sciml 0.0.9__py3-none-any.whl → 0.0.10__py3-none-any.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.
- sciml/__init__.py +2 -2
- sciml/ccc.py +36 -0
- sciml/metrics.py +123 -0
- sciml/models.py +275 -276
- sciml/pipelines.py +226