bella-companion 0.0.10__tar.gz → 0.0.12__tar.gz

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  1. {bella_companion-0.0.10 → bella_companion-0.0.12}/PKG-INFO +2 -2
  2. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/fbd_empirical/data/change_times.csv +0 -10
  3. bella_companion-0.0.12/bella_companion/fbd_empirical/data/traits.csv +122 -0
  4. bella_companion-0.0.12/bella_companion/fbd_empirical/data/trees.nwk +100 -0
  5. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/fbd_empirical/run_beast.py +31 -9
  6. {bella_companion-0.0.10 → bella_companion-0.0.12}/pyproject.toml +2 -2
  7. bella_companion-0.0.10/bella_companion/fbd_empirical/data/body_mass.csv +0 -1378
  8. bella_companion-0.0.10/bella_companion/fbd_empirical/data/sampling_change_times.csv +0 -6
  9. bella_companion-0.0.10/bella_companion/fbd_empirical/data/trees.nwk +0 -100
  10. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/__init__.py +0 -0
  11. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/cli.py +0 -0
  12. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/fbd_empirical/__init__.py +0 -0
  13. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/fbd_empirical/__pycache__/run_beast.cpython-311.pyc +0 -0
  14. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/fbd_empirical/__pycache__/run_mlp.cpython-311.pyc +0 -0
  15. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/fbd_empirical/__pycache__/run_nonparametric.cpython-311.pyc +0 -0
  16. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/fbd_empirical/__pycache__/summarize_logs.cpython-311.pyc +0 -0
  17. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/fbd_empirical/results.py +0 -0
  18. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/fbd_empirical/summarize_logs.py +0 -0
  19. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/__init__.py +0 -0
  20. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/__pycache__/__init__.cpython-310.pyc +0 -0
  21. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/__pycache__/__init__.cpython-311.pyc +0 -0
  22. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/__pycache__/features.cpython-310.pyc +0 -0
  23. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/__pycache__/features.cpython-311.pyc +0 -0
  24. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/__pycache__/generate_data.cpython-310.pyc +0 -0
  25. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/__pycache__/generate_data.cpython-311.pyc +0 -0
  26. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/__pycache__/run_beast.cpython-311.pyc +0 -0
  27. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/__pycache__/summarize_logs.cpython-311.pyc +0 -0
  28. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/features.py +0 -0
  29. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/__init__.py +0 -0
  30. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/__pycache__/__init__.cpython-311.pyc +0 -0
  31. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/__pycache__/epi_explainations.cpython-311.pyc +0 -0
  32. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/__pycache__/epi_predictions.cpython-311.pyc +0 -0
  33. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/__pycache__/epi_simulations.cpython-311.pyc +0 -0
  34. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/__pycache__/fbd_explainations.cpython-311.pyc +0 -0
  35. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/__pycache__/fbd_predictions.cpython-311.pyc +0 -0
  36. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/__pycache__/fbd_simulations.cpython-311.pyc +0 -0
  37. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/__pycache__/figure1.cpython-311.pyc +0 -0
  38. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/__pycache__/plot.cpython-311.pyc +0 -0
  39. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/__pycache__/scenarios.cpython-311.pyc +0 -0
  40. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/__pycache__/utils.cpython-311.pyc +0 -0
  41. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/epi_multitype_results.py +0 -0
  42. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/epi_skyline_results.py +0 -0
  43. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/explain/__init__.py +0 -0
  44. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/explain/pdp.py +0 -0
  45. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/explain/shap.py +0 -0
  46. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/fbd_2traits_results.py +0 -0
  47. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/fbd_no_traits_results.py +0 -0
  48. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/scenarios.py +0 -0
  49. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/figures/utils.py +0 -0
  50. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/generate_data.py +0 -0
  51. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/generate_figures.py +0 -0
  52. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/metrics.py +0 -0
  53. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/run_beast.py +0 -0
  54. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__init__.py +0 -0
  55. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__pycache__/__init__.cpython-310.pyc +0 -0
