestResult.__init__", "kind": "function", "doc": "\n", "signature": "(\tx: causy.interfaces.NodeInterface,\ty: causy.interfaces.NodeInterface,\taction: causy.interfaces.TestResultAction,\tdata: Optional[Dict] = None)"}, "causy.interfaces.TestResult.x": {"fullname": "causy.interfaces.TestResult.x", "modulename": "causy.interfaces", "qualname": "TestResult.x", "kind": "variable", "doc": "\n", "annotation": ": causy.interfaces.NodeInterface"}, "causy.interfaces.TestResult.y": {"fullname": "causy.interfaces.TestResult.y", "modulename": "causy.interfaces", "qualname": "TestResult.y", "kind": "variable", "doc": "\n", "annotation": ": causy.interfaces.NodeInterface"}, "causy.interfaces.TestResult.action": {"fullname": "causy.interfaces.TestResult.action", "modulename": "causy.interfaces", "qualname": "TestResult.action", "kind": "variable", "doc": "\n", "annotation": ": causy.interfaces.TestResultAction"}, "causy.interfaces.TestResult.data": {"fullname": "causy.interfaces.TestResult.data", "modulename": "causy.interfaces", "qualname": "TestResult.data", "kind": "variable", "doc": "\n", "annotation": ": Optional[Dict]", "default_value": "None"}, "causy.interfaces.TestResult.to_dict": {"fullname": "causy.interfaces.TestResult.to_dict", "modulename": "causy.interfaces", "qualname": "TestResult.to_dict", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface": {"fullname": "causy.interfaces.BaseGraphInterface", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "abc.ABC"}, "causy.interfaces.BaseGraphInterface.nodes": {"fullname": "causy.interfaces.BaseGraphInterface.nodes", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.nodes", "kind": "variable", "doc": "\n", "annotation": ": Dict[str, causy.interfaces.NodeInterface]"}, "causy.interfaces.BaseGraphInterface.edges": {"fullname": "causy.interfaces.BaseGraphInterface.edges", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.edges", "kind": "variable", "doc": "\n", "annotation": ": Dict[str, Dict[str, Dict]]"}, "causy.interfaces.BaseGraphInterface.retrieve_edge_history": {"fullname": "causy.interfaces.BaseGraphInterface.retrieve_edge_history", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.retrieve_edge_history", "kind": "function", "doc": "\n", "signature": "(\tself,\tu,\tv,\taction: causy.interfaces.TestResultAction) -> List[causy.interfaces.TestResult]:", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.add_edge_history": {"fullname": "causy.interfaces.BaseGraphInterface.add_edge_history", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.add_edge_history", "kind": "function", "doc": "\n", "signature": "(self, u, v, action: causy.interfaces.TestResultAction):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.add_edge": {"fullname": "causy.interfaces.BaseGraphInterface.add_edge", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.add_edge", "kind": "function", "doc": "\n", "signature": "(self, u, v, w):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.remove_edge": {"fullname": "causy.interfaces.BaseGraphInterface.remove_edge", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.remove_edge", "kind": "function", "doc": "\n", "signature": "(self, u, v):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.remove_directed_edge": {"fullname": "causy.interfaces.BaseGraphInterface.remove_directed_edge", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.remove_directed_edge", "kind": "function", "doc": "\n", "signature": "(self, u, v):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.update_edge": {"fullname": "causy.interfaces.BaseGraphInterface.update_edge", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.update_edge", "kind": "function", "doc": "\n", "signature": "(self, u, v, w):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.add_node": {"fullname": "causy.interfaces.BaseGraphInterface.add_node", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.add_node", "kind": "function", "doc": "\n", "signature": "(self, name, values):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.edge_value": {"fullname": "causy.interfaces.BaseGraphInterface.edge_value", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.edge_value", "kind": "function", "doc": "\n", "signature": "(self, u, v):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.undirected_edge_exists": {"fullname": "causy.interfaces.BaseGraphInterface.undirected_edge_exists", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.undirected_edge_exists", "kind": "function", "doc": "\n", "signature": "(self, u, v):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.directed_edge_exists": {"fullname": "causy.interfaces.BaseGraphInterface.directed_edge_exists", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.directed_edge_exists", "kind": "function", "doc": "\n", "signature": "(self, u, v):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.edge_exists": {"fullname": "causy.interfaces.BaseGraphInterface.edge_exists", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.edge_exists", "kind": "function", "doc": "\n", "signature": "(self, u, v):", "funcdef": "def"}, "causy.interfaces.GraphModelInterface": {"fullname": "causy.interfaces.GraphModelInterface", "modulename": "causy.interfaces", "qualname": "GraphModelInterface", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "abc.ABC"}, "causy.interfaces.GraphModelInterface.pool": {"fullname": "causy.interfaces.GraphModelInterface.pool", "modulename": "causy.interfaces", "qualname": "GraphModelInterface.pool", "kind": "variable", "doc": "\n", "annotation": ": <bound method BaseContext.Pool of <multiprocessing.context.DefaultContext object at 0x1073a5e10>>"}, "causy.interfaces.GraphModelInterface.create_graph_from_data": {"fullname": "causy.interfaces.GraphModelInterface.create_graph_from_data", "modulename": "causy.interfaces", "qualname": "GraphModelInterface.create_graph_from_data", "kind": "function", "doc": "\n", "signature": "(self, data: List[Dict]):", "funcdef": "def"}, "causy.interfaces.GraphModelInterface.execute_pipeline_steps": {"fullname": "causy.interfaces.GraphModelInterface.execute_pipeline_steps", "modulename": "causy.interfaces", "qualname": "GraphModelInterface.execute_pipeline_steps", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "causy.interfaces.GraphModelInterface.execute_pipeline_step": {"fullname": "causy.interfaces.GraphModelInterface.execute_pipeline_step", "modulename": "causy.interfaces", "qualname": "GraphModelInterface.execute_pipeline_step", "kind": "function", "doc": "\n", "signature": "(self, step):", "funcdef": "def"}, "causy.interfaces.GeneratorInterface": {"fullname": "causy.interfaces.GeneratorInterface", "modulename": "causy.interfaces", "qualname": "GeneratorInterface", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "abc.ABC"}, "causy.interfaces.GeneratorInterface.comparison_settings": {"fullname": "causy.interfaces.GeneratorInterface.comparison_settings", "modulename": "causy.interfaces", "qualname": "GeneratorInterface.comparison_settings", "kind": "variable", "doc": "\n", "annotation": ": causy.interfaces.ComparisonSettings"}, "causy.interfaces.GeneratorInterface.chunked": {"fullname": "causy.interfaces.GeneratorInterface.chunked", "modulename": "causy.interfaces", "qualname": "GeneratorInterface.chunked", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, "causy.interfaces.GeneratorInterface.generate": {"fullname": "causy.interfaces.GeneratorInterface.generate", "modulename": "causy.interfaces", "qualname": "GeneratorInterface.generate", "kind": "function", "doc": "\n", "signature": "(\tself,\tgraph: causy.interfaces.BaseGraphInterface,\tgraph_model_instance_: dict):", "funcdef": "def"}, "causy.interfaces.GeneratorInterface.serialize": {"fullname": "causy.interfaces.GeneratorInterface.serialize", "modulename": "causy.interfaces", "qualname": "GeneratorInterface.serialize", "kind": "function", "doc": "\n", "signature": "(self) -> dict:", "funcdef": "def"}, "causy.interfaces.IndependenceTestInterface": {"fullname": "causy.interfaces.IndependenceTestInterface", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "abc.ABC"}, "causy.interfaces.IndependenceTestInterface.NUM_OF_COMPARISON_ELEMENTS": {"fullname": "causy.interfaces.IndependenceTestInterface.NUM_OF_COMPARISON_ELEMENTS", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface.NUM_OF_COMPARISON_ELEMENTS", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "0"}, "causy.interfaces.IndependenceTestInterface.GENERATOR": {"fullname": "causy.interfaces.IndependenceTestInterface.GENERATOR", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface.GENERATOR", "kind": "variable", "doc": "\n", "annotation": ": Optional[causy.interfaces.GeneratorInterface]", "default_value": "None"}, "causy.interfaces.IndependenceTestInterface.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.interfaces.IndependenceTestInterface.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "1"}, "causy.interfaces.IndependenceTestInterface.PARALLEL": {"fullname": "causy.interfaces.IndependenceTestInterface.PARALLEL", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface.PARALLEL", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "True"}, "causy.interfaces.IndependenceTestInterface.threshold": {"fullname": "causy.interfaces.IndependenceTestInterface.threshold", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface.threshold", "kind": "variable", "doc": "\n"}, "causy.interfaces.IndependenceTestInterface.test": {"fullname": "causy.interfaces.IndependenceTestInterface.test", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface.test", "kind": "function", "doc": "Test if x and y are independent
