nimbus 2.2.1 → 2.3.0
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- checksums.yaml +7 -0
- data/CODE_OF_CONDUCT.md +7 -0
- data/CONTRIBUTING.md +46 -0
- data/MIT-LICENSE.txt +1 -1
- data/README.md +131 -21
- data/bin/nimbus +2 -2
- data/lib/nimbus.rb +2 -6
- data/lib/nimbus/classification_tree.rb +9 -12
- data/lib/nimbus/configuration.rb +22 -22
- data/lib/nimbus/forest.rb +8 -8
- data/lib/nimbus/loss_functions.rb +11 -0
- data/lib/nimbus/regression_tree.rb +8 -10
- data/lib/nimbus/tree.rb +54 -12
- data/lib/nimbus/version.rb +1 -1
- data/spec/classification_tree_spec.rb +47 -47
- data/spec/configuration_spec.rb +55 -55
- data/spec/fixtures/{classification_config.yml → classification/config.yml} +3 -3
- data/spec/fixtures/classification/random_forest.yml +1174 -0
- data/spec/fixtures/{classification_testing.data → classification/testing.data} +0 -0
- data/spec/fixtures/{classification_training.data → classification/training.data} +0 -0
- data/spec/fixtures/{regression_config.yml → regression/config.yml} +4 -4
- data/spec/fixtures/regression/random_forest.yml +2737 -0
- data/spec/fixtures/{regression_testing.data → regression/testing.data} +0 -0
- data/spec/fixtures/{regression_training.data → regression/training.data} +0 -0
- data/spec/forest_spec.rb +39 -39
- data/spec/individual_spec.rb +3 -3
- data/spec/loss_functions_spec.rb +31 -13
- data/spec/nimbus_spec.rb +2 -2
- data/spec/regression_tree_spec.rb +44 -44
- data/spec/training_set_spec.rb +3 -3
- data/spec/tree_spec.rb +4 -4
- metadata +37 -34
- data/spec/fixtures/classification_random_forest.yml +0 -922
- data/spec/fixtures/regression_random_forest.yml +0 -1741
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#Input files
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input:
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training:
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testing:
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forest:
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training: training.data
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testing: testing.data
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forest: random_forest.yml
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#Forest parameters
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forest:
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forest_size: 3 #how many trees
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SNP_sample_size_mtry: 60 #mtry
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SNP_total_count: 200
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node_min_size: 5
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node_min_size: 5
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- two
|
|
1897
|
+
- -0.8813
|
|
1898
|
+
- two
|
|
1899
|
+
- 148:
|
|
1900
|
+
- 122:
|
|
1901
|
+
- 99:
|
|
1902
|
+
- 100:
|
|
1903
|
+
- 13:
|
|
1904
|
+
- 15:
|
|
1905
|
+
- -0.15595
|
|
1906
|
+
- two
|
|
1907
|
+
- 3:
|
|
1908
|
+
- 0.0693
|
|
1909
|
+
- two
|
|
1910
|
+
- 0.0041
|
|
1911
|
+
- two
|
|
1912
|
+
- 0.436
|
|
1913
|
+
- two
|
|
1914
|
+
- 163:
|
|
1915
|
+
- -0.7244
|
|
1916
|
+
- two
|
|
1917
|
+
- -0.42378
|
|
1918
|
+
- two
|
|
1919
|
+
- 1.13595
|
|
1920
|
+
- zero