  56. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__pycache__/__init__.cpython-311.pyc +0 -0
  57. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__pycache__/common.cpython-310.pyc +0 -0
  58. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__pycache__/common.cpython-311.pyc +0 -0
  59. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__pycache__/epi_multitype.cpython-310.pyc +0 -0
  60. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__pycache__/epi_multitype.cpython-311.pyc +0 -0
  61. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__pycache__/epi_skyline.cpython-310.pyc +0 -0
  62. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__pycache__/epi_skyline.cpython-311.pyc +0 -0
  63. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__pycache__/fbd_2traits.cpython-310.pyc +0 -0
  64. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__pycache__/fbd_2traits.cpython-311.pyc +0 -0
  65. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__pycache__/fbd_no_traits.cpython-310.pyc +0 -0
  66. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__pycache__/fbd_no_traits.cpython-311.pyc +0 -0
  67. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__pycache__/scenario.cpython-310.pyc +0 -0
  68. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__pycache__/scenario.cpython-311.pyc +0 -0
  69. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/__pycache__/utils.cpython-311.pyc +0 -0
  70. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/common.py +0 -0
  71. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/epi_multitype.py +0 -0
  72. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/epi_skyline.py +0 -0
  73. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/fbd_2traits.py +0 -0
  74. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/fbd_no_traits.py +0 -0
  75. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/scenarios/scenario.py +0 -0
  76. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/simulations/summarize_logs.py +0 -0
  77. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/utils/__init__.py +0 -0
  78. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/utils/beast.py +0 -0
  79. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/utils/explain.py +0 -0
  80. {bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/utils/slurm.py +0 -0
{bella_companion-0.0.10 → bella_companion-0.0.12}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: bella-companion
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- Version: 0.0.10
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+ Version: 0.0.12
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  Summary:
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  Author: gabriele-marino
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  Author-email: gabmarino.8601@gmail.com
@@ -12,5 +12,5 @@ Classifier: Programming Language :: Python :: 3.12
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  Requires-Dist: arviz (>=0.22.0,<0.23.0)
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  Requires-Dist: bella-lumiere (>=0.0.13,<0.0.14)
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  Requires-Dist: dotenv (>=0.9.9,<0.10.0)
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- Requires-Dist: phylogenie (>=2.1.29,<3.0.0)
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+ Requires-Dist: phylogenie (>=2.1.30,<3.0.0)
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  Requires-Dist: seaborn (>=0.13.2,<0.14.0)
{bella_companion-0.0.10 → bella_companion-0.0.12}/bella_companion/fbd_empirical/data/change_times.csv RENAMED
@@ -1,4 +1,3 @@
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- 0.0117
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  0.126
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  0.781
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  1.80
@@ -11,12 +10,3 @@
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  15.97
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  20.44
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  23.03
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- 28.1
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- 33.9
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- 37.8
17
- 41.2
18
- 47.8
19
- 56.0
20
- 59.2
21
- 61.6
22
- 66.0
bella_companion-0.0.12/bella_companion/fbd_empirical/data/traits.csv ADDED
@@ -0,0 +1,122 @@
1
+ species BM log10BM log10BM-cat midlat midlat-cat type
2
+ Acrecebus_fraileyi 12000.0 4.08 3 NA 1 3_1
3
+ Alouatta_belzebul 6395.0 3.81 3 -5.17 1 3_1
4
+ Alouatta_caraya 5375.0 3.73 3 -19.77 1 3_1
5
+ Alouatta_coibensis NA NA NA NA 2 ?
6
+ Alouatta_guariba 5362.5 3.73 3 -22.27 1 3_1
7
+ Alouatta_macconnelli 6292.5 3.8 3 3.74 1 3_1
8
+ Alouatta_nigerrima NA NA NA -5.48 1 ?
9
+ Alouatta_palliata 6250.0 3.8 3 7.12 1 3_1
10
+ Alouatta_pigra 8915.0 3.95 3 18.3 2 3_2
11
+ Alouatta_sara 6123.0 3.79 3 -14.07 1 3_1
12
+ Alouatta_seniculus 5950.0 3.77 3 0.6 1 3_1
13
+ Antillothrix_bernensis 1500.0 3.18 2 18.37 2 2_2
14
+ Aotus_azarae 1205.0 3.08 2 -12.84 1 2_1
15
+ Aotus_dindensis 1054.0 3.02 2 -3.22 1 2_1
16
+ Aotus_griseimembra 966.0 2.98 1 6.65 1 1_1
17
+ Aotus_infulatus NA NA NA NA 1 ?
