sequenzo 0.1.17__cp39-cp39-macosx_10_9_universal2.whl → 0.1.18__cp39-cp39-macosx_10_9_universal2.whl

sequenzo/with_event_history_analysis/sequence_history_analysis.py

@@ -0,0 +1,283 @@
+"""
+@Author  : Yuqi Liang 梁彧祺
+@File    : sequence_history_analysis.py
+@Time    : 30/09/2025 21:08
+@Desc    : Sequence History Analysis - Convert person-level sequence data to person-period format
+"""
+
+import numpy as np
+import pandas as pd
+
+
+def person_level_to_person_period(data, id_col="id", period_col="time", event_col="event"):
+    """
+    Convert person-level data to person-period format.
+    
+    This function expands each person's single row into multiple rows,
+    one for each time period they are observed.
+    
+    Parameters
+    ----------
+    data : pandas.DataFrame
+        Input data with one row per person
+    id_col : str, optional
+        Name of the ID column (default: "id")
+    period_col : str, optional
+        Name of the time period column (default: "time")
+    event_col : str, optional
+        Name of the event indicator column (default: "event")
+    
+    Returns
+    -------
+    pandas.DataFrame
+        Expanded data with one row per person-period
+    
+    Examples
+    --------
+    >>> data = pd.DataFrame({'id': [1, 2], 'time': [3, 2], 'event': [True, False]})
+    >>> person_level_to_person_period(data)
+       id  time  event
+    0   1     1  False
+    1   1     2  False
+    2   1     3   True
+    3   2     1  False
+    4   2     2  False
+    """
+    # Check for missing values in critical columns
+    if data[[id_col, period_col, event_col]].isna().any().any():
+        raise ValueError("Cannot handle missing data in the time or event variables")
+    
+    # Create an index that repeats each row based on the time value
+    # For example, if time=3, that row will be repeated 3 times
+    index = np.repeat(np.arange(len(data)), data[period_col].values)
+    
+    # Find the cumulative sum to identify which rows should have the event
+    idmax = np.cumsum(data[period_col].values) - 1
+    
+    # Expand the data by repeating rows
+    dat = data.iloc[index].copy()
+    dat.reset_index(drop=True, inplace=True)
+    
+    # Create sequential time periods for each ID (1, 2, 3, ...)
+    dat[period_col] = dat.groupby(id_col).cumcount() + 1
+    
+    # Set all events to False initially
+    dat[event_col] = False
+    
+    # Set events to True only at the final period for each person
+    # Convert to bool to avoid dtype incompatibility warning
+    dat.loc[idmax, event_col] = data[event_col].values.astype(bool)
+    
+    return dat
+
+
+def _extract_sequence_dataframe(seqdata):
+    """
+    Extract sequence DataFrame from various input types.
+    
+    Parameters
+    ----------
+    seqdata : SequenceData, pandas.DataFrame, or numpy.ndarray
+        Input sequence data
+    
+    Returns
+    -------
+    pandas.DataFrame
+        Sequence data as a DataFrame
+    """
+    # Check if input is a SequenceData object
+    if hasattr(seqdata, 'seqdata'):
+        # This is a SequenceData object
+        return seqdata.seqdata.copy()
+    elif isinstance(seqdata, pd.DataFrame):
+        return seqdata.copy()
+    else:
+        # Assume it's array-like
+        return pd.DataFrame(seqdata)
+
+
+def seqsha(seqdata, time, event, include_present=False, align_end=False, covar=None):
+    """
+    Sequence History Analysis: Create person-period format with sequence history.
+    
+    This function converts sequence data into a person-period format where each
+    row represents a time point for a person, with columns showing their sequence
+    history up to that point.
+    
+    Parameters
+    ----------
+    seqdata : SequenceData, pandas.DataFrame, or numpy.ndarray
+        Sequence data where each row is a person and each column is a time point.
+        Can be a SequenceData object, DataFrame, or array.
+    time : array-like
+        Duration or time until event for each person. Length should equal the 
+        number of sequences. Each value indicates how many time periods that 
+        person is observed. For example, if all persons are observed for the 
+        full sequence length, use: np.full(n_persons, sequence_length)
+    event : array-like
+        Event indicator for each person (True/False or 1/0). Length should 
+        equal the number of sequences.
