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

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.

This version of sequenzo might be problematic. Click here for more details.

Files changed (86) hide show
  1. sequenzo/__init__.py +25 -1
  2. sequenzo/big_data/clara/clara.py +1 -1
  3. sequenzo/big_data/clara/utils/get_weighted_diss.c +157 -157
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-darwin.so +0 -0
  5. sequenzo/clustering/hierarchical_clustering.py +202 -8
  6. sequenzo/define_sequence_data.py +34 -2
  7. sequenzo/dissimilarity_measures/c_code.cpython-39-darwin.so +0 -0
  8. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  9. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  10. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  11. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  12. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  13. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  14. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  15. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  16. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  58. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +157 -157
  59. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-39-darwin.so +0 -0
  60. sequenzo/dissimilarity_measures/utils/seqconc.c +157 -157
  61. sequenzo/dissimilarity_measures/utils/seqconc.cpython-39-darwin.so +0 -0
  62. sequenzo/dissimilarity_measures/utils/seqdss.c +157 -157
  63. sequenzo/dissimilarity_measures/utils/seqdss.cpython-39-darwin.so +0 -0
  64. sequenzo/dissimilarity_measures/utils/seqdur.c +157 -157
  65. sequenzo/dissimilarity_measures/utils/seqdur.cpython-39-darwin.so +0 -0
  66. sequenzo/dissimilarity_measures/utils/seqlength.c +157 -157
  67. sequenzo/dissimilarity_measures/utils/seqlength.cpython-39-darwin.so +0 -0
  68. sequenzo/sequence_characteristics/__init__.py +4 -0
  69. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  70. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  71. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  72. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  73. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  74. sequenzo/sequence_characteristics/turbulence.py +47 -67
  75. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  76. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  77. sequenzo/visualization/plot_sequence_index.py +58 -35
  78. sequenzo/visualization/plot_state_distribution.py +57 -36
  79. sequenzo/with_event_history_analysis/__init__.py +35 -0
  80. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  81. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  82. {sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/METADATA +7 -6
  83. {sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/RECORD +86 -79
  84. {sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/WHEEL +0 -0
  85. {sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/licenses/LICENSE +0 -0
  86. {sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/top_level.txt +0 -0
sequenzo/__init__.py CHANGED
@@ -85,6 +85,7 @@ from .sequence_characteristics import (
85
85
  get_number_of_transitions,
86
86
 
87
87
  get_turbulence,
88
+ get_complexity_index,
88
89
  get_within_sequence_entropy,
89
90
  get_spell_duration_variance,
90
91
  get_state_freq_and_entropy_per_seq,
@@ -95,6 +96,18 @@ from .sequence_characteristics import (
95
96
 
96
97
  )
97
98
 
99
+ # Event History Analysis (SAMM)
100
+ from .with_event_history_analysis import (
101
+ SAMM,
102
+ sequence_analysis_multi_state_model,
103
+ plot_samm,
104
+ seqsammseq,
105
+ set_typology,
106
+ seqsammeha,
107
+ # Keep old names for backward compatibility
108
+ seqsamm
109
+ )
110
+
98
111
  # Define `__all__` to specify the public API when using `from sequenzo import *`
99
112
  __all__ = [
100
113
  # Datasets
@@ -175,10 +188,21 @@ __all__ = [
175
188
  "get_subsequences_all_sequences",
176
189
  "get_number_of_transitions",
177
190
  "get_turbulence",
191
+ "get_complexity_index",
178
192
  "get_within_sequence_entropy",
179
193
  "get_spell_duration_variance",
180
194
  "get_state_freq_and_entropy_per_seq",
181
195
  "get_cross_sectional_entropy",
182
196
  "plot_longitudinal_characteristics",
183
- "plot_cross_sectional_characteristics"
197
+ "plot_cross_sectional_characteristics",
198
+
199
+ # Event History Analysis (SAMM)
200
+ "SAMM",
201
+ "sequence_analysis_multi_state_model",
202
+ "plot_samm",
203
+ "seqsammseq",
204
+ "set_typology",
205
+ "seqsammeha",
206
+ # Keep old names for backward compatibility
207
+ "seqsamm"
184
208
  ]
sequenzo/big_data/clara/clara.py CHANGED
@@ -439,7 +439,7 @@ if __name__ == '__main__':
439
439
  # ===============================
440
440
  # detailed
441
441
  # ===============================
442
- df = pd.read_csv("D:/college/research/QiQi/sequenzo/data_and_output/sampled_data_sets/detailed_data/sampled_1000_data.csv")
442
+ df = pd.read_csv("/Users/xinyi/Projects/sequenzo/sequenzo/data_and_output/sampled_data_sets/detailed_data/sampled_1000_data.csv")
443
443
  time = list(df.columns)[4:]
444
444
  states = ['data', 'data & intensive math', 'hardware', 'research', 'software', 'software & hardware', 'support & test']
445
445
  sequence_data = SequenceData(df[['worker_id', 'C1', 'C2', 'C3', 'C4', 'C5', 'C6', 'C7', 'C8', 'C9', 'C10']],