18
+ Aotus_lemurinus 896.0 2.95 1 1.86 1 1_1
19
+ Aotus_nancymaae 787.0 2.9 1 -5.44 1 1_1
20
+ Aotus_nigriceps 957.5 2.98 1 -7.89 1 1_1
21
+ Aotus_trivirgatus 774.5 2.89 1 2.28 1 1_1
22
+ Aotus_vociferans 703.0 2.85 1 -0.96 1 1_1
23
+ Ateles_belzebuth 7770.0 3.89 3 -0.33 1 3_1
24
+ Ateles_chamek 9370.0 3.97 3 -9.71 1 3_1
25
+ Ateles_fusciceps 9025.0 3.96 3 4.04 1 3_1
26
+ Ateles_geoffroyi 7535.0 3.88 3 15.66 2 3_2
27
+ Ateles_hybridus 8700.5 3.94 3 8.27 1 3_1
28
+ Ateles_paniscus 8775.0 3.94 3 2.57 1 3_1
29
+ Brachyteles_arachnoides 8840.0 3.95 3 -23.9 0 3_0
30
+ Brachyteles_hypoxanthus 8874.5 3.95 3 -19.05 1 3_1
31
+ Branisella_boliviana 1000.0 3.0 2 -17.1 1 2_1
32
+ Cacajao_ayresi NA NA NA -0.1 1 ?
33
+ Cacajao_calvus 3165.0 3.5 3 -6.61 1 3_1
34
+ Cacajao_hosomi 3800.0 3.58 3 1.38 1 3_1
35
+ Cacajao_melanocephalus 2935.0 3.47 2 0.06 1 2_1
36
+ Caipora_bambuiorum 24000.0 4.38 3 -10.16 1 3_1
37
+ Callicebus_brunneus 829.5 2.92 1 -10.58 1 1_1
38
+ Callicebus_caligatus 880.0 2.94 1 -4.95 1 1_1
39
+ Callicebus_coimbrai NA NA NA -11.19 1 ?
40
+ Callicebus_cupreus 1070.0 3.03 2 -6.67 1 2_1
41
+ Callicebus_donacophilus 950.0 2.98 1 -14.8 1 1_1
42
+ Callicebus_hoffmansi 1060.0 3.03 2 -4.18 1 2_1
43
+ Callicebus_lugens 1090.0 3.04 2 3.42 1 2_1
44
+ Callicebus_moloch 988.0 2.99 1 -7.86 1 1_1
45
+ Callicebus_nigrifrons NA NA NA -21.32 1 ?
46
+ Callicebus_personatus 1245.0 3.1 2 -18.76 1 2_1
47
+ Callicebus_torquatus 1245.0 3.1 2 -1.68 1 2_1
48
+ Callimico_goeldii 483.5 2.68 0 -5.6 1 0_1
49
+ Callithrix_aurita 429.0 2.63 0 -21.99 1 0_1
50
+ Callithrix_geoffroyi 359.0 2.56 0 -17.9 1 0_1
51
+ Callithrix_jacchus 320.5 2.51 0 -7.86 1 0_1
52
+ Callithrix_kuhlii 375.0 2.57 0 -15.1 1 0_1
53
+ Callithrix_penicillata 325.5 2.51 0 -14.87 1 0_1
54
+ Canaanimico 2000.0 3.3 2 -7.35 1 2_1
55
+ Carlocebus_carmenensis 3500.0 3.54 3 -47.02 0 3_0
56
+ Cartelles_coimbrafilhoi 23500.0 4.37 3 -10.16 1 3_1
57
+ Cebuella_pygmaea 116.0 2.06 0 -5.09 1 0_1
58
+ Cebupithecia_sarmientoi 1602.0 3.2 2 -3.22 1 2_1
59
+ Cebus_albifrons 2735.0 3.44 2 -1.52 1 2_1
60
+ Cebus_capucinus 3110.0 3.49 3 7.75 1 3_1
61
+ Cebus_olivaceus 2905.0 3.46 2 4.5 1 2_1
62
+ Chilecebus_carrascoensis 1000.0 3.0 2 -34.88 0 2_0
63
+ Chiropotes_chiropotes 2740.0 3.44 2 2.45 1 2_1
64
+ Chiropotes_israelita NA NA NA NA 1 ?