+    include_present : bool, optional
+        If True, include the current time point in the history (default: False)
+        If False, only include past time points (recommended for most analyses)
+    align_end : bool, optional
+        If True, align sequences from the end (right-aligned) (default: False)
+        If False, align sequences from the start (left-aligned)
+    covar : pandas.DataFrame or numpy.ndarray, optional
+        Additional covariates to merge with the output (default: None)
+        Should have the same number of rows as seqdata
+    
+    Returns
+    -------
+    pandas.DataFrame
+        Person-period data with the following columns:
+        - id: Person identifier
+        - time: Time period within person
+        - event: Event indicator (True only at the final period for each person)
+        - Sequence history columns (varies based on align_end parameter)
+        - Additional covariate columns (if covar is provided)
+    
+    Raises
+    ------
+    ValueError
+        If maximum time exceeds the length of the longest sequence
+    
+    Examples
+    --------
+    Example 1: Basic usage with DataFrame
+    >>> import pandas as pd
+    >>> import numpy as np
+    >>> seqdata = pd.DataFrame([[1, 2, 3, 4], [1, 1, 2, 2]])
+    >>> time = np.array([3, 2])
+    >>> event = np.array([True, False])
+    >>> result = seqsha(seqdata, time, event)
+    
+    Example 2: Usage with SequenceData object (recommended)
+    >>> from sequenzo import SequenceData, load_dataset
+    >>> df = load_dataset('pairfam_family')
+    >>> time_cols = [str(i) for i in range(1, 265)]
+    >>> seq_data = SequenceData(df, time=time_cols, id_col='id', 
+    ...                          states=list(range(1, 10)))
+    >>> # All persons observed for 264 months
+    >>> time = np.full(len(df), 264)
+    >>> event = df['highschool'].values
+    >>> result = seqsha(seq_data, time, event)
+    
+    Example 3: With covariates
+    >>> covar = df[['sex', 'yeduc', 'east']]
+    >>> result = seqsha(seq_data, time, event, covar=covar)
+    
+    Example 4: Right-aligned sequences
+    >>> result = seqsha(seq_data, time, event, align_end=True)
+    
+    Notes
+    -----
+    - The time parameter represents observation duration, not calendar time
+    - When include_present=False (default), only past states are included
+    - Use align_end=True when analyzing sequences leading up to an event
+    - Missing values in the original sequence are converted to "NA_orig"
+    """
+    # Extract sequence DataFrame from input (handles SequenceData, DataFrame, or array)
+    seq_df = _extract_sequence_dataframe(seqdata)
+    
+    # Convert time and event to numpy arrays for consistency
+    time_array = np.asarray(time)
+    event_array = np.asarray(event)
+    
+    # Check that dimensions match
+    n_sequences = len(seq_df)
+    if len(time_array) != n_sequences:
+        raise ValueError(
+            f"Length of 'time' ({len(time_array)}) must match number of sequences ({n_sequences})"
+        )
+    if len(event_array) != n_sequences:
+        raise ValueError(
+            f"Length of 'event' ({len(event_array)}) must match number of sequences ({n_sequences})"
+        )
+    
+    # Create base time data: one row per person with their time and event
+    basetime = pd.DataFrame({
+        'id': np.arange(1, n_sequences + 1),
+        'time': time_array,
+        'event': event_array
+    })
+    
+    # Convert to person-period format (expand rows)
+    persper = person_level_to_person_period(basetime, "id", "time", "event")
+    
+    # Convert sequence data to matrix and handle missing values
+    sdata = seq_df.values.astype(str)
+    sdata[pd.isna(seq_df.values)] = "NA_orig"
+    
+    # Get the time periods for each row in person-period data
+    age = persper['time'].values
+    ma = int(np.max(age))
+    
+    # Check if time values are valid
+    if ma > seq_df.shape[1]:
+        raise ValueError("Maximum time of event occurrence is higher than the longest sequence!")