|
|
1921
|
+
- 154:
|
|
1922
|
+
- -2.1213
|
|
1923
|
+
- two
|
|
1924
|
+
- 45:
|
|
1925
|
+
- -0.98177
|
|
1926
|
+
- zero
|
|
1927
|
+
- -0.1997
|
|
1928
|
+
- zero
|
|
1929
|
+
- 30:
|
|
1930
|
+
- 6:
|
|
1931
|
+
- 107:
|
|
1932
|
+
- -1.06677
|
|
1933
|
+
- two
|
|
1934
|
+
- 2:
|
|
1935
|
+
- -1.2307
|
|
1936
|
+
- two
|
|
1937
|
+
- -1.1728
|
|
1938
|
+
- zero
|
|
1939
|
+
- -0.7271
|
|
1940
|
+
- two
|
|
1941
|
+
- -1.4882
|
|
1942
|
+
- two
|
|
1943
|
+
- 28:
|
|
1944
|
+
- 125:
|
|
1945
|
+
- 13:
|
|
1946
|
+
- -0.2253
|
|
1947
|
+
- two
|
|
1948
|
+
- -1.6078
|
|
1949
|
+
- two
|
|
1950
|
+
- 30:
|
|
1951
|
+
- 0.74175
|
|
1952
|
+
- two
|
|
1953
|
+
- 12:
|
|
1954
|
+
- -0.289
|
|
1955
|
+
- two
|
|
1956
|
+
- 14:
|
|
1957
|
+
- 0.2494
|
|
1958
|
+
- zero
|
|
1959
|
+
- 0.2014
|
|
1960
|
+
- zero
|
|
1961
|
+
- -1.2424
|
|
1962
|
+
- zero
|
|
1963
|
+
- 110:
|
|
1964
|
+
- 193:
|
|
1965
|
+
- 107:
|
|
1966
|
+
- 176:
|
|
1967
|
+
- 68:
|
|
1968
|
+
- 0.7696
|
|
1969
|
+
- zero
|
|
1970
|
+
- 60:
|
|
1971
|
+
- 29:
|
|
1972
|
+
- 0.1378
|
|
1973
|
+
- zero
|
|
1974
|
+
- -0.0272
|
|
1975
|
+
- two
|
|
1976
|
+
- -0.25215
|
|
1977
|
+
- two
|
|
1978
|
+
- -0.84207
|
|
1979
|
+
- two
|
|
1980
|
+
- 133:
|
|
1981
|
+
- 6:
|
|
1982
|
+
- 12:
|
|
1983
|
+
- 0.541
|
|
1984
|
+
- two
|
|
1985
|
+
- 0.6594
|
|
1986
|
+
- two
|
|
1987
|
+
- 1.30743
|
|
1988
|
+
- zero
|
|
1989
|
+
- -0.13735
|
|
1990
|
+
- zero
|
|
1991
|
+
- 120:
|
|
1992
|
+
- 141:
|
|
1993
|
+
- 179:
|
|
1994
|
+
- 25:
|
|
1995
|
+
- -0.59535
|
|
1996
|
+
- two
|
|
1997
|
+
- -0.1483
|
|
1998
|
+
- zero
|
|
1999
|
+
- -1.20805
|
|
2000
|
+
- zero
|
|
2001
|
+
- -1.868
|
|
2002
|
+
- two
|
|
2003
|
+
- 94:
|
|
2004
|
+
- 63:
|
|
2005
|
+
- -1.20543
|
|
2006
|
+
- zero
|
|
2007
|
+
- 16:
|
|
2008
|
+
- 42:
|
|
2009
|
+
- 3:
|
|
2010
|
+
- -0.2611
|
|
2011
|
+
- two
|
|
2012
|
+
- -0.3755
|
|
2013
|
+
- zero
|
|
2014
|
+
- -0.0753
|
|
2015
|
+
- two
|
|
2016
|
+
- 1.0944
|
|
2017
|
+
- zero
|
|
2018
|
+
- 20:
|
|
2019
|
+
- 0.6182
|
|
2020
|
+
- two
|
|
2021
|
+
- 3:
|
|
2022
|
+
- 0.187
|
|
2023
|
+
- two
|
|
2024
|
+
- 0.1633
|
|
2025
|
+
- two
|
|
2026
|
+
- 19:
|
|
2027
|
+
- 22:
|
|
2028
|
+
- 16:
|
|
2029
|
+
- 58:
|
|
2030
|
+
- 0.4023
|
|
2031
|
+
- zero
|
|
2032
|
+
- 86:
|
|
2033
|
+
- 0.1456
|
|
2034
|
+
- zero
|
|
2035
|
+
- 158:
|
|
2036
|
+
- -1.13285
|
|
2037
|
+
- two
|
|
2038
|
+
- -0.54573
|
|
2039
|
+
- two
|
|
2040
|
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- 46:
|
|
2041
|
+
- 0.7033
|
|
2042
|
+
- two
|
|
2043
|
+
- 0.55235
|
|
2044
|
+
- two
|
|
2045
|
+
- 197:
|
|
2046
|
+
- 158:
|
|
2047
|
+
- 24:
|
|
2048
|
+
- 3:
|
|
2049
|
+
- 1.3888
|
|
2050
|
+
- two
|
|
2051
|
+
- 1.56813
|
|
2052
|
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- zero
|
|
2053
|
+
- 0.9291
|
|
2054
|
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- two
|
|
2055
|
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- 17:
|
|
2056
|
+
- 29:
|
|
2057
|
+
- 1.3846
|
|
2058
|
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- zero
|
|
2059
|
+
- 1.07973
|
|
2060
|
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- zero
|
|
2061
|
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- 88:
|
|
2062
|
+
