sequenzo 0.1.20__cp311-cp311-win_amd64.whl → 0.1.21__cp311-cp311-win_amd64.whl
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- sequenzo/big_data/clara/utils/get_weighted_diss.c +192 -191
- sequenzo/big_data/clara/utils/get_weighted_diss.cp311-win_amd64.pyd +0 -0
- sequenzo/clustering/clustering_c_code.cp311-win_amd64.pyd +0 -0
- sequenzo/clustering/hierarchical_clustering.py +1 -1
- sequenzo/define_sequence_data.py +4 -4
- sequenzo/dissimilarity_measures/c_code.cp311-win_amd64.pyd +0 -0
- sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +169 -169
- sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp311-win_amd64.pyd +0 -0
- sequenzo/dissimilarity_measures/utils/seqconc.c +231 -230
- sequenzo/dissimilarity_measures/utils/seqconc.cp311-win_amd64.pyd +0 -0
- sequenzo/dissimilarity_measures/utils/seqdss.c +324 -323
- sequenzo/dissimilarity_measures/utils/seqdss.cp311-win_amd64.pyd +0 -0
- sequenzo/dissimilarity_measures/utils/seqdur.c +324 -323
- sequenzo/dissimilarity_measures/utils/seqdur.cp311-win_amd64.pyd +0 -0
- sequenzo/dissimilarity_measures/utils/seqlength.c +224 -222
- sequenzo/dissimilarity_measures/utils/seqlength.cp311-win_amd64.pyd +0 -0
- sequenzo/multidomain/association_between_domains.py +1 -1
- sequenzo/multidomain/combt.py +4 -4
- sequenzo/multidomain/linked_polyad.py +3 -3
- sequenzo/prefix_tree/__init__.py +1 -1
- sequenzo/prefix_tree/individual_level_indicators.py +2 -2
- sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +2 -2
- sequenzo/sequence_characteristics/plot_characteristics.py +2 -2
- sequenzo/sequence_characteristics/simple_characteristics.py +2 -2
- sequenzo/suffix_tree/__init__.py +1 -1
- sequenzo/suffix_tree/individual_level_indicators.py +3 -3
- sequenzo/visualization/plot_single_medoid.py +2 -2
- sequenzo/visualization/plot_transition_matrix.py +1 -1
- sequenzo/visualization/utils/utils.py +2 -2
- sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +1 -1
- {sequenzo-0.1.20.dist-info → sequenzo-0.1.21.dist-info}/METADATA +11 -8
- {sequenzo-0.1.20.dist-info → sequenzo-0.1.21.dist-info}/RECORD +35 -41
- sequenzo/big_data/clara/utils/get_weighted_diss.pyx +0 -16
- sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.pyx +0 -95
- sequenzo/dissimilarity_measures/utils/seqconc.pyx +0 -26
- sequenzo/dissimilarity_measures/utils/seqdss.pyx +0 -33
- sequenzo/dissimilarity_measures/utils/seqdur.pyx +0 -34
- sequenzo/dissimilarity_measures/utils/seqlength.pyx +0 -19
- {sequenzo-0.1.20.dist-info → sequenzo-0.1.21.dist-info}/WHEEL +0 -0
- {sequenzo-0.1.20.dist-info → sequenzo-0.1.21.dist-info}/licenses/LICENSE +0 -0
- {sequenzo-0.1.20.dist-info → sequenzo-0.1.21.dist-info}/top_level.txt +0 -0
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import numpy as np
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cimport numpy as cnp
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from sequenzo.define_sequence_data import SequenceData
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from libc.stdint cimport int32_t
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def seqdur(seqdata):
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if not isinstance(seqdata, SequenceData):
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raise ValueError("data is not a sequence object, see SequenceData to create one")
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cdef cnp.ndarray[int32_t, ndim=2] seqdatanum = seqdata.values.copy().astype(np.int32, copy=False)
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cdef int n = seqdatanum.shape[0], m = seqdatanum.shape[1]
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cdef int i, j
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cdef cnp.ndarray[int32_t, ndim=2] ffill = seqdatanum.copy()
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for j in range(1, m):
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ffill[:, j] = np.where(seqdatanum[:, j] < 0, ffill[:, j - 1], seqdatanum[:, j])
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cdef cnp.ndarray[char, ndim=2] boundaries = np.concatenate(
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[np.ones((n, 1), dtype=bool), ffill[:, 1:] != ffill[:, :-1]], axis=1
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)
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cdef cnp.ndarray[int32_t, ndim=2] group_ids = np.cumsum(boundaries, axis=1).astype(np.int32, copy=False)
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cdef cnp.ndarray[char, ndim=2] valid = seqdatanum >= 0
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cdef cnp.ndarray[int32_t, ndim=2] group_durations = np.zeros((n, m), dtype=np.int32)
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for i in range(n):
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counts = np.bincount(group_ids[i][valid[i]])
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counts = counts[1:] if counts.size > 0 else np.array([], dtype=int)
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group_durations[i, :len(counts)] = counts
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return group_durations
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import pandas as pd
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import numpy as np
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cimport numpy as cnp
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from sequenzo.define_sequence_data import SequenceData
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from libc.stdint cimport int32_t
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def seqlength(seqdata):
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if isinstance(seqdata, SequenceData):
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seqdata = seqdata.seqdata.replace(np.nan, -99)
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cdef cnp.ndarray[int32_t, ndim=2] seqarray_long
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if isinstance(seqdata, pd.DataFrame):
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seqarray_long = seqdata.to_numpy(dtype=np.int32)
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return np.sum(seqarray_long > 0, axis=1)
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else:
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seqarray_long = seqdata
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return np.sum(seqarray_long > 0, axis=1)
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