phylojunction.utility package

Submodules

phylojunction.utility.exception_classes module

exception phylojunction.utility.exception_classes.AnnotatedTreeIncorrectAnnotationError(message: str)

Bases: Exception

message: str

exception phylojunction.utility.exception_classes.AnnotatedTreeMissingNodeName

Bases: Exception

message: str

exception phylojunction.utility.exception_classes.AnnotatedTreeMisspecError(message: str)

Bases: Exception

message: str

exception phylojunction.utility.exception_classes.AnnotatedTreeNodeMissingAttrError(nd_name: str, attr_name: str, message: str)

Bases: Exception

message: str

exception phylojunction.utility.exception_classes.DAGCannotAddNodeError(node_name: str, message: str)

Bases: Exception

message: str

exception phylojunction.utility.exception_classes.DAGCannotInitialize(message: str)

Bases: Exception

message: str

exception phylojunction.utility.exception_classes.DimensionalityError(dn_name: str, par_name: str | None = '')

Bases: Exception

dn_name: str

message: str

par_name: str

exception phylojunction.utility.exception_classes.DimensionalityWarning(rv_name: str, dn_name: str, message: str = '')

Bases: Exception

dn_name: str

message: str

rv_name: str

exception phylojunction.utility.exception_classes.FunctionArgsMismatchError(fn_name: str, message: str)

Bases: Exception

fn_name: str

message: str

exception phylojunction.utility.exception_classes.GenerateFailError(dn_name: str, message: str)

Bases: Exception

message: str

exception phylojunction.utility.exception_classes.IncorrectDimensionError(container_name: str, obs_len: int, exp_len: int = 0)

Bases: Exception

container_name: str

exp_len: int

message: str

obs_len: int

exception phylojunction.utility.exception_classes.InexistentVariableError(rv_name: str)

Bases: Exception

message: str

rv_name: str

exception phylojunction.utility.exception_classes.InvalidMCMCChainLength(message: str)

Bases: Exception

message: str

exception phylojunction.utility.exception_classes.MaxNFailedAttemptsLimit(max_n_attempts: int)

Bases: Exception

exception phylojunction.utility.exception_classes.MissingColumnName(col_name: str, message: str)

Bases: Exception

message: str

exception phylojunction.utility.exception_classes.NoPlatingAllowedError(det_name: str, problematic_node_dag_name: str, message: str = '')

Bases: Exception

det_name: str

message: str

node_dag_name: str

exception phylojunction.utility.exception_classes.NodeDAGStatCantFloatError(node_name: str)

Bases: Exception

message: str

exception phylojunction.utility.exception_classes.NodeInferenceDimensionalityError(node_name: str)

Bases: Exception

message: str

node_name: str

exception phylojunction.utility.exception_classes.NotBetweenZeroAndOneError(par_name: str, message: str = '')

Bases: Exception

message: str

par_name: str

exception phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError(obj_name: str, container_name: str, obs_len: int, exp_len: int = 0, at_least: bool = False)

Bases: Exception

at_least: bool

exp_len: int

message: str

obj_name: str

obs_len: int

exception phylojunction.utility.exception_classes.ObjInitInvalidArgError(obj_name: str, par_name: str, message: str | None = '')

Bases: Exception

message: str

obj_name: str

exception phylojunction.utility.exception_classes.ObjInitMissingParameterError(obj_name: str, par_name: str, message: str | None = '')

Bases: Exception

message: str

obj_name: str

exception phylojunction.utility.exception_classes.ObjInitMissingStateDependentParameterError(epoch_missing_param: int, symmetric_diff_set: Set[Any])

Bases: Exception

message: str

symmetric_diff_str: str

exception phylojunction.utility.exception_classes.ObjInitRepeatedStateDependentParameterError(epoch_w_repeated_param: int, repeated_param: Tuple[Tuple[int], Enum])

Bases: Exception

message: str

exception phylojunction.utility.exception_classes.ObjInitRequireNonZeroStateDependentParameterError(obj_name: str, dimension_idx: int)

Bases: Exception

message: str

obj_name: str

exception phylojunction.utility.exception_classes.ObjInitRequireSameParameterTypeError(obj_name: str, n_diff_par: int)

Bases: Exception

message: str

n_diff_par: int

obj_name: str

exception phylojunction.utility.exception_classes.PJCLIInvalidInputError(par_name: str, message: str)

Bases: Exception

message: str

par_name: str

exception phylojunction.utility.exception_classes.PJCLISampleOutOfRangeError(range_str: str)

Bases: Exception

exception phylojunction.utility.exception_classes.PJIOFileDoesNotExistError(fn_name: str, file_path: str)

Bases: Exception

exception phylojunction.utility.exception_classes.ParseCtFnInitFailError(ct_fn_name: str, message: str)

Bases: Exception

ct_fn_name: str

message: str

exception phylojunction.utility.exception_classes.ParseDetFnInitFailError(det_fn_name: str, message: str)

Bases: Exception

det_fn_name: str

message: str

exception phylojunction.utility.exception_classes.ParseDnInitFailError(dn_name: str, message: str)

Bases: Exception

dn_name: str

message: str

exception phylojunction.utility.exception_classes.ParseFunctionArgError(par_name: str, message: str)

Bases: Exception

message: str

par_name: str

exception phylojunction.utility.exception_classes.ParseInvalidArgumentError(par_name: str, invalid_arg: str, message: str)