- 0.67103
|
|
2063
|
+
- zero
|
|
2064
|
+
- -0.041
|
|
2065
|
+
- two
|
|
2066
|
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- 139:
|
|
2067
|
+
- 77:
|
|
2068
|
+
- 1.543
|
|
2069
|
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- two
|
|
2070
|
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- 20:
|
|
2071
|
+
- -0.109
|
|
2072
|
+
- two
|
|
2073
|
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- 6:
|
|
2074
|
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- 0.7526
|
|
2075
|
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- zero
|
|
2076
|
+
- 0.7268
|
|
2077
|
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- zero
|
|
2078
|
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- 197:
|
|
2079
|
+
- 155:
|
|
2080
|
+
- 165:
|
|
2081
|
+
- 5:
|
|
2082
|
+
- 0.4736
|
|
2083
|
+
- two
|
|
2084
|
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- 0.4535
|
|
2085
|
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- zero
|
|
2086
|
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- 16:
|
|
2087
|
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- 1:
|
|
2088
|
+
- 0.1159
|
|
2089
|
+
- two
|
|
2090
|
+
- 0.123
|
|
2091
|
+
- two
|
|
2092
|
+
- -0.0497
|
|
2093
|
+
- two
|
|
2094
|
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- -0.31825
|
|
2095
|
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- zero
|
|
2096
|
+
- -1.595
|
|
2097
|
+
- two
|
|
2098
|
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- 72:
|
|
2099
|
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- 50:
|
|
2100
|
+
- -0.65195
|
|
2101
|
+
- two
|
|
2102
|
+
- -1.0076
|
|
2103
|
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- two
|
|
2104
|
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- 0.6762
|
|
2105
|
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- zero
|
|
2106
|
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- 55:
|
|
2107
|
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- 130:
|
|
2108
|
+
- 38:
|
|
2109
|
+
- 1:
|
|
2110
|
+
- 0.10073
|
|
2111
|
+
- two
|
|
2112
|
+
- 22:
|
|
2113
|
+
- -0.2959
|
|
2114
|
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- two
|
|
2115
|
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- -0.57205
|
|
2116
|
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- two
|
|
2117
|
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- 12:
|
|
2118
|
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- 5:
|
|
2119
|
+
- -0.85003
|
|
2120
|
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- two
|
|
2121
|
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- -0.9571
|
|
2122
|
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- two
|
|
2123
|
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- -0.6209
|
|
2124
|
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- zero
|
|
2125
|
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- 85:
|
|
2126
|
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- 15:
|
|
2127
|
+
- 0.7004
|
|
2128
|
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- two
|
|
2129
|
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- 2:
|
|
2130
|
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- 0.4458
|
|
2131
|