+    
+    # Create empty matrix to store past sequence states
+    past = np.full((len(persper), seq_df.shape[1]), np.nan, dtype=object)
+    
+    if align_end:
+        # Right-align the sequences (align from the end)
+        start = 1 if include_present else 2
+        
+        for aa in range(start, ma + 1):
+            # Find rows where time equals aa
+            cond = age == aa
+            # Get the person IDs for these rows
+            ids_a = persper.loc[cond, 'id'].values - 1  # Subtract 1 for 0-based indexing
+            
+            if include_present:
+                # Include current time point: fill from (ncol-aa) to end
+                past[cond, (seq_df.shape[1] - aa):seq_df.shape[1]] = sdata[ids_a, 0:aa]
+            else:
+                # Exclude current time point: fill from (ncol-aa+1) to end
+                past[cond, (seq_df.shape[1] - aa + 1):seq_df.shape[1]] = sdata[ids_a, 0:(aa - 1)]
+        
+        # Create column names counting backwards
+        col_names = [f"Tm{i}" for i in range(seq_df.shape[1], 0, -1)]
+    else:
+        # Left-align the sequences (align from the start)
+        for aa in range(1, ma + 1):
+            if include_present:
+                # Include present: use time > aa
+                cond = age > aa
+            else:
+                # Exclude present: use time >= aa
+                cond = age >= aa
+            
+            # Get the person IDs for these rows
+            ids_a = persper.loc[cond, 'id'].values - 1  # Subtract 1 for 0-based indexing
+            
+            # Fill in the sequence state at position aa-1 (0-based)
+            past[cond, aa - 1] = sdata[ids_a, aa - 1]
+        
+        # Use original column names or create default ones
+        if seq_df.columns is not None and len(seq_df.columns) > 0:
+            col_names = [str(col) for col in seq_df.columns[:ma]]
+            # Pad with additional column names if needed
+            col_names += [f"col_{i}" for i in range(ma, seq_df.shape[1])]
+        else:
+            col_names = [f"col_{i}" for i in range(seq_df.shape[1])]
+    
+    # Convert past matrix to DataFrame
+    past_df = pd.DataFrame(past, columns=col_names)
+    
+    # Combine person-period data with sequence history
+    alldata = pd.concat([persper.reset_index(drop=True), past_df], axis=1)
+    
+    # Add covariates if provided
+    if covar is not None:
+        # Merge covariates based on the ID (subtract 1 for 0-based indexing)
+        if isinstance(covar, pd.DataFrame):
+            covar_subset = covar.iloc[alldata['id'].values - 1].reset_index(drop=True)
+            alldata = pd.concat([alldata, covar_subset], axis=1)
+        else:
+            covar_array = np.array(covar)
+            covar_subset = covar_array[alldata['id'].values - 1]
+            alldata = pd.concat([alldata, pd.DataFrame(covar_subset)], axis=1)
+    
+    return alldata

{sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sequenzo
-Version: 0.1.17
+Version: 0.1.18
 Summary: A fast, scalable and intuitive Python package for social sequence analysis.
 Author-email: Yuqi Liang <yuqi.liang.1900@gmail.com>, Xinyi Li <1836724126@qq.com>, Jan Heinrich Ernst Meyerhoff-Liang <jan.meyerhoff1@gmail.com>
 License: BSD 3-Clause License
@@ -58,6 +58,7 @@ Requires-Dist: joblib>=1.0.1
 Requires-Dist: docutils>=0.17
 Requires-Dist: tqdm<5.0.0,>=4.62.3
 Requires-Dist: missingno<0.6.0,>=0.5.2
+Requires-Dist: rpy2
 Provides-Extra: dev
 Requires-Dist: pytest>=6.2.5; extra == "dev"
 Requires-Dist: flake8>=3.9.2; extra == "dev"
@@ -123,12 +124,12 @@ Perfect for research, policy, and business, enabling seamless analysis of catego
 
 Sequenzo provides pre-built Python wheels for maximum compatibility — no need to compile from source.
 
-| Platform         | Architecture                  | Python Versions      | Status            |
+| Platform         | Architecture                  | Python Versions       | Status            |
 |------------------|-------------------------------|-----------------------|-------------------|
-| **macOS**        | `universal2` (Intel + Apple Silicon) | 3.9, 3.11       | ✅ Pre-built wheel |
-| **Windows**      | `AMD64` (64-bit)              | 3.9, 3.10, 3.11       | ✅ Pre-built wheel |
-| **Linux (glibc)**| `x86_64` (standard Linux)     | 3.9, 3.10, 3.11       | ✅ Pre-built wheel |
-| **Linux (musl)** | `x86_64` (Alpine Linux)       | 3.9, 3.10, 3.11       | ✅ Pre-built wheel |
+| **macOS**        | `universal2` (Intel + Apple Silicon) | 3.9, 3.10, 3.11, 3.12 | ✅ Pre-built wheel |
+| **Windows**      | `AMD64` (64-bit)              | 3.9, 3.10, 3.11, 3.12 | ✅ Pre-built wheel |
+| **Linux (glibc)**| `x86_64` (standard Linux)     | 3.9, 3.10, 3.11, 3.12 | ✅ Pre-built wheel |
+| **Linux (musl)** | `x86_64` (Alpine Linux)       | 3.9, 3.10, 3.11, 3.12 | ✅ Pre-built wheel |
 
 
 What do these terms mean?

{sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/RECORD

@@ -1,20 +1,20 @@
-sequenzo/__init__.py,sha256=OQ0-cfOGB-cHDWM18fMNk4OXHInmGawk29dOEIQVcGM,5743
-sequenzo/define_sequence_data.py,sha256=cDBn74UTIxpo6658ZhrfYVZpJfnlfPafyUOtyPlNzpI,25749
+sequenzo/__init__.py,sha256=TRZc7i5NYjA8IqdaWQV7E0xH9X8iWGo4oF1SLzrynJk,6279
+sequenzo/define_sequence_data.py,sha256=EioGt7wKRtSt_F85icbli7CmmPzFGfRtuEa2jeAiN_I,28211
 sequenzo/big_data/__init__.py,sha256=iSZnGboYhbvsFf75uL8D8XDucXRxYypmFNN1uX5MxJo,152
 sequenzo/big_data/clara/__init__.py,sha256=pDR5_TSDisEhPtsA2gXGaXXBNTmWidJC_nnd9QMkz-U,700
-sequenzo/big_data/clara/clara.py,sha256=28qy9J48UYp1Dm2P5zy51V4z-Ed7LOCyZy4LCinXJQ8,18818
+sequenzo/big_data/clara/clara.py,sha256=67KaOUrmUxzUJrSe7O3VtW4URIhYZUHe3_QlokQTGds,18824
 sequenzo/big_data/clara/visualization.py,sha256=EpSmtAxRHVqcXlcXvSGiUuBjEETR7zK_gnLZgjlbXB8,3211
 sequenzo/big_data/clara/utils/__init__.py,sha256=2_o1tz8HFZVKFy8w8oJWdWlVKtwGjGY3z4PQylHKjt0,726
 sequenzo/big_data/clara/utils/aggregatecases.py,sha256=ul97pbnRlwxbFbX_0M4j-Bkyxkp7zMAKatSo4eanO24,2899
 sequenzo/big_data/clara/utils/davies_bouldin.py,sha256=4Y6VFjqopG3CaftQ8tDxQPjxxupJ6Hgv-yTXwCvgN7w,3037
-sequenzo/big_data/clara/utils/get_weighted_diss.c,sha256=U9OkbU5M9RS1zrPnYtc2UYnZPv0XWqFQdZYohMQBWNk,466603
-sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-darwin.so,sha256=mYvCcfYm0SaxkIrUVmYCT9Bml_NHlUJZENnjtsO2Yas,104280
+sequenzo/big_data/clara/utils/get_weighted_diss.c,sha256=xKcmRuFHEVlppw71SsyzahwKO87Iu1Cq-AiioswujYI,466603
+sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-darwin.so,sha256=aYyHmzFZ0u6tpGPjw4QFNqHASqiTSfPcV5687hypdtM,104280
 sequenzo/big_data/clara/utils/get_weighted_diss.pyx,sha256=UYR-u8MDQEuWID3inKhSpBsuxu7qTFmEwLrjNPBMmUw,430
 sequenzo/big_data/clara/utils/wfcmdd.py,sha256=-1H6CbTteTW-CeuQ_ehVDhnKH3ozcCkUobxoCSRIpYg,7074
 sequenzo/clustering/KMedoids.py,sha256=8EcBIeW4071b6hBa2p4p3ivanMwqUGIv97s8n0lScoQ,6181
 sequenzo/clustering/__init__.py,sha256=duEY0Hq0-7Kc_lv0uFDK3D8IEXby-7Z0Rjff0EgO0KM,875
 sequenzo/clustering/clustering_c_code.cpython-39-darwin.so,sha256=Fj5RvS-gmqEooFTeW6wUe4SEhMPyFmr0S0-Pajl1hGk,362760
-sequenzo/clustering/hierarchical_clustering.py,sha256=ZmijK9xZRR6z1kwItcRLqo6WQ1Ryl0NrYeeuknVBfS0,47646
+sequenzo/clustering/hierarchical_clustering.py,sha256=ZFx4jAN_aUUAJBrpAEKQov7ZL1uLaZpnpWWGSs7kf0Y,56496
 sequenzo/clustering/src/KMedoid.cpp,sha256=Bb4LaRes004T9vyCmUknRS0NUaNr4ZoEpWvtkYGq-jw,9299
 sequenzo/clustering/src/PAM.cpp,sha256=UFXdTy1wMWheYa-fUoi8ASQPmn0Ew-AO7fqVQVxn_E8,8357
 sequenzo/clustering/src/PAMonce.cpp,sha256=C9HqGBRenmF2tnQofALjjU1As02dTw2oqEnuvdhoJIk,7943
@@ -46,16 +46,17 @@ sequenzo/datasets/polyadic_samplep1.csv,sha256=-2HvKSmevfqe1rWFVJlbnjousEgJRU_PH
 sequenzo/datasets/polyadic_seqc1.csv,sha256=ydZ-U8NTszR4lNBN4hhsH_dHfq0w5VZSMM7t9C5Uado,7028
 sequenzo/datasets/polyadic_seqp1.csv,sha256=sydXCR0JBKJlbMxJyGa46cic9XQstUpYFOtHaLmkp_0,7681
 sequenzo/dissimilarity_measures/__init__.py,sha256=qkWAQ1sBpS2aayO-FSA8Zha7rQ_vjs0_KIHEB60bVg4,958
-sequenzo/dissimilarity_measures/c_code.cpython-39-darwin.so,sha256=4X3Q-T8CbSZECQnqCbtX4-tDEv2hC4VnomCdwr7Ldkw,345304
+sequenzo/dissimilarity_measures/c_code.cpython-39-darwin.so,sha256=s6h-gzYX6kK55Hf5KXr-39QXd-QyEEvwxf_Z6YLJpoY,345992
 sequenzo/dissimilarity_measures/get_distance_matrix.py,sha256=bRlmBHkVAo48hAm9kuFarXH1p-eEXORgG-nOi96CH14,30017
-sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py,sha256=NcwKUY3l7zLMR4rqaYUuCjCJHXR3fv3HG-NBAdz6Cb4,9529
+sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py,sha256=A2ohhpJw-dznmjfsjctVnO5BOzajRBm3Ffj-oPYEvJ4,9551
 sequenzo/dissimilarity_measures/setup.py,sha256=OLo8Zw65euUVytr-SjjkOrgIHgHe98DdWCUynsTDPXQ,758
-sequenzo/dissimilarity_measures/src/DHDdistance.cpp,sha256=YYZMnnOKHricMP0B2aDPCy5vVdjhq6vBty5vLSG1kWA,5471
-sequenzo/dissimilarity_measures/src/LCPdistance.cpp,sha256=W2g9m6krNoEyhG-SkL8nok4Dif8Pbc6RunJyyHIEc04,3988
-sequenzo/dissimilarity_measures/src/OMdistance.cpp,sha256=rkZoDn-1WP0KSB-gfPu5aZ71w9erJVCxDlBACTwOJxw,9823
-sequenzo/dissimilarity_measures/src/OMspellDistance.cpp,sha256=eO0wjWa_LvrTEYo42OY2p_nuTFx_BbL6xv2jZwQ471E,8248
+sequenzo/dissimilarity_measures/src/DHDdistance.cpp,sha256=RbWbSaELxlJiw5ST_JaD-wPx_sD7PGV2VdK4qEhOcxE,4714
+sequenzo/dissimilarity_measures/src/LCPdistance.cpp,sha256=VCqRm_mbI2IOm6KiO7SACHDOpZXBTkDdyr1Fo39zJVE,3231
+sequenzo/dissimilarity_measures/src/OMdistance.cpp,sha256=0HxjF4VFXkCtrV2zV7Kb_URVMWrjgt_W-4ugf1O7cDo,8726
+sequenzo/dissimilarity_measures/src/OMspellDistance.cpp,sha256=EbtrWCTNK5mq5hfTJUwcgD4aUm3VbVCjzIA1J_3wNP0,9877
 sequenzo/dissimilarity_measures/src/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sequenzo/dissimilarity_measures/src/dist2matrix.cpp,sha256=spUINWdfJyXR3uWaQ66tLPifrZT0VPfylX5SkKdQ3RQ,1759
+sequenzo/dissimilarity_measures/src/dp_utils.h,sha256=mghKkQlXhl3F4dXuO-4INGBkWiYfyxBawVv-PtBCkZw,4466
 sequenzo/dissimilarity_measures/src/module.cpp,sha256=A8SheP33EUcBATXzVcb1W_bqevxYOFoj0yJxdVDLT7M,1729
 sequenzo/dissimilarity_measures/src/setup.py,sha256=HTMiDG0P6sCLdAQBgyp8Jd5iNvQimzvNoTHE4QP0XVs,579
 sequenzo/dissimilarity_measures/src/utils.h,sha256=Hw_VLkhFvoXLFoJ9FsdFMuflnI5Zm6-6gAwspnzA5TI,803
@@ -389,59 +390,61 @@ sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h
 sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h,sha256=rsHZiQKOqWBd-ptCJyOP2Ju5uDc9Vm7V8SoUJQcSUR8,16505
 sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h,sha256=5K91T9EDnVCqWxNogT4GN6g3ieIx9uoJ3_4Y-UkBeF0,4312
 sequenzo/dissimilarity_measures/src/xsimd/.github/cmake-test/main.cpp,sha256=2CGojY-vyRREHQGI6-Wytz1Yq9dk5bLVvlz_FM10TXY,57
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp,sha256=pq1cZpXyhC15orjwj22KgnSHCX6uFRFpbaQOCMaO7SQ,2616
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp,sha256=GphfuEIWQsJD9LDCOP--XlfV1Dac-6Jsavq3v6yrwNA,88059
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp,sha256=NqZ1H-sgeY1NL2_R0qgFbXCQcWF-_7EakjdexTe3PKI,43390
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 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512cd.hpp,sha256=xBQYj_r0XVrrO5ZeGndBarz5N4kWAYaXWO9kGJmA2sk,979
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 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512ifma.hpp,sha256=HO39AdydUnMCg9NDElzZuml9DDHxJYPrHXMODiRrvFw,939
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512pf.hpp,sha256=Df3HEkrfatmU5GEQpdxWpZy3oSbxJqqjL3Lo8OEsDBw,933
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-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp,sha256=kHaHDq8Dc4No_vZ-dy9r9kxxkKEVs8TCQb3LvRqw0fQ,3176
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 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vnni_avx512bw.hpp,sha256=GKWN2MD1An0VGTSxLCSVEc2WTNxxRE4FBga_khzlEFA,968
