measures

Module containing Inter Rater Agreement Measures.

human_protocol_sdk.agreement.measures.agreement(annotations, measure='krippendorffs_alpha', labels=None, bootstrap_method=None, bootstrap_kwargs=None, measure_kwargs=None)

Calculates agreement across the given data using the given method.

Parameters:
- annotations (Sequence) – Annotation data. Must be a N x M Matrix, where N is the number of annotated items and M is the number of annotators. Missing values must be indicated by nan.
- measure – Specifies the method to use. Must be one of ‘cohens_kappa’, ‘percentage’, ‘fleiss_kappa’, ‘sigma’ or ‘krippendorffs_alpha’.
- labels (Optional[Sequence]) – List of labels to use for the annotation. If set to None, labels are inferred from the data. If provided, values not in the labels are set to nan.
- bootstrap_method (Optional[str]) – Name of the bootstrap method to use for calculating confidence intervals. If set to None, no confidence intervals are calculated. If provided, must be one of ‘percentile’ or ‘bca’.
- bootstrap_kwargs (Optional[dict]) – Dictionary of keyword arguments to be passed to the bootstrap function.
- measure_kwargs (Optional[dict]) – Dictionary of keyword arguments to be passed to the measure function.
Return type: dict
Returns: A dictionary containing the keys “results” and “config”. Results contains the scores, while config contains parameters that produced the results.

Example:

from human_protocol_sdk.agreement import agreement

annotations = [
    ['cat', 'not', 'cat'],
    ['cat', 'cat', 'cat'],
    ['not', 'not', 'not'],
    ['cat', 'nan', 'not'],
]

agreement_report = agreement(annotations, measure="fleiss_kappa")
print(agreement_report)
# {
#     'results': {
#         'measure': 'fleiss_kappa',
#         'score': 0.3950000000000001,
#         'ci': None,
#         'confidence_level': None
#     },
#     'config': {
#         'measure': 'fleiss_kappa',
#         'labels': array(['cat', 'not'], dtype='<U3'),
#         'data': array([['cat', 'not', 'cat'],
#                        ['cat', 'cat', 'cat'],
#                        ['not', 'not', 'not'],
#                        ['cat', '', 'not']], dtype='<U3'),
#         'bootstrap_method': None,
#         'bootstrap_kwargs': {},
#         'measure_kwargs': {}
#     }
# }

human_protocol_sdk.agreement.measures.cohens_kappa(annotations)

Returns Cohen’s Kappa for the provided annotations.

Parameters: annotations (ndarray) – Annotation data. Must be a N x M Matrix, where N is the number of annotated items and M is the number of annotators. Missing values must be indicated by nan.
Return type: float
Returns: Value between -1.0 and 1.0, indicating the degree of agreement between both raters.

Example:

from human_protocol_sdk.agreement.measures import cohens_kappa
import numpy as np

annotations = np.asarray([
        ["cat", "cat"],
        ["cat", "cat"],
        ["not", "cat"],
        ["not", "cat"],
        ["cat", "not"],
        ["not", "not"],
        ["not", "not"],
        ["not", "not"],
        ["not", "not"],
        ["not", "not"],
])
print(cohens_kappa(annotations))
# 0.348

human_protocol_sdk.agreement.measures.fleiss_kappa(annotations)

Returns Fleisss’ Kappa for the provided annotations.

Parameters: annotations (ndarray) – Annotation data. Must be a N x M Matrix, where N is the number of items and M is the number of annotators.
Return type: float
Returns: Value between -1.0 and 1.0, indicating the degree of agreement between all raters.

Example:

from human_protocol_sdk.agreement.measures import fleiss_kappa
import numpy as np

# 3 raters, 2 classes
annotations = np.asarray([
    ["cat", "not", "cat"],
    ["cat", "cat", "cat"],
    ["not", "not", "not"],
    ["cat", "cat", "not"],
])
print(f"{fleiss_kappa(annotations):.3f}")
# 0.395

human_protocol_sdk.agreement.measures.krippendorffs_alpha(annotations, distance_function)

Calculates Krippendorff’s Alpha for the given annotations (item-value pairs), using the given distance function.

Parameters:
- annotations (ndarray) – Annotation data. Must be a N x M Matrix, where N is the number of annotated items and M is the number of annotators. Missing values must be indicated by nan.
- distance_function (Union[Callable, str]) – Function to calculate distance between two values. Calling distance_fn(annotations[i, j], annotations[p, q]) must return a number. Can also be one of ‘nominal’, ‘ordinal’, ‘interval’ or ‘ratio’ for default functions pertaining to the level of measurement of the data.
Return type: float
Returns: Value between -1.0 and 1.0, indicating the degree of agreement.

Example:

from human_protocol_sdk.agreement.measures import krippendorffs_alpha
import numpy as np

annotations = np.asarray([
    [0, 0, 0],
    [0, 1, 1]]
)
print(krippendorffs_alpha(annotations, distance_function="nominal"))
# 0.375

human_protocol_sdk.agreement.measures.percentage(annotations)

Returns the overall agreement percentage observed across the data.

Parameters: annotations (ndarray) – Annotation data. Must be a N x M Matrix, where N is the number of annotated items and M is the number of annotators. Missing values must be indicated by nan.
Return type: float
Returns: Value between 0.0 and 1.0, indicating the percentage of agreement.

Example:

from human_protocol_sdk.agreement.measures import percentage
import numpy as np

annotations = np.asarray([
    ["cat", "not", "cat"],
    ["cat", "cat", "cat"],
    ["not", "not", "not"],
    ["cat", "cat", "not"],
])
print(percentage(annotations))
# 0.7

human_protocol_sdk.agreement.measures.sigma(annotations, distance_function, p=0.05)

Calculates the Sigma Agreement Measure for the given annotations (item-value pairs), using the given distance function. For details, see https://dl.acm.org/doi/fullHtml/10.1145/3485447.3512242.

Parameters:
- annotations (ndarray) – Annotation data. Must be a N x M Matrix, where N is the number of annotated items and M is the number of annotators. Missing values must be indicated by nan.
- distance_function (Union[Callable, str]) – Function to calculate distance between two values. Calling distance_fn(annotations[i, j], annotations[p, q]) must return a number. Can also be one of ‘nominal’, ‘ordinal’, ‘interval’ or ‘ratio’ for default functions pertaining to the level of measurement of the data.
- p – Probability threshold between 0.0 and 1.0 determining statistical significant difference. The lower, the stricter.
Return type: float
Returns: Value between 0.0 and 1.0, indicating the degree of agreement.

Example:

from human_protocol_sdk.agreement.measures import sigma
import numpy as np

np.random.seed(42)
n_items = 500
n_annotators = 5

# create annotations
annotations = np.random.rand(n_items, n_annotators)
means = np.random.rand(n_items, 1) * 100
scales = np.random.randn(n_items, 1) * 10
annotations = annotations * scales + means
d = "interval"

print(sigma(annotations, d))
# 0.6538

Last updated 1 month ago