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- zero
|
|
2132
|
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- 0.2446
|
|
2133
|
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- two
|
|
2134
|
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- 3:
|
|
2135
|
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- -0.5292
|
|
2136
|
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- two
|
|
2137
|
+
- -0.13
|
|
2138
|
+
- two
|
|
2139
|
+
- 90:
|
|
2140
|
+
- 34:
|
|
2141
|
+
- 96:
|
|
2142
|
+
- 56:
|
|
2143
|
+
- 29:
|
|
2144
|
+
- 76:
|
|
2145
|
+
- 20:
|
|
2146
|
+
- 13:
|
|
2147
|
+
- -1.14883
|
|
2148
|
+
- two
|
|
2149
|
+
- -0.9854
|
|
2150
|
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- two
|
|
2151
|
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- -1.5471
|
|
2152
|
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- two
|
|
2153
|
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- -0.4978
|
|
2154
|
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- zero
|
|
2155
|
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- -1.8612
|
|
2156
|
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- zero
|
|
2157
|
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- 14:
|
|
2158
|
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- 0.16185
|
|
2159
|
+
- zero
|
|
2160
|
+
- -0.3719
|
|
2161
|
+
- two
|
|
2162
|
+
- 2.2543
|
|
2163
|
+
- two
|
|
2164
|
+
- 110:
|
|
2165
|
+
- 4:
|
|
2166
|
+
- -1.25715
|
|
2167
|
+
- zero
|
|
2168
|
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- 111:
|
|
2169
|
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- 1:
|
|
2170
|
+
- -2.1193
|
|
2171
|
+
- two
|
|
2172
|
+
- -2.3286
|
|
2173
|
+
- two
|
|
2174
|
+
- -1.78225
|
|
2175
|
+
- two
|
|
2176
|
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- 93:
|
|
2177
|
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- 51:
|
|
2178
|
+
- -1.7294
|
|
2179
|
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- zero
|
|
2180
|
+
- -1.31197
|
|
2181
|
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- two
|
|
2182
|
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- 20:
|
|
2183
|
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- -0.9702
|
|
2184
|
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- two
|
|
2185
|
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- -0.4259
|
|
2186
|
+
- zero
|
|
2187
|
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- 195:
|
|
2188
|
+
- 89:
|
|
2189
|
+
- 49:
|
|
2190
|
+
- 5:
|
|
2191
|
+
- -0.7449
|
|
2192
|
+
- two
|
|
2193
|
+
- -1.0922
|
|
2194
|
+
- two
|
|
2195
|
+
- -1.46498
|
|
2196
|
+
- two
|
|
2197
|
+
- 0.2135
|
|
2198
|
+
- zero
|
|
2199
|
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- 84:
|
|
2200
|
+
- 58:
|
|
2201
|
+
- -0.9042
|
|
2202
|
+
- zero
|
|
2203
|
+
- 7:
|
|
2204
|
+
- 0.6958
|
|
2205
|
+
- zero
|
|
2206
|
+
- 126:
|
|
2207
|
+
- 5:
|
|
2208
|
+
- 11:
|
|
2209
|
+
- 8:
|
|
2210
|
+
- -0.0616
|
|
2211
|
+
- zero
|
|
2212
|
+
- -0.0499
|
|
2213
|
+
- zero
|
|
2214
|
+
- -0.1084
|
|
2215
|
+
- zero
|
|
2216
|
+
- -0.2489
|
|
2217
|
+
- two
|
|
2218
|
+
- 0.2809
|
|
2219
|
+
- zero
|
|
2220
|
+
- 0.99907
|
|
2221
|
+
- zero
|
|
2222
|
+
- 111:
|
|
2223
|
+
- 177:
|
|
2224