Bases: Exception

message: str

par_name: str

exception phylojunction.utility.exception_classes.ParseInvalidNewickStringError(par_name: str, message: str = '')

Bases: Exception

message: str

par_name: str

exception phylojunction.utility.exception_classes.ParseMissingArgumentError(par_name: str, arg_name: str = '')

Bases: Exception

message: str

par_name: str

exception phylojunction.utility.exception_classes.ParseMissingParameterError(par_name: str)

Bases: Exception

message: str

par_name: str

exception phylojunction.utility.exception_classes.ParseMissingSpecificationError(obj2spec_name: str)

Bases: Exception

message: str

exception phylojunction.utility.exception_classes.ParseMutuallyExclusiveParametersError(par_name: str, mutually_exclusive_par_name: str, message: str = '')

Bases: Exception

message: str

mutually_exclusive_par_name: str

par_name: str

exception phylojunction.utility.exception_classes.ParseNotAParameterError(par_name: str)

Bases: Exception

message: str

par_name: str

exception phylojunction.utility.exception_classes.ParsePathDoesNotExistError(par_name: str, path_str: str, message: str | None = '')

Bases: Exception

message: str

par_name: str

path_str: str

exception phylojunction.utility.exception_classes.ParseRequireIntegerError(obj_name: str, arg: str)

Bases: Exception

message: str

obj_name: str

exception phylojunction.utility.exception_classes.ParseRequireNumericError(obj_name: str, arg: str)

Bases: Exception

message: str

obj_name: str

exception phylojunction.utility.exception_classes.ParseRequirePositiveIntegerError(obj_name: str, arg: str)

Bases: Exception

message: str

obj_name: str

exception phylojunction.utility.exception_classes.ParseRequireSingleValueError(obj_name: str, arg: str)

Bases: Exception

message: str

obj_name: str

exception phylojunction.utility.exception_classes.ReplicateNumberError(node_name, message='')

Bases: Exception

message: str

node_name: str

exception phylojunction.utility.exception_classes.RunTimeLimit(runtime_limit: float)

Bases: Exception

exception phylojunction.utility.exception_classes.SSEStashMisspec(message: str)

Bases: Exception

message: str

exception phylojunction.utility.exception_classes.ScriptSyntaxError(cmd_line: str, message: str)

Bases: Exception

cmd_line: str

message: str

exception phylojunction.utility.exception_classes.StateDependentParameterMisspec(message: str = '')

Bases: Exception

message: str

exception phylojunction.utility.exception_classes.VariableAssignmentError(rv_name: str, message: str = '')

Bases: Exception

message: str

rv_name: str

exception phylojunction.utility.exception_classes.VariableMisspec(rv_name: str)

Bases: Exception

message: str

rv_name: str

phylojunction.utility.helper_functions module

phylojunction.utility.helper_functions.autovivify(levels=1, final=<class 'dict'>) → DefaultDict

phylojunction.utility.helper_functions.check_and_vectorize_if_must(param_list: int | float | str | List[int | float | str], dn_name: str, size_to_grow: int = 1) → List[List[int | float | str]]

Check number of provided values and vectorize if necessary.

Parameters:

• param_list (tuple) – Parameter values (could be scalar

• integers –

• floats –

• strings –

• list). (or any of those in a) –

• dn_name (str) – Name of the distribution whose parameter values we are checking.

• size_to_grow (int) – Number of values we need, which is the specified number of simulations (‘n_samples’ in DistributionDAG). Defaults to 1.

Returns:

Two-dimensional list of potentially vectorized

parameter values. First dimension are samples (simulations), second dimension are replicates.

Return type:

(list)

phylojunction.utility.helper_functions.create_str_defaultdict() → defaultdict

phylojunction.utility.helper_functions.get_covg(full_cov_df: DataFrame, par_name: str) → float

Return coverage from ‘within_hpd’ column in DataFrame.

Parameters:

• full_cov_df (pandas.DataFrame) – DataFrame object containing column named ‘within_hpd’ with 0’s or 1’s for parameters outside and inside an HPD, respectively.

• par_name (str) – Name of the focal parameter for error printing.

Returns:

Bayesian coverage for the parameter

Return type:

float

phylojunction.utility.helper_functions.get_ellapsed_time_in_seconds(start: float, end: float) → int

Calculate ellapsed time in seconds.

Parameters:

• start (float) – Start of time window

• end (float) – End of time window

Returns:

Ellapsed time in seconds in time window

Return type:

int

phylojunction.utility.helper_functions.is_val_in_interval(val: int | float | float64, lower: int | float | float64, upper: int | float | float64) → bool

Return True/False if numerical value is in (lower, upper].

Parameters:

• val (ty.Union[int, float, np.float64]t) – Numerical value

• lower (ty.Union[int, float, np.float64]) – Lower end of interval

• upper (ty.Union[int, float, np.float64]) – Upper end of interval

Returns:

Whether val is in (lower, upper]

Return type:

bool

phylojunction.utility.helper_functions.print_progress(idx: int, iterator_len: int) → None

Print progress bar on iteration for longer tests

Parameters:

• idx (int) – Index to keep track of where in iteration one is

• iterator_len (int) – Size of the iterator whose progress is keeping track of

phylojunction.utility.helper_functions.symmetric_difference(set1: Set[Any], set2: Set[Any]) → Set[Any]

Return symmetric difference among two sets

Module contents