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vnni_avx512vbmi2.hpp,sha256=Gs2IqCq_ZgJJjWgqVKOA1EKrICB40sUTWitS1z1cZCQ,975
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avxvnni.hpp,sha256=b9XOSCmcZcNdWNxs0UUdTEMUpYSCt69Y5wC7Nt2F0sw,930
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp,sha256=UqTtqe21YMVkmhUS-DijTor-NQp-3e0ZU3954YqtR7M,1153
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp,sha256=cpFjOSIN6h6BX5ZWeVWdZWHCYz5upqqbsOZRRZw__3A,2737
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp,sha256=jSIS29Xfm34Wd9NlDnrw3HJzY204eTmFOttHtic1VQ8,14092
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp,sha256=h_VC-mjPsqLaokmt87dX1oalcIoVPU3KvI2RigwibSc,36204
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp,sha256=1mjc_5evkSyJeyl4cjy9a6WbuPlJc1B3aqScAdlPn-Q,3042
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 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx2.hpp,sha256=cU1qT6VBmLW-LUFiLJIKQQow1QsXHPOYs30RRFSXwCQ,1592
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp,sha256=roaWDy9e8knDZF1r8UcJl0jO5Crl6sVgC2OwHhmwyn0,3041
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp,sha256=pr3MIsqNEGVatJvB4uFwCR6reQLj2zHOW24Vsv6cTwg,2957
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+sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp,sha256=b8THgymg0NPIjQTcir5i9AvAg-wqsbzPJeYplVIMJm8,3461
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_i8mm_neon64.hpp,sha256=OChPwZc_MGK-9mTOMyLVszuhDKgihN8NhQaeEZCSASo,901
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp,sha256=vwQpCnkASeQ_UJGJQT4z5ROSSIw31I9FaVgKZDP8JEI,2768
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp,sha256=W5sHoHjwaQNZip8JpXvr1KG_cBhqbSq-ROFl1B6QGOg,126707
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp,sha256=-BHZqOdi_naDZmA6WGS2PYUqERvdKG1PjGc20mIBA-Q,61941
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp,sha256=DEl-wMCkt5wWpN4Y1KGgClhqOTzmmmhXn25nsbxr0oo,70518
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp,sha256=vRec_I2FFO08TOc9qzX9bVKO5tySgojlIDewIyyxUIg,36502
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp,sha256=ouYp7iokhwnlipC_F-LQnGYSWHMnwm2jG7diik0Y1oo,78475
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp,sha256=HJa3Z2dGgnNKzWnUpxe17H1jWGFLmasY7wy7gx7ax2A,2102
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+sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp,sha256=KKyskeg7Q96G9epwqUxTeXgwfG2OWsg1yq1VlZvrFhA,71057
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 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse4_1.hpp,sha256=OpXAmc-2deMiqa2PBltJ6L2ObDK8HaJPLBsEPNrOFOo,14045
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse4_2.hpp,sha256=gK3_yY9vcjyac0LDUFB5-i7jNQraKxC2PwmQtEukD0E,1697
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp,sha256=vv9t_UrBwqADio-VgrlRpShs-JOEg_JoUjowMr51uE0,7945
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp,sha256=RA86okzM4MzxPXHsCAsWhm8bnY7OI7wJqtlWUH0MnwU,48947
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp,sha256=yUtqTqMyf-I6JWs7MBtlsBsRRqOByTcdZUZ5cMEwBlw,72155
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp,sha256=XF5DGDsbxGx7VQC6PDBohV_aYRN9fz-nOFNLwDlD4SU,10081
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp,sha256=xFL0kBf-V6gLDqXRY_3vzUaAg-B9dcdmklsgC_HjZTA,4007