|
+
- 37:
|
|
2225
|
+
- 112:
|
|
2226
|
+
- 0.90065
|
|
2227
|
+
- zero
|
|
2228
|
+
- 20:
|
|
2229
|
+
- 2:
|
|
2230
|
+
- -1.6357
|
|
2231
|
+
- two
|
|
2232
|
+
- -1.7456
|
|
2233
|
+
- two
|
|
2234
|
+
- 1:
|
|
2235
|
+
- -1.1642
|
|
2236
|
+
- two
|
|
2237
|
+
- -0.8326
|
|
2238
|
+
- zero
|
|
2239
|
+
- 182:
|
|
2240
|
+
- 2:
|
|
2241
|
+
- 24:
|
|
2242
|
+
- 8:
|
|
2243
|
+
- 0.2566
|
|
2244
|
+
- two
|
|
2245
|
+
- 0.8685
|
|
2246
|
+
- two
|
|
2247
|
+
- 14:
|
|
2248
|
+
- 1.3171
|
|
2249
|
+
- zero
|
|
2250
|
+
- 1.64803
|
|
2251
|
+
- zero
|
|
2252
|
+
- 0.00897
|
|
2253
|
+
- zero
|
|
2254
|
+
- 187:
|
|
2255
|
+
- 34:
|
|
2256
|
+
- 1:
|
|
2257
|
+
- -0.96818
|
|
2258
|
+
- two
|
|
2259
|
+
- -0.9391
|
|
2260
|
+
- two
|
|
2261
|
+
- -1.3004
|
|
2262
|
+
- zero
|
|
2263
|
+
- 121:
|
|
2264
|
+
- 73:
|
|
2265
|
+
- -0.46507
|
|
2266
|
+
- zero
|
|
2267
|
+
- 12:
|
|
2268
|
+
- 0.21928
|
|
2269
|
+
- two
|
|
2270
|
+
- -0.0348
|
|
2271
|
+
- two
|
|
2272
|
+
- 28:
|
|
2273
|
+
- 0.7291
|
|
2274
|
+
- two
|
|
2275
|
+
- 21:
|
|
2276
|
+
- 0.3669
|
|
2277
|
+
- zero
|
|
2278
|
+
- 0.4967
|
|
2279
|
+
- two
|
|
2280
|
+
- 132:
|
|
2281
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|
2663
|
+
- 112:
|
|
2664
|
+
- 17:
|
|
2665
|
+
- -0.5577
|
|
2666
|
+
- zero
|
|
2667
|
+
- -0.33755
|
|
2668
|
+
- zero
|
|
2669
|
+
- -0.1509
|
|
2670
|
+
- two
|
|
2671
|
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- 6:
|
|
2672
|
+
- -0.42835
|
|
2673
|
+
- zero
|
|
2674
|
+
- -1.1814
|
|
2675
|
+
- zero
|
|
2676
|
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- 1:
|
|
2677
|
+
- 16:
|
|
2678
|
+
- 0.6825
|
|
2679
|
+
- two
|
|
2680
|
+
- 0.3287
|
|
2681
|
+
- two
|
|
2682
|
+
- 1.7749
|
|
2683
|
+
- two
|
|
2684
|
+
- 37:
|
|
2685
|
+
- 1.1693
|
|
2686
|
+
- zero
|
|
2687
|
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- 83:
|
|
2688
|
+
- 15:
|
|
2689
|
+
- -0.423
|
|
2690
|
+
- two
|
|
2691
|
+
- -1.0997
|
|
2692
|
+
- two
|
|
2693
|
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- 180:
|
|
2694
|
+
- -0.15085
|
|
2695
|
+
- two
|
|
2696
|
+
- -0.4069
|
|
2697
|
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- zero
|
|
2698
|
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- 197:
|
|
2699
|
+
- 67:
|
|
2700
|
+
- 125:
|
|
2701
|
+
- 30:
|
|
2702
|
+
- 2.1744
|
|
2703
|
+
- two
|
|
2704
|
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- 1.39935
|
|
2705
|
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- zero
|
|
2706
|
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- 10:
|
|
2707
|
+
- 2.30633
|
|
2708
|
+
- two
|
|
2709
|
+
- 3.5375
|
|
2710
|
+
- zero
|
|
2711
|
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- 22:
|
|
2712
|
+
- 0.1782
|
|
2713
|
+
- two
|
|
2714
|
+
- 15:
|
|
2715
|
+
- 1.0276
|
|
2716
|
+
- zero
|
|
2717
|
+
- 1.2606
|
|
2718
|
+
- two
|
|
2719
|
+
- 17:
|
|
2720
|
+
- 1.3228
|
|
2721
|
+
- zero
|
|
2722
|
+
- 149:
|
|
2723
|
+
- 54:
|
|
2724
|
+
- 93:
|
|
2725
|
+
- 0.453
|
|
2726
|
+
- two
|
|
2727
|
+
- 6:
|
|
2728
|
+
- 0.34043
|
|
2729
|
+
- zero
|
|
2730
|
+
- 0.3473
|
|
2731
|
+
- two
|
|
2732
|
+
- 0.6184
|
|
2733
|
+
- two
|
|
2734
|
+
- 4:
|
|
2735
|
+
- 1.0034
|
|
2736
|
+
- zero
|
|
2737
|
+
- 0.63835
|