\n\n\n\n", "signature": "(\tself,\tnodes: List[str],\tgraph: causy.interfaces.BaseGraphInterface) -> Optional[causy.interfaces.TestResult]:", "funcdef": "def"}, "causy.interfaces.IndependenceTestInterface.serialize": {"fullname": "causy.interfaces.IndependenceTestInterface.serialize", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface.serialize", "kind": "function", "doc": "\n", "signature": "(self) -> dict:", "funcdef": "def"}, "causy.interfaces.LogicStepInterface": {"fullname": "causy.interfaces.LogicStepInterface", "modulename": "causy.interfaces", "qualname": "LogicStepInterface", "kind": "class", "doc": "True if independent, False otherwise
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "abc.ABC"}, "causy.interfaces.LogicStepInterface.execute": {"fullname": "causy.interfaces.LogicStepInterface.execute", "modulename": "causy.interfaces", "qualname": "LogicStepInterface.execute", "kind": "function", "doc": "\n", "signature": "(\tself,\tgraph: causy.interfaces.BaseGraphInterface,\tgraph_model_instance_: dict):", "funcdef": "def"}, "causy.interfaces.LogicStepInterface.serialize": {"fullname": "causy.interfaces.LogicStepInterface.serialize", "modulename": "causy.interfaces", "qualname": "LogicStepInterface.serialize", "kind": "function", "doc": "\n", "signature": "(self) -> dict:", "funcdef": "def"}, "causy.interfaces.ExitConditionInterface": {"fullname": "causy.interfaces.ExitConditionInterface", "modulename": "causy.interfaces", "qualname": "ExitConditionInterface", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "abc.ABC"}, "causy.interfaces.ExitConditionInterface.check": {"fullname": "causy.interfaces.ExitConditionInterface.check", "modulename": "causy.interfaces", "qualname": "ExitConditionInterface.check", "kind": "function", "doc": "\n\n", "signature": "(\tself,\tgraph: causy.interfaces.BaseGraphInterface,\tgraph_model_instance_: dict,\tactions_taken: List[causy.interfaces.TestResult],\titeration: int) -> bool:", "funcdef": "def"}, "causy.interfaces.ExitConditionInterface.serialize": {"fullname": "causy.interfaces.ExitConditionInterface.serialize", "modulename": "causy.interfaces", "qualname": "ExitConditionInterface.serialize", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "causy.orientation_tests": {"fullname": "causy.orientation_tests", "modulename": "causy.orientation_tests", "kind": "module", "doc": "\n"}, "causy.orientation_tests.ColliderTest": {"fullname": "causy.orientation_tests.ColliderTest", "modulename": "causy.orientation_tests", "qualname": "ColliderTest", "kind": "class", "doc": "True if you want to break an iteration, False otherwise
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.orientation_tests.ColliderTest.GENERATOR": {"fullname": "causy.orientation_tests.ColliderTest.GENERATOR", "modulename": "causy.orientation_tests", "qualname": "ColliderTest.GENERATOR", "kind": "variable", "doc": "\n", "default_value": "<causy.generators.AllCombinationsGenerator object>"}, "causy.orientation_tests.ColliderTest.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.orientation_tests.ColliderTest.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.orientation_tests", "qualname": "ColliderTest.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "1"}, "causy.orientation_tests.ColliderTest.PARALLEL": {"fullname": "causy.orientation_tests.ColliderTest.PARALLEL", "modulename": "causy.orientation_tests", "qualname": "ColliderTest.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "False"}, "causy.orientation_tests.ColliderTest.test": {"fullname": "causy.orientation_tests.ColliderTest.test", "modulename": "causy.orientation_tests", "qualname": "ColliderTest.test", "kind": "function", "doc": "We call triples x, y, z of nodes v structures if x and y that are NOT adjacent but share an adjacent node z.\nV structures looks like this in the undirected skeleton: (x - z - y).\nWe now check if z is in the separating set.\nIf z is not in the separating set, we know that x and y are uncorrelated given z.\nSo, the edges must be oriented from x to z and from y to z (x -> z <- y).
\n\nHelper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.orientation_tests.NonColliderTest.GENERATOR": {"fullname": "causy.orientation_tests.NonColliderTest.GENERATOR", "modulename": "causy.orientation_tests", "qualname": "NonColliderTest.GENERATOR", "kind": "variable", "doc": "\n", "default_value": "<causy.generators.AllCombinationsGenerator object>"}, "causy.orientation_tests.NonColliderTest.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.orientation_tests.NonColliderTest.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.orientation_tests", "qualname": "NonColliderTest.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "1"}, "causy.orientation_tests.NonColliderTest.PARALLEL": {"fullname": "causy.orientation_tests.NonColliderTest.PARALLEL", "modulename": "causy.orientation_tests", "qualname": "NonColliderTest.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "False"}, "causy.orientation_tests.NonColliderTest.test": {"fullname": "causy.orientation_tests.NonColliderTest.test", "modulename": "causy.orientation_tests", "qualname": "NonColliderTest.test", "kind": "function", "doc": "Further orientation rule: all v structures that are colliders are already oriented.\nWe now orient all v structures that have a single alternative to being a collider.
\n\nHelper class that provides a standard way to create an ABC using\ninheritance.
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\n\nHelper class that provides a standard way to create an ABC using\ninheritance.
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\n\nHelper class that provides a standard way to create an ABC using\ninheritance.
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\n\n\n\n", "signature": "(*lists):", "funcdef": "def"}, "causy.utils.backward_substituion": {"fullname": "causy.utils.backward_substituion", "modulename": "causy.utils", "qualname": "backward_substituion", "kind": "function", "doc": "list (sum of lists)
\n
\n\n", "signature": "(R, b, n):", "funcdef": "def"}, "causy.utils.get_regression_coefficients": {"fullname": "causy.utils.get_regression_coefficients", "modulename": "causy.utils", "qualname": "get_regression_coefficients", "kind": "function", "doc": "Matrix, n-dimensional regression coefficient vector
\n
\n\n", "signature": "(x, Z):", "funcdef": "def"}, "causy.utils.get_residuals": {"fullname": "causy.utils.get_residuals", "modulename": "causy.utils", "qualname": "get_residuals", "kind": "function", "doc": "sympy matrix, regression coefficients from regressing x on Z
\n
\n\n\nresidual \u2013 list (length = # of samples)
\n
CAUTION: Z must have full rank\nTODO: add optional check
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\n\nSupports the following objects and types by default:
\n\n+-------------------+---------------+\n| Python | JSON |\n+===================+===============+\n| dict | object |\n+-------------------+---------------+\n| list, tuple | array |\n+-------------------+---------------+\n| str | string |\n+-------------------+---------------+\n| int, float | number |\n+-------------------+---------------+\n| True | true |\n+-------------------+---------------+\n| False | false |\n+-------------------+---------------+\n| None | null |\n+-------------------+---------------+
\n\nTo extend this to recognize other objects, subclass and implement a\n.default()
method with another method that returns a serializable\nobject for o
if possible, otherwise it should call the superclass\nimplementation (to raise TypeError
).