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp,sha256=zdRWq1Tn9iNCDqNg85J7GAwRwu52INcq3xieq1wND9U,15339
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp,sha256=Pu5xs-A5ZGZ0k-kcl7uwj2F1TKidWoGahzVbvJtITcQ,8350
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp,sha256=x0g_ywqi5l6jWGhpJsKe1GDSi0-6U2F9VKW_CZeRgNw,114906
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp,sha256=hLQT4FmSS1dmrLICJzs5LlH_r_EM9sEmIXmhexCm764,40475
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+sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp,sha256=mqcXzs6CSdv9SzfOMLx6qJ5myVvXuwa_y34M8QAkd8w,4070
+sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp,sha256=_mD-smC8FQRgWofxuuhtjhsUeFWO1fHj9XUVA6wERF8,15802
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+sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp,sha256=7TDTegY1TC02GEMz6tolupM244dHmnjPPpi1uh17jWI,116975
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 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_rounding.hpp,sha256=h7MJ6xC3jzjX1Ur9lCutOU8SAZfHRSeFhfDmqoCF8nQ,2772
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp,sha256=ey1phD8M9b_Fxp3Y_48yE2m5oT7gabDVIgnS1RqK_KU,45031
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp,sha256=wR6k9p-mvu9z7fF5nZYNwGrxrdWa8qUXrOQysrtTmlQ,8192
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp,sha256=zD1WSYBj2ujcpbXxTkJP8feZdnIIQzo8hfkuR_BCmzM,10517
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp,sha256=L10EvW4rHG2OtqVcNNQO6vAx7Xzzzd3vV4YEDPlutAw,9163
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp,sha256=VlwbeY8M3F6kK5tN5l3_LZQJ0z2rIEnXmz1-8408zis,1028
+sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp,sha256=mygsN-TfId4EmTLEdUjqE-PjtEiHN5nmS8qBGO6sHs4,9876
+sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp,sha256=vproKQRWczMTzEqu58exB2ZBnynrnV5IhSs4qn15XhU,45215
+sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp,sha256=1tYXZvcPoIXq2JQn9zCLssZJxw78ujtCJzIgP_3aLFM,8357
+sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp,sha256=mLDtLMxrLg_VvE2VLzXgdbZaubB-i8zigxR2xwgYy2Y,10819
+sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp,sha256=wRwLPkFnMMbT2jNkN3HBzQF6Qem7cqG-btBGsN2eQbc,9243
+sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp,sha256=G4txGeFYlaJ6eJV7-ZuyfDDGwNK_xixG-yF3QYofuEE,1127
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/math/xsimd_rem_pio2.hpp,sha256=8HLQvmN5LyevGa5_oHmvh1DpIfcx5vhOyNMEemyusac,25630
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/memory/xsimd_aligned_allocator.hpp,sha256=FjurT6RViugW6JYw-dTZ4BGQeeDfoj15fjl8EdG_q44,11463
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/memory/xsimd_alignment.hpp,sha256=daZBsGCBL-dy_z6sNIaJnFMolvYyOn9XNexjKq_vNtQ,2610
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp,sha256=Xe3Nr4YJ9tBFvRswGszEU79pPvRDJB1F9S1WIt-epa0,1943
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp,sha256=w48GY_8uwmEqL3KkF9Dhj9E320zB-tb9IljDAtGehlQ,91528
+sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp,sha256=dFsghzwm8dkyfGOlAZalxpsaZ48F8OkJ4-WBQ04oQIM,1978
+sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp,sha256=BgUmz6rVac01w0MThpdEzAlX7WaLKCJph88hYDSyaVU,94022
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx2_register.hpp,sha256=Bv7gezr-leUFuxJwqNw4HN28LuvJ1MjRnfw_IaL5hsA,1441