65
+ Chiropotes_utahicki 2740.0 3.44 2 -3.49 1 2_1
66
+ Dolichocebus_gaimanensis 2700.0 3.43 2 -43.36 0 2_0
67
+ Homunculus_patagonicus 2700.0 3.43 2 -51.22 0 2_0
68
+ Insulacebus_toussentiana 4805.0 3.68 3 18.33 2 3_2
69
+ Killikaike_blakei 2000.0 3.3 2 -51.57 0 2_0
70
+ Lagonimico_conclucatus 595.0 2.77 1 -3.22 1 1_1
71
+ Lagothrix_cana 8571.5 3.93 3 -8.58 1 3_1
72
+ Lagothrix_lagotricha 7150.0 3.85 3 -0.15 1 3_1
73
+ Laventiana_annectens 605.0 2.78 1 -3.22 1 1_1
74
+ Leontopithecus_chrysomelas 577.5 2.76 1 -15.07 1 1_1
75
+ Leontopithecus_chrysopygus 577.5 2.76 1 -23.24 1 1_1
76
+ Leontopithecus_rosalia 609.0 2.78 1 -22.64 1 1_1
77
+ Mazzonicebus_almendrae 1602.0 3.2 2 -45.71 0 2_0
78
+ Mico_argentatus 346.5 2.54 0 -2.83 1 0_1
79
+ Mico_emiliae 321.5 2.51 0 -9.83 1 0_1
80
+ Mico_humeralifer 473.5 2.68 0 -4.36 1 0_1
81
+ Mico_mauesi 371.5 2.57 0 -5.35 1 0_1
82
+ Micodon_kyotensis 400.0 2.6 0 -3.22 1 0_1
83
+ Miocallicebus_villaviejai 1500.0 3.18 2 -3.22 1 2_1
84
+ Mohanamico_hershkovitzi 1000.0 3.0 2 -3.22 1 2_1
85
+ Neosaimiri_fieldsi 768.0 2.89 1 -3.22 1 1_1
86
+ Nuciruptor_rubricae 2000.0 3.3 2 -3.22 1 2_1
87
+ Panamacebus_transitus 2700.0 3.43 2 9.03 2 2_2
88
+ Paralouatta_varonai 8444.0 3.93 3 22.4 2 3_2
89
+ Patasola_magdalenae 480.0 2.68 0 -3.22 1 0_1
90
+ Perupithecus_ucayaliensis 400.0 2.6 0 -9.49 1 0_1
91
+ Pithecia_irrorata 2160.0 3.33 2 -7.54 1 2_1
92
+ Pithecia_monachus 2360.0 3.37 2 -4.87 1 2_1
93
+ Pithecia_pithecia 1760.0 3.25 2 2.47 1 2_1
94
+ Proteropithecia_neuquenensis 1600.0 3.2 2 -40.04 0 2_0
95
+ Saguinus_bicolor 429.0 2.63 0 -2.95 1 0_1
96
+ Saguinus_fuscicollis 350.5 2.54 0 -6.22 1 0_1
97
+ Saguinus_geoffroyi 492.0 2.69 0 6.58 1 0_1
98
+ Saguinus_graellsi 474.5 2.68 0 -1.96 1 0_1
99
+ Saguinus_imperator 585.0 2.77 1 -9.7 1 1_1
100
+ Saguinus_labiatus 514.5 2.71 1 -6.49 1 1_1
101
+ Saguinus_martinsi 492.0 2.69 0 -1.68 1 0_1
102
+ Saguinus_melanoleucus NA NA NA -8.41 1 ?
103
+ Saguinus_midas 545.0 2.74 1 1.77 1 1_1
104
+ Saguinus_mystax 524.5 2.72 1 -6.14 1 1_1
105
+ Saguinus_nigricollis 476.0 2.68 0 -0.82 1 0_1
106
+ Saguinus_oedipus 411.0 2.61 0 8.98 2 0_2
107
+ Saguinus_tripartitus 871.5 2.94 1 -1.42 1 1_1
108
+ Saimiri_boliviensis 788.5 2.9 1 -10.31 1 1_1
109
+ Saimiri_oerstedii 767.25 2.88 1 8.91 2 1_2
110
+ Saimiri_sciureus 852.5 2.93 1 -3.33 1 1_1
111
+ Saimiri_ustus 800.0 2.9 1 -8.69 1 1_1
112
+ Sapajus_apella 3085.0 3.49 3 -2.76 1 3_1
113
+ Sapajus_libidinosus 2509.779135 3.4 2 -11.96 1 2_1
114
+ Sapajus_robustus 2730.833333 3.44 2 -17.73 1 2_1
115
+ Sapajus_xanthosternos 2440.47619 3.39 2 -12.75 1 2_1
116
+ Solimoea_acrensis 8000.0 3.9 3 -10.93 1 3_1
117
+ Soriacebus_ameghinorum 1483.0 3.17 2 -47.02 0 2_0
118
+ Stirtonia_tatacoensis 5513.0 3.74 3 -3.22 1 3_1
119
+ Stirtonia_victoriae 10000.0 4.0 3 -3.22 1 3_1
120
+ Szalatavus_attricuspis 550.0 2.74 1 -17.1 1 1_1
121
+ Tremacebus_harringtoni 1800.0 3.26 2 -42.52 0 2_0
122
+ Xenothrix_mcgregori 5720.0 3.76 3 17.73 2 3_2