Implement this method in a subclass such that it returns\na serializable object for o
, or calls the base implementation\n(to raise a TypeError
).
For example, to support arbitrary iterators, you could\nimplement default like this::
\n\ndef default(self, o):\n try:\n iterable = iter(o)\n except TypeError:\n pass\n else:\n return list(iterable)\n # Let the base class default method raise the TypeError\n return JSONEncoder.default(self, o)\n
\n", "signature": "(self, obj):", "funcdef": "def"}, "causy.cli.eject": {"fullname": "causy.cli.eject", "modulename": "causy.cli", "qualname": "eject", "kind": "function", "doc": "\n", "signature": "(algorithm: str, output_file: str):", "funcdef": "def"}, "causy.cli.execute": {"fullname": "causy.cli.execute", "modulename": "causy.cli", "qualname": "execute", "kind": "function", "doc": "\n", "signature": "(\tdata_file: str,\tpipeline: str = None,\talgorithm: str = None,\toutput_file: str = None,\trender_save_file: str = None,\tlog_level: str = 'ERROR'):", "funcdef": "def"}, "causy.cli.visualize": {"fullname": "causy.cli.visualize", "modulename": "causy.cli", "qualname": "visualize", "kind": "function", "doc": "\n", "signature": "(output: str):", "funcdef": "def"}, "causy.exit_conditions": {"fullname": "causy.exit_conditions", "modulename": "causy.exit_conditions", "kind": "module", "doc": "\n"}, "causy.exit_conditions.ExitOnNoActions": {"fullname": "causy.exit_conditions.ExitOnNoActions", "modulename": "causy.exit_conditions", "qualname": "ExitOnNoActions", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.ExitConditionInterface"}, "causy.exit_conditions.ExitOnNoActions.check": {"fullname": "causy.exit_conditions.ExitOnNoActions.check", "modulename": "causy.exit_conditions", "qualname": "ExitOnNoActions.check", "kind": "function", "doc": "Check if there are no actions taken in the last iteration and if so, break the loop\nIf it is the first iteration, do not break the loop (we need to execute the first step)
\n\n\n\n", "signature": "(self, graph, graph_model_instance_, actions_taken, iteration):", "funcdef": "def"}, "causy.generators": {"fullname": "causy.generators", "modulename": "causy.generators", "kind": "module", "doc": "\n"}, "causy.generators.logger": {"fullname": "causy.generators.logger", "modulename": "causy.generators", "qualname": "logger", "kind": "variable", "doc": "\n", "default_value": "<Logger causy.generators (WARNING)>"}, "causy.generators.AllCombinationsGenerator": {"fullname": "causy.generators.AllCombinationsGenerator", "modulename": "causy.generators", "qualname": "AllCombinationsGenerator", "kind": "class", "doc": "True if you want to break an iteration, False otherwise
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.GeneratorInterface"}, "causy.generators.AllCombinationsGenerator.generate": {"fullname": "causy.generators.AllCombinationsGenerator.generate", "modulename": "causy.generators", "qualname": "AllCombinationsGenerator.generate", "kind": "function", "doc": "\n", "signature": "(\tself,\tgraph: causy.interfaces.BaseGraphInterface,\tgraph_model_instance_: causy.interfaces.GraphModelInterface):", "funcdef": "def"}, "causy.generators.PairsWithNeighboursGenerator": {"fullname": "causy.generators.PairsWithNeighboursGenerator", "modulename": "causy.generators", "qualname": "PairsWithNeighboursGenerator", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.GeneratorInterface"}, "causy.generators.PairsWithNeighboursGenerator.__init__": {"fullname": "causy.generators.PairsWithNeighboursGenerator.__init__", "modulename": "causy.generators", "qualname": "PairsWithNeighboursGenerator.__init__", "kind": "function", "doc": "\n", "signature": "(\tcomparison_settings: causy.interfaces.ComparisonSettings,\tchunked: bool = None,\tshuffle_combinations: bool = None)"}, "causy.generators.PairsWithNeighboursGenerator.shuffle_combinations": {"fullname": "causy.generators.PairsWithNeighboursGenerator.shuffle_combinations", "modulename": "causy.generators", "qualname": "PairsWithNeighboursGenerator.shuffle_combinations", "kind": "variable", "doc": "\n", "default_value": "True"}, "causy.generators.PairsWithNeighboursGenerator.chunked": {"fullname": "causy.generators.PairsWithNeighboursGenerator.chunked", "modulename": "causy.generators", "qualname": "PairsWithNeighboursGenerator.chunked", "kind": "variable", "doc": "\n", "default_value": "True"}, "causy.generators.PairsWithNeighboursGenerator.to_dict": {"fullname": "causy.generators.PairsWithNeighboursGenerator.to_dict", "modulename": "causy.generators", "qualname": "PairsWithNeighboursGenerator.to_dict", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "causy.generators.PairsWithNeighboursGenerator.generate": {"fullname": "causy.generators.PairsWithNeighboursGenerator.generate", "modulename": "causy.generators", "qualname": "PairsWithNeighboursGenerator.generate", "kind": "function", "doc": "\n", "signature": "(\tself,\tgraph: causy.interfaces.BaseGraphInterface,\tgraph_model_instance_: causy.interfaces.GraphModelInterface):", "funcdef": "def"}, "causy.graph": {"fullname": "causy.graph", "modulename": "causy.graph", "kind": "module", "doc": "\n"}, "causy.graph.logger": {"fullname": "causy.graph.logger", "modulename": "causy.graph", "qualname": "logger", "kind": "variable", "doc": "\n", "default_value": "<Logger causy.graph (WARNING)>"}, "causy.graph.Node": {"fullname": "causy.graph.Node", "modulename": "causy.graph", "qualname": "Node", "kind": "class", "doc": "\n", "bases": "causy.interfaces.NodeInterface"}, "causy.graph.Node.__init__": {"fullname": "causy.graph.Node.__init__", "modulename": "causy.graph", "qualname": "Node.__init__", "kind": "function", "doc": "\n", "signature": "(name: str, id: str, values: torch.Tensor)"}, "causy.graph.Node.name": {"fullname": "causy.graph.Node.name", "modulename": "causy.graph", "qualname": "Node.name", "kind": "variable", "doc": "\n", "annotation": ": str"}, "causy.graph.Node.id": {"fullname": "causy.graph.Node.id", "modulename": "causy.graph", "qualname": "Node.id", "kind": "variable", "doc": "\n", "annotation": ": str"}, "causy.graph.Node.values": {"fullname": "causy.graph.Node.values", "modulename": "causy.graph", "qualname": "Node.values", "kind": "variable", "doc": "\n", "annotation": ": torch.Tensor"}, "causy.graph.UndirectedGraphError": {"fullname": "causy.graph.UndirectedGraphError", "modulename": "causy.graph", "qualname": "UndirectedGraphError", "kind": "class", "doc": "Common base class for all non-exit exceptions.