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512bw_register.hpp,sha256=I5SuqGKd_eNjPz13FMvPPImFscpX_LKSSYiFZ_QBB7I,1658
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512cd_register.hpp,sha256=rzJzLBBiU2oykdVnL98u1lM_WVJvkDQNuGRpWos0oUo,1653
@@ -456,7 +459,7 @@ sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vnni_a
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vnni_avx512vbmi2_register.hpp,sha256=ip1yV_HIBIQq0oDMYpiJLYC2D--4pvL0jN6cZAaR5xE,1871
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx_register.hpp,sha256=PALy0fEfHn5HzQXrtK06KsnBcbWTjbi3Mjwwfe4jAP4,2403
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avxvnni_register.hpp,sha256=y7c7Odk5jYAvPK7Gw_K719kgfS3WiM4BS9ap-2nhx0I,1473
-sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp,sha256=AXt0NsbLvK70coeK3kbZSeDVDdXL3t3zg2NtJxVwDYs,54278
+sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp,sha256=E3nUHaiHNOzQtAI32u144bE7AQXJRW6ODiFj0rvV-QQ,55252
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch_constant.hpp,sha256=EHJK2Wg3mR2qOKrqKXJvLSiWrWmU48zxhaNF3_SrsZ0,11442
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_common_arch.hpp,sha256=mQ1R_I4sR2tOo6MndNkpK171somx0OwEMl0wfszSdbw,1837
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_emulated_register.hpp,sha256=JHsYwTCOXgxhbKeI4lrdN9Zltzlzgl6-Uw7lGoHCfoM,2958
@@ -468,32 +471,33 @@ sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_i8mm_neon64_
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_neon64_register.hpp,sha256=dWUugWN9Gxr36Q1msPnfHP0u6EPCqc-VuLKorU_x028,1847
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_neon_register.hpp,sha256=c6ncY5lAnYamrQI7ezH9Mkm0QfM-3bQoUE1-wKOZmpk,5615
 sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_register.hpp,sha256=0nY6CpGYVZSttQiRxXbjasCX3e8gPKDYkGvmxfPBIlQ,4204
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 sequenzo/dissimilarity_measures/utils/seqlength.pyx,sha256=y-792z6X1L4zychHJj5IQVHOfM5JibQ_ITFnkYHJO3c,564
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 sequenzo/multidomain/association_between_domains.py,sha256=V4I_ILAAwf3cfz2i0HdLF8otAqPtF2LfjcCKo1IkfHA,10855
@@ -506,15 +510,15 @@ sequenzo/prefix_tree/__init__.py,sha256=YxMzr5UwM22DmpMDMAmKYI-vjhikDI8Gft_cJ9h1
 sequenzo/prefix_tree/individual_level_indicators.py,sha256=9JPINoPU50UGh9-D2QOAr7GQsxAkZ6qDmhKQtVwvZsU,52788
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 sequenzo/prefix_tree/utils.py,sha256=7DETf9i_OclRnWel680qD4wO1b8SffJVKq2Kx0zkTaQ,1489
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 sequenzo/suffix_tree/system_level_indicators.py,sha256=N4DrjM9fBHFqqcjDN1TAkwbkoDnlZSK2F8F2ERCizIQ,16962
@@ -524,14 +528,17 @@ sequenzo/visualization/plot_mean_time.py,sha256=5K1iBNCYTs4JrPlxaiZ1WF-0p-paDHPf
 sequenzo/visualization/plot_modal_state.py,sha256=wTAhdlu4px-dJdxM9LSSgDQioW46r-N08pt2hhSeU9c,9919
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 sequenzo/visualization/plot_single_medoid.py,sha256=yqKzUANkmA-f-oreDZuAVAzMrALxn_uGjg815HAjKag,5971
-sequenzo/visualization/plot_state_distribution.py,sha256=vMNryhsvnWFjaYwk7UdJM9N7uHon5sFigwqjnXRuwVU,24926
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 sequenzo/visualization/plot_transition_matrix.py,sha256=0DDOBZ2xu7lLb4Pz_18FvIaylkI8_7DttdXy_In6KTk,6895
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