\n", "bases": "builtins.Exception"}, "causy.graph.UndirectedGraph": {"fullname": "causy.graph.UndirectedGraph", "modulename": "causy.graph", "qualname": "UndirectedGraph", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.BaseGraphInterface"}, "causy.graph.UndirectedGraph.nodes": {"fullname": "causy.graph.UndirectedGraph.nodes", "modulename": "causy.graph", "qualname": "UndirectedGraph.nodes", "kind": "variable", "doc": "\n", "annotation": ": Dict[str, causy.graph.Node]"}, "causy.graph.UndirectedGraph.edges": {"fullname": "causy.graph.UndirectedGraph.edges", "modulename": "causy.graph", "qualname": "UndirectedGraph.edges", "kind": "variable", "doc": "\n", "annotation": ": Dict[str, Dict[str, Dict]]"}, "causy.graph.UndirectedGraph.edge_history": {"fullname": "causy.graph.UndirectedGraph.edge_history", "modulename": "causy.graph", "qualname": "UndirectedGraph.edge_history", "kind": "variable", "doc": "\n", "annotation": ": Dict[Tuple[str, str], List[causy.interfaces.TestResult]]"}, "causy.graph.UndirectedGraph.action_history": {"fullname": "causy.graph.UndirectedGraph.action_history", "modulename": "causy.graph", "qualname": "UndirectedGraph.action_history", "kind": "variable", "doc": "\n", "annotation": ": List[Dict[str, List[causy.interfaces.TestResult]]]"}, "causy.graph.UndirectedGraph.add_edge": {"fullname": "causy.graph.UndirectedGraph.add_edge", "modulename": "causy.graph", "qualname": "UndirectedGraph.add_edge", "kind": "function", "doc": "Add an edge to the graph
\n\nRetrieve the edge history
\n\nRemove an edge from the graph
\n\nRemove an edge from the graph
\n\nUpdate an edge in the graph
\n\nUpdate an edge in the graph
\n\nCheck if any edge exists between u and v. Cases: u -> v, u <-> v, u <- v
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.directed_edge_exists": {"fullname": "causy.graph.UndirectedGraph.directed_edge_exists", "modulename": "causy.graph", "qualname": "UndirectedGraph.directed_edge_exists", "kind": "function", "doc": "True if any edge exists, False otherwise
\n
Check if a directed edge exists between u and v. Cases: u -> v, u <-> v
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.only_directed_edge_exists": {"fullname": "causy.graph.UndirectedGraph.only_directed_edge_exists", "modulename": "causy.graph", "qualname": "UndirectedGraph.only_directed_edge_exists", "kind": "function", "doc": "True if a directed edge exists, False otherwise
\n
Check if a directed edge exists between u and v, but no directed edge exists between v and u. Case: u -> v
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.undirected_edge_exists": {"fullname": "causy.graph.UndirectedGraph.undirected_edge_exists", "modulename": "causy.graph", "qualname": "UndirectedGraph.undirected_edge_exists", "kind": "function", "doc": "True if only directed edge exists, False otherwise
\n
Check if an undirected edge exists between u and v. Note: currently, an undirected edges is implemented just as\na directed edge. However, they are two functions as they mean different things in different algorithms.\nCurrently, this function is used in the PC algorithm, where an undirected edge is an edge which could not be\noriented in any direction by orientation rules.\nLater, a cohersive naming scheme should be implemented.
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.bidirected_edge_exists": {"fullname": "causy.graph.UndirectedGraph.bidirected_edge_exists", "modulename": "causy.graph", "qualname": "UndirectedGraph.bidirected_edge_exists", "kind": "function", "doc": "True if an undirected edge exists, False otherwise
\n
Check if a bidirected edge exists between u and v. Note: currently, a bidirected edges is implemented just as\nan undirected edge. However, they are two functions as they mean different things in different algorithms.\nThis function will be used for the FCI algorithm for now, where a bidirected edge is an edge between two nodes\nthat have been identified to have a common cause by orientation rules.\nLater, a cohersive naming scheme should be implemented.
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.edge_value": {"fullname": "causy.graph.UndirectedGraph.edge_value", "modulename": "causy.graph", "qualname": "UndirectedGraph.edge_value", "kind": "function", "doc": "\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.add_node": {"fullname": "causy.graph.UndirectedGraph.add_node", "modulename": "causy.graph", "qualname": "UndirectedGraph.add_node", "kind": "function", "doc": "True if a bidirected edge exists, False otherwise
\n
Add a node to the graph
\n\nCheck if a directed path from u to v exists
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.directed_paths": {"fullname": "causy.graph.UndirectedGraph.directed_paths", "modulename": "causy.graph", "qualname": "UndirectedGraph.directed_paths", "kind": "function", "doc": "True if a directed path exists, False otherwise
\n
Return all directed paths from u to v
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.UndirectedGraph.inducing_path_exists": {"fullname": "causy.graph.UndirectedGraph.inducing_path_exists", "modulename": "causy.graph", "qualname": "UndirectedGraph.inducing_path_exists", "kind": "function", "doc": "list of directed paths
\n
Check if an inducing path from u to v exists.\nAn inducing path from u to v is a directed path from u to v on which all mediators are colliders.
\n\n\n\n", "signature": "(self, u: causy.graph.Node, v: causy.graph.Node):", "funcdef": "def"}, "causy.graph.unpack_run": {"fullname": "causy.graph.unpack_run", "modulename": "causy.graph", "qualname": "unpack_run", "kind": "function", "doc": "\n", "signature": "(args):", "funcdef": "def"}, "causy.graph.AbstractGraphModel": {"fullname": "causy.graph.AbstractGraphModel", "modulename": "causy.graph", "qualname": "AbstractGraphModel", "kind": "class", "doc": "True if an inducing path exists, False otherwise
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.GraphModelInterface, abc.ABC"}, "causy.graph.AbstractGraphModel.__init__": {"fullname": "causy.graph.AbstractGraphModel.__init__", "modulename": "causy.graph", "qualname": "AbstractGraphModel.__init__", "kind": "function", "doc": "\n", "signature": "(\tgraph=None,\tpipeline_steps: Optional[List[causy.interfaces.IndependenceTestInterface]] = None)"}, "causy.graph.AbstractGraphModel.pipeline_steps": {"fullname": "causy.graph.AbstractGraphModel.pipeline_steps", "modulename": "causy.graph", "qualname": "AbstractGraphModel.pipeline_steps", "kind": "variable", "doc": "\n", "annotation": ": List[causy.interfaces.IndependenceTestInterface]"}, "causy.graph.AbstractGraphModel.graph": {"fullname": "causy.graph.AbstractGraphModel.graph", "modulename": "causy.graph", "qualname": "AbstractGraphModel.graph", "kind": "variable", "doc": "\n", "annotation": ": causy.interfaces.BaseGraphInterface"}, "causy.graph.AbstractGraphModel.pool": {"fullname": "causy.graph.AbstractGraphModel.pool", "modulename": "causy.graph", "qualname": "AbstractGraphModel.pool", "kind": "variable", "doc": "\n", "annotation": ": <bound method BaseContext.Pool of <multiprocessing.context.DefaultContext object at 0x10a2f5a10>>"}, "causy.graph.AbstractGraphModel.create_graph_from_data": {"fullname": "causy.graph.AbstractGraphModel.create_graph_from_data", "modulename": "causy.graph", "qualname": "AbstractGraphModel.create_graph_from_data", "kind": "function", "doc": "Create a graph from data
\n\nCreate all possible nodes
\n\nExecute all pipeline_steps
\n\n\n\n", "signature": "(self):", "funcdef": "def"}, "causy.graph.AbstractGraphModel.execute_pipeline_step": {"fullname": "causy.graph.AbstractGraphModel.execute_pipeline_step", "modulename": "causy.graph", "qualname": "AbstractGraphModel.execute_pipeline_step", "kind": "function", "doc": "the steps taken during the step execution
\n
Filter the graph
\n\nCreate a graph model
\n\n\n\n", "signature": "(\tpipeline_steps: Optional[List[causy.interfaces.IndependenceTestInterface]] = None) -> type[causy.graph.AbstractGraphModel]:", "funcdef": "def"}, "causy.graph.Loop": {"fullname": "causy.graph.Loop", "modulename": "causy.graph", "qualname": "Loop", "kind": "class", "doc": "the graph model
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.LogicStepInterface"}, "causy.graph.Loop.__init__": {"fullname": "causy.graph.Loop.__init__", "modulename": "causy.graph", "qualname": "Loop.__init__", "kind": "function", "doc": "\n", "signature": "(\tpipeline_steps: Optional[List[causy.interfaces.IndependenceTestInterface]] = None,\texit_condition: causy.interfaces.ExitConditionInterface = None)"}, "causy.graph.Loop.execute": {"fullname": "causy.graph.Loop.execute", "modulename": "causy.graph", "qualname": "Loop.execute", "kind": "function", "doc": "\n", "signature": "(\tself,\tgraph: causy.interfaces.BaseGraphInterface,\tgraph_model_instance_: causy.interfaces.GraphModelInterface):", "funcdef": "def"}, "causy.graph.Loop.pipeline_steps": {"fullname": "causy.graph.Loop.pipeline_steps", "modulename": "causy.graph", "qualname": "Loop.pipeline_steps", "kind": "variable", "doc": "\n"}, "causy.graph.Loop.exit_condition": {"fullname": "causy.graph.Loop.exit_condition", "modulename": "causy.graph", "qualname": "Loop.exit_condition", "kind": "variable", "doc": "\n"}, "causy.graph.Loop.serialize": {"fullname": "causy.graph.Loop.serialize", "modulename": "causy.graph", "qualname": "Loop.serialize", "kind": "function", "doc": "\n", "signature": "(self) -> dict:", "funcdef": "def"}, "causy.independence_tests": {"fullname": "causy.independence_tests", "modulename": "causy.independence_tests", "kind": "module", "doc": "\n"}, "causy.independence_tests.logger": {"fullname": "causy.independence_tests.logger", "modulename": "causy.independence_tests", "qualname": "logger", "kind": "variable", "doc": "\n", "default_value": "<Logger causy.independence_tests (WARNING)>"}, "causy.independence_tests.CalculateCorrelations": {"fullname": "causy.independence_tests.CalculateCorrelations", "modulename": "causy.independence_tests", "qualname": "CalculateCorrelations", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.independence_tests.CalculateCorrelations.GENERATOR": {"fullname": "causy.independence_tests.CalculateCorrelations.GENERATOR", "modulename": "causy.independence_tests", "qualname": "CalculateCorrelations.GENERATOR", "kind": "variable", "doc": "\n", "default_value": "<causy.generators.AllCombinationsGenerator object>"}, "causy.independence_tests.CalculateCorrelations.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.independence_tests.CalculateCorrelations.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.independence_tests", "qualname": "CalculateCorrelations.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "1"}, "causy.independence_tests.CalculateCorrelations.PARALLEL": {"fullname": "causy.independence_tests.CalculateCorrelations.PARALLEL", "modulename": "causy.independence_tests", "qualname": "CalculateCorrelations.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "False"}, "causy.independence_tests.CalculateCorrelations.test": {"fullname": "causy.independence_tests.CalculateCorrelations.test", "modulename": "causy.independence_tests", "qualname": "CalculateCorrelations.test", "kind": "function", "doc": "Calculate the correlation between each pair of nodes and store it to the respective edge.
\n\n\n\n", "signature": "(\tself,\tnodes: Tuple[str],\tgraph: causy.interfaces.BaseGraphInterface) -> causy.interfaces.TestResult:", "funcdef": "def"}, "causy.independence_tests.CorrelationCoefficientTest": {"fullname": "causy.independence_tests.CorrelationCoefficientTest", "modulename": "causy.independence_tests", "qualname": "CorrelationCoefficientTest", "kind": "class", "doc": "A TestResult with the action to take
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.independence_tests.CorrelationCoefficientTest.GENERATOR": {"fullname": "causy.independence_tests.CorrelationCoefficientTest.GENERATOR", "modulename": "causy.independence_tests", "qualname": "CorrelationCoefficientTest.GENERATOR", "kind": "variable", "doc": "\n", "default_value": "<causy.generators.AllCombinationsGenerator object>"}, "causy.independence_tests.CorrelationCoefficientTest.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.independence_tests.CorrelationCoefficientTest.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.independence_tests", "qualname": "CorrelationCoefficientTest.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "1"}, "causy.independence_tests.CorrelationCoefficientTest.PARALLEL": {"fullname": "causy.independence_tests.CorrelationCoefficientTest.PARALLEL", "modulename": "causy.independence_tests", "qualname": "CorrelationCoefficientTest.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "False"}, "causy.independence_tests.CorrelationCoefficientTest.test": {"fullname": "causy.independence_tests.CorrelationCoefficientTest.test", "modulename": "causy.independence_tests", "qualname": "CorrelationCoefficientTest.test", "kind": "function", "doc": "Test if x and y are independent and delete edge in graph if they are.
\n\n\n\n", "signature": "(\tself,\tnodes: List[str],\tgraph: causy.interfaces.BaseGraphInterface) -> Optional[causy.interfaces.TestResult]:", "funcdef": "def"}, "causy.independence_tests.PartialCorrelationTest": {"fullname": "causy.independence_tests.PartialCorrelationTest", "modulename": "causy.independence_tests", "qualname": "PartialCorrelationTest", "kind": "class", "doc": "A TestResult with the action to take
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.independence_tests.PartialCorrelationTest.GENERATOR": {"fullname": "causy.independence_tests.PartialCorrelationTest.GENERATOR", "modulename": "causy.independence_tests", "qualname": "PartialCorrelationTest.GENERATOR", "kind": "variable", "doc": "\n", "default_value": "<causy.generators.AllCombinationsGenerator object>"}, "causy.independence_tests.PartialCorrelationTest.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.independence_tests.PartialCorrelationTest.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.independence_tests", "qualname": "PartialCorrelationTest.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "1"}, "causy.independence_tests.PartialCorrelationTest.PARALLEL": {"fullname": "causy.independence_tests.PartialCorrelationTest.PARALLEL", "modulename": "causy.independence_tests", "qualname": "PartialCorrelationTest.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "False"}, "causy.independence_tests.PartialCorrelationTest.test": {"fullname": "causy.independence_tests.PartialCorrelationTest.test", "modulename": "causy.independence_tests", "qualname": "PartialCorrelationTest.test", "kind": "function", "doc": "Test if nodes x,y are independent given node z based on a partial correlation test.\nWe use this test for all combinations of 3 nodes because it is faster than the extended test (which supports combinations of n nodes). We can\nuse it to remove edges between nodes which are not independent given another node and so reduce the number of combinations for the extended test.
\n\n\n\n\nA TestResult with the action to take
\n
TODO: we are testing (C and E given B) and (E and C given B), we just need one of these, remove redundant tests.
\n", "signature": "(\tself,\tnodes: Tuple[str],\tgraph: causy.interfaces.BaseGraphInterface) -> Optional[List[causy.interfaces.TestResult]]:", "funcdef": "def"}, "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestLinearRegression", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.GENERATOR": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.GENERATOR", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestLinearRegression.GENERATOR", "kind": "variable", "doc": "\n", "default_value": "<causy.generators.AllCombinationsGenerator object>"}, "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestLinearRegression.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "1000"}, "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.PARALLEL": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.PARALLEL", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestLinearRegression.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "True"}, "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.test": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestLinearRegression.test", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestLinearRegression.test", "kind": "function", "doc": "Test if nodes x,y are independent given Z (set of nodes) based on partial correlation using linear regression and a correlation test on the residuals.\nWe use this test for all combinations of more than 3 nodes because it is slower.
\n\n\n\n\nA TestResult with the action to take
\n
TODO: Does not run in reasonable time yet.
\n", "signature": "(\tself,\tnodes: List[str],\tgraph: causy.interfaces.BaseGraphInterface) -> Optional[List[causy.interfaces.TestResult]]:", "funcdef": "def"}, "causy.independence_tests.ExtendedPartialCorrelationTestMatrix": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestMatrix", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestMatrix", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.GENERATOR": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.GENERATOR", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestMatrix.GENERATOR", "kind": "variable", "doc": "\n", "default_value": "<causy.generators.PairsWithNeighboursGenerator object>"}, "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestMatrix.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "1000"}, "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.PARALLEL": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.PARALLEL", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestMatrix.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "False"}, "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.test": {"fullname": "causy.independence_tests.ExtendedPartialCorrelationTestMatrix.test", "modulename": "causy.independence_tests", "qualname": "ExtendedPartialCorrelationTestMatrix.test", "kind": "function", "doc": "Test if nodes x,y are independent given Z (set of nodes) based on partial correlation using the inverted covariance matrix (precision matrix).\nhttps://en.wikipedia.org/wiki/Partial_correlation#Using_matrix_inversion\nWe use this test for all combinations of more than 3 nodes because it is slower.
\n\n\n\n", "signature": "(\tself,\tnodes: List[str],\tgraph: causy.interfaces.BaseGraphInterface) -> Optional[causy.interfaces.TestResult]:", "funcdef": "def"}, "causy.independence_tests.PlaceholderTest": {"fullname": "causy.independence_tests.PlaceholderTest", "modulename": "causy.independence_tests", "qualname": "PlaceholderTest", "kind": "class", "doc": "A TestResult with the action to take
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.independence_tests.PlaceholderTest.NUM_OF_COMPARISON_ELEMENTS": {"fullname": "causy.independence_tests.PlaceholderTest.NUM_OF_COMPARISON_ELEMENTS", "modulename": "causy.independence_tests", "qualname": "PlaceholderTest.NUM_OF_COMPARISON_ELEMENTS", "kind": "variable", "doc": "\n", "default_value": "2"}, "causy.independence_tests.PlaceholderTest.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.independence_tests.PlaceholderTest.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.independence_tests", "qualname": "PlaceholderTest.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "10"}, "causy.independence_tests.PlaceholderTest.PARALLEL": {"fullname": "causy.independence_tests.PlaceholderTest.PARALLEL", "modulename": "causy.independence_tests", "qualname": "PlaceholderTest.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "False"}, "causy.independence_tests.PlaceholderTest.test": {"fullname": "causy.independence_tests.PlaceholderTest.test", "modulename": "causy.independence_tests", "qualname": "PlaceholderTest.test", "kind": "function", "doc": "Placeholder test for testing purposes
\n\nEnum where members are also (and must be) strings
\n", "bases": "enum.StrEnum"}, "causy.interfaces.TestResultAction.REMOVE_EDGE_UNDIRECTED": {"fullname": "causy.interfaces.TestResultAction.REMOVE_EDGE_UNDIRECTED", "modulename": "causy.interfaces", "qualname": "TestResultAction.REMOVE_EDGE_UNDIRECTED", "kind": "variable", "doc": "\n", "default_value": "<TestResultAction.REMOVE_EDGE_UNDIRECTED: 'REMOVE_EDGE_UNDIRECTED'>"}, "causy.interfaces.TestResultAction.UPDATE_EDGE": {"fullname": "causy.interfaces.TestResultAction.UPDATE_EDGE", "modulename": "causy.interfaces", "qualname": "TestResultAction.UPDATE_EDGE", "kind": "variable", "doc": "\n", "default_value": "<TestResultAction.UPDATE_EDGE: 'UPDATE_EDGE'>"}, "causy.interfaces.TestResultAction.UPDATE_EDGE_DIRECTED": {"fullname": "causy.interfaces.TestResultAction.UPDATE_EDGE_DIRECTED", "modulename": "causy.interfaces", "qualname": "TestResultAction.UPDATE_EDGE_DIRECTED", "kind": "variable", "doc": "\n", "default_value": "<TestResultAction.UPDATE_EDGE_DIRECTED: 'UPDATE_EDGE_DIRECTED'>"}, "causy.interfaces.TestResultAction.DO_NOTHING": {"fullname": "causy.interfaces.TestResultAction.DO_NOTHING", "modulename": "causy.interfaces", "qualname": "TestResultAction.DO_NOTHING", "kind": "variable", "doc": "\n", "default_value": "<TestResultAction.DO_NOTHING: 'DO_NOTHING'>"}, "causy.interfaces.TestResultAction.REMOVE_EDGE_DIRECTED": {"fullname": "causy.interfaces.TestResultAction.REMOVE_EDGE_DIRECTED", "modulename": "causy.interfaces", "qualname": "TestResultAction.REMOVE_EDGE_DIRECTED", "kind": "variable", "doc": "\n", "default_value": "<TestResultAction.REMOVE_EDGE_DIRECTED: 'REMOVE_EDGE_DIRECTED'>"}, "causy.interfaces.TestResult": {"fullname": "causy.interfaces.TestResult", "modulename": "causy.interfaces", "qualname": "TestResult", "kind": "class", "doc": "\n"}, "causy.interfaces.TestResult.__init__": {"fullname": "causy.interfaces.TestResult.__init__", "modulename": "causy.interfaces", "qualname": "TestResult.__init__", "kind": "function", "doc": "\n", "signature": "(\tx: causy.interfaces.NodeInterface,\ty: causy.interfaces.NodeInterface,\taction: causy.interfaces.TestResultAction,\tdata: Optional[Dict] = None)"}, "causy.interfaces.TestResult.x": {"fullname": "causy.interfaces.TestResult.x", "modulename": "causy.interfaces", "qualname": "TestResult.x", "kind": "variable", "doc": "\n", "annotation": ": causy.interfaces.NodeInterface"}, "causy.interfaces.TestResult.y": {"fullname": "causy.interfaces.TestResult.y", "modulename": "causy.interfaces", "qualname": "TestResult.y", "kind": "variable", "doc": "\n", "annotation": ": causy.interfaces.NodeInterface"}, "causy.interfaces.TestResult.action": {"fullname": "causy.interfaces.TestResult.action", "modulename": "causy.interfaces", "qualname": "TestResult.action", "kind": "variable", "doc": "\n", "annotation": ": causy.interfaces.TestResultAction"}, "causy.interfaces.TestResult.data": {"fullname": "causy.interfaces.TestResult.data", "modulename": "causy.interfaces", "qualname": "TestResult.data", "kind": "variable", "doc": "\n", "annotation": ": Optional[Dict]", "default_value": "None"}, "causy.interfaces.TestResult.to_dict": {"fullname": "causy.interfaces.TestResult.to_dict", "modulename": "causy.interfaces", "qualname": "TestResult.to_dict", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface": {"fullname": "causy.interfaces.BaseGraphInterface", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "abc.ABC"}, "causy.interfaces.BaseGraphInterface.nodes": {"fullname": "causy.interfaces.BaseGraphInterface.nodes", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.nodes", "kind": "variable", "doc": "\n", "annotation": ": Dict[str, causy.interfaces.NodeInterface]"}, "causy.interfaces.BaseGraphInterface.edges": {"fullname": "causy.interfaces.BaseGraphInterface.edges", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.edges", "kind": "variable", "doc": "\n", "annotation": ": Dict[str, Dict[str, Dict]]"}, "causy.interfaces.BaseGraphInterface.retrieve_edge_history": {"fullname": "causy.interfaces.BaseGraphInterface.retrieve_edge_history", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.retrieve_edge_history", "kind": "function", "doc": "\n", "signature": "(\tself,\tu,\tv,\taction: causy.interfaces.TestResultAction) -> List[causy.interfaces.TestResult]:", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.add_edge_history": {"fullname": "causy.interfaces.BaseGraphInterface.add_edge_history", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.add_edge_history", "kind": "function", "doc": "\n", "signature": "(self, u, v, action: causy.interfaces.TestResultAction):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.add_edge": {"fullname": "causy.interfaces.BaseGraphInterface.add_edge", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.add_edge", "kind": "function", "doc": "\n", "signature": "(self, u, v, w):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.remove_edge": {"fullname": "causy.interfaces.BaseGraphInterface.remove_edge", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.remove_edge", "kind": "function", "doc": "\n", "signature": "(self, u, v):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.remove_directed_edge": {"fullname": "causy.interfaces.BaseGraphInterface.remove_directed_edge", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.remove_directed_edge", "kind": "function", "doc": "\n", "signature": "(self, u, v):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.update_edge": {"fullname": "causy.interfaces.BaseGraphInterface.update_edge", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.update_edge", "kind": "function", "doc": "\n", "signature": "(self, u, v, w):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.add_node": {"fullname": "causy.interfaces.BaseGraphInterface.add_node", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.add_node", "kind": "function", "doc": "\n", "signature": "(self, name, values):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.edge_value": {"fullname": "causy.interfaces.BaseGraphInterface.edge_value", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.edge_value", "kind": "function", "doc": "\n", "signature": "(self, u, v):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.undirected_edge_exists": {"fullname": "causy.interfaces.BaseGraphInterface.undirected_edge_exists", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.undirected_edge_exists", "kind": "function", "doc": "\n", "signature": "(self, u, v):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.directed_edge_exists": {"fullname": "causy.interfaces.BaseGraphInterface.directed_edge_exists", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.directed_edge_exists", "kind": "function", "doc": "\n", "signature": "(self, u, v):", "funcdef": "def"}, "causy.interfaces.BaseGraphInterface.edge_exists": {"fullname": "causy.interfaces.BaseGraphInterface.edge_exists", "modulename": "causy.interfaces", "qualname": "BaseGraphInterface.edge_exists", "kind": "function", "doc": "\n", "signature": "(self, u, v):", "funcdef": "def"}, "causy.interfaces.GraphModelInterface": {"fullname": "causy.interfaces.GraphModelInterface", "modulename": "causy.interfaces", "qualname": "GraphModelInterface", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "abc.ABC"}, "causy.interfaces.GraphModelInterface.pool": {"fullname": "causy.interfaces.GraphModelInterface.pool", "modulename": "causy.interfaces", "qualname": "GraphModelInterface.pool", "kind": "variable", "doc": "\n", "annotation": ": <bound method BaseContext.Pool of <multiprocessing.context.DefaultContext object at 0x10a2f5a10>>"}, "causy.interfaces.GraphModelInterface.create_graph_from_data": {"fullname": "causy.interfaces.GraphModelInterface.create_graph_from_data", "modulename": "causy.interfaces", "qualname": "GraphModelInterface.create_graph_from_data", "kind": "function", "doc": "\n", "signature": "(self, data: List[Dict]):", "funcdef": "def"}, "causy.interfaces.GraphModelInterface.execute_pipeline_steps": {"fullname": "causy.interfaces.GraphModelInterface.execute_pipeline_steps", "modulename": "causy.interfaces", "qualname": "GraphModelInterface.execute_pipeline_steps", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "causy.interfaces.GraphModelInterface.execute_pipeline_step": {"fullname": "causy.interfaces.GraphModelInterface.execute_pipeline_step", "modulename": "causy.interfaces", "qualname": "GraphModelInterface.execute_pipeline_step", "kind": "function", "doc": "\n", "signature": "(self, step):", "funcdef": "def"}, "causy.interfaces.GeneratorInterface": {"fullname": "causy.interfaces.GeneratorInterface", "modulename": "causy.interfaces", "qualname": "GeneratorInterface", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "abc.ABC"}, "causy.interfaces.GeneratorInterface.comparison_settings": {"fullname": "causy.interfaces.GeneratorInterface.comparison_settings", "modulename": "causy.interfaces", "qualname": "GeneratorInterface.comparison_settings", "kind": "variable", "doc": "\n", "annotation": ": causy.interfaces.ComparisonSettings"}, "causy.interfaces.GeneratorInterface.chunked": {"fullname": "causy.interfaces.GeneratorInterface.chunked", "modulename": "causy.interfaces", "qualname": "GeneratorInterface.chunked", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "False"}, "causy.interfaces.GeneratorInterface.generate": {"fullname": "causy.interfaces.GeneratorInterface.generate", "modulename": "causy.interfaces", "qualname": "GeneratorInterface.generate", "kind": "function", "doc": "\n", "signature": "(\tself,\tgraph: causy.interfaces.BaseGraphInterface,\tgraph_model_instance_: dict):", "funcdef": "def"}, "causy.interfaces.GeneratorInterface.serialize": {"fullname": "causy.interfaces.GeneratorInterface.serialize", "modulename": "causy.interfaces", "qualname": "GeneratorInterface.serialize", "kind": "function", "doc": "\n", "signature": "(self) -> dict:", "funcdef": "def"}, "causy.interfaces.IndependenceTestInterface": {"fullname": "causy.interfaces.IndependenceTestInterface", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "abc.ABC"}, "causy.interfaces.IndependenceTestInterface.NUM_OF_COMPARISON_ELEMENTS": {"fullname": "causy.interfaces.IndependenceTestInterface.NUM_OF_COMPARISON_ELEMENTS", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface.NUM_OF_COMPARISON_ELEMENTS", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "0"}, "causy.interfaces.IndependenceTestInterface.GENERATOR": {"fullname": "causy.interfaces.IndependenceTestInterface.GENERATOR", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface.GENERATOR", "kind": "variable", "doc": "\n", "annotation": ": Optional[causy.interfaces.GeneratorInterface]", "default_value": "None"}, "causy.interfaces.IndependenceTestInterface.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.interfaces.IndependenceTestInterface.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "annotation": ": int", "default_value": "1"}, "causy.interfaces.IndependenceTestInterface.PARALLEL": {"fullname": "causy.interfaces.IndependenceTestInterface.PARALLEL", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface.PARALLEL", "kind": "variable", "doc": "\n", "annotation": ": bool", "default_value": "True"}, "causy.interfaces.IndependenceTestInterface.threshold": {"fullname": "causy.interfaces.IndependenceTestInterface.threshold", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface.threshold", "kind": "variable", "doc": "\n"}, "causy.interfaces.IndependenceTestInterface.test": {"fullname": "causy.interfaces.IndependenceTestInterface.test", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface.test", "kind": "function", "doc": "Test if x and y are independent
\n\n\n\n", "signature": "(\tself,\tnodes: List[str],\tgraph: causy.interfaces.BaseGraphInterface) -> Optional[causy.interfaces.TestResult]:", "funcdef": "def"}, "causy.interfaces.IndependenceTestInterface.serialize": {"fullname": "causy.interfaces.IndependenceTestInterface.serialize", "modulename": "causy.interfaces", "qualname": "IndependenceTestInterface.serialize", "kind": "function", "doc": "\n", "signature": "(self) -> dict:", "funcdef": "def"}, "causy.interfaces.LogicStepInterface": {"fullname": "causy.interfaces.LogicStepInterface", "modulename": "causy.interfaces", "qualname": "LogicStepInterface", "kind": "class", "doc": "True if independent, False otherwise
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "abc.ABC"}, "causy.interfaces.LogicStepInterface.execute": {"fullname": "causy.interfaces.LogicStepInterface.execute", "modulename": "causy.interfaces", "qualname": "LogicStepInterface.execute", "kind": "function", "doc": "\n", "signature": "(\tself,\tgraph: causy.interfaces.BaseGraphInterface,\tgraph_model_instance_: dict):", "funcdef": "def"}, "causy.interfaces.LogicStepInterface.serialize": {"fullname": "causy.interfaces.LogicStepInterface.serialize", "modulename": "causy.interfaces", "qualname": "LogicStepInterface.serialize", "kind": "function", "doc": "\n", "signature": "(self) -> dict:", "funcdef": "def"}, "causy.interfaces.ExitConditionInterface": {"fullname": "causy.interfaces.ExitConditionInterface", "modulename": "causy.interfaces", "qualname": "ExitConditionInterface", "kind": "class", "doc": "Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "abc.ABC"}, "causy.interfaces.ExitConditionInterface.check": {"fullname": "causy.interfaces.ExitConditionInterface.check", "modulename": "causy.interfaces", "qualname": "ExitConditionInterface.check", "kind": "function", "doc": "\n\n", "signature": "(\tself,\tgraph: causy.interfaces.BaseGraphInterface,\tgraph_model_instance_: dict,\tactions_taken: List[causy.interfaces.TestResult],\titeration: int) -> bool:", "funcdef": "def"}, "causy.interfaces.ExitConditionInterface.serialize": {"fullname": "causy.interfaces.ExitConditionInterface.serialize", "modulename": "causy.interfaces", "qualname": "ExitConditionInterface.serialize", "kind": "function", "doc": "\n", "signature": "(self):", "funcdef": "def"}, "causy.orientation_tests": {"fullname": "causy.orientation_tests", "modulename": "causy.orientation_tests", "kind": "module", "doc": "\n"}, "causy.orientation_tests.ColliderTest": {"fullname": "causy.orientation_tests.ColliderTest", "modulename": "causy.orientation_tests", "qualname": "ColliderTest", "kind": "class", "doc": "True if you want to break an iteration, False otherwise
\n
Helper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.orientation_tests.ColliderTest.GENERATOR": {"fullname": "causy.orientation_tests.ColliderTest.GENERATOR", "modulename": "causy.orientation_tests", "qualname": "ColliderTest.GENERATOR", "kind": "variable", "doc": "\n", "default_value": "<causy.generators.AllCombinationsGenerator object>"}, "causy.orientation_tests.ColliderTest.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.orientation_tests.ColliderTest.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.orientation_tests", "qualname": "ColliderTest.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "1"}, "causy.orientation_tests.ColliderTest.PARALLEL": {"fullname": "causy.orientation_tests.ColliderTest.PARALLEL", "modulename": "causy.orientation_tests", "qualname": "ColliderTest.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "False"}, "causy.orientation_tests.ColliderTest.test": {"fullname": "causy.orientation_tests.ColliderTest.test", "modulename": "causy.orientation_tests", "qualname": "ColliderTest.test", "kind": "function", "doc": "We call triples x, y, z of nodes v structures if x and y that are NOT adjacent but share an adjacent node z.\nV structures looks like this in the undirected skeleton: (x - z - y).\nWe now check if z is in the separating set.\nIf z is not in the separating set, we know that x and y are uncorrelated given z.\nSo, the edges must be oriented from x to z and from y to z (x -> z <- y).
\n\nHelper class that provides a standard way to create an ABC using\ninheritance.
\n", "bases": "causy.interfaces.IndependenceTestInterface"}, "causy.orientation_tests.NonColliderTest.GENERATOR": {"fullname": "causy.orientation_tests.NonColliderTest.GENERATOR", "modulename": "causy.orientation_tests", "qualname": "NonColliderTest.GENERATOR", "kind": "variable", "doc": "\n", "default_value": "<causy.generators.AllCombinationsGenerator object>"}, "causy.orientation_tests.NonColliderTest.CHUNK_SIZE_PARALLEL_PROCESSING": {"fullname": "causy.orientation_tests.NonColliderTest.CHUNK_SIZE_PARALLEL_PROCESSING", "modulename": "causy.orientation_tests", "qualname": "NonColliderTest.CHUNK_SIZE_PARALLEL_PROCESSING", "kind": "variable", "doc": "\n", "default_value": "1"}, "causy.orientation_tests.NonColliderTest.PARALLEL": {"fullname": "causy.orientation_tests.NonColliderTest.PARALLEL", "modulename": "causy.orientation_tests", "qualname": "NonColliderTest.PARALLEL", "kind": "variable", "doc": "\n", "default_value": "False"}, "causy.orientation_tests.NonColliderTest.test": {"fullname": "causy.orientation_tests.NonColliderTest.test", "modulename": "causy.orientation_tests", "qualname": "NonColliderTest.test", "kind": "function", "doc": "Further orientation rule: all v structures that are colliders are already oriented.\nWe now orient all v structures that have a single alternative to being a collider.
\n\nHelper class that provides a standard way to create an ABC using\ninheritance.
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\n\nHelper class that provides a standard way to create an ABC using\ninheritance.
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\n\nHelper class that provides a standard way to create an ABC using\ninheritance.
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\n\n\n\n", "signature": "(*lists):", "funcdef": "def"}, "causy.utils.backward_substituion": {"fullname": "causy.utils.backward_substituion", "modulename": "causy.utils", "qualname": "backward_substituion", "kind": "function", "doc": "list (sum of lists)
\n
\n\n", "signature": "(R, b, n):", "funcdef": "def"}, "causy.utils.get_regression_coefficients": {"fullname": "causy.utils.get_regression_coefficients", "modulename": "causy.utils", "qualname": "get_regression_coefficients", "kind": "function", "doc": "Matrix, n-dimensional regression coefficient vector
\n
\n\n", "signature": "(x, Z):", "funcdef": "def"}, "causy.utils.get_residuals": {"fullname": "causy.utils.get_residuals", "modulename": "causy.utils", "qualname": "get_residuals", "kind": "function", "doc": "sympy matrix, regression coefficients from regressing x on Z
\n
\n\n\nresidual \u2013 list (length = # of samples)
\n
CAUTION: Z must have full rank\nTODO: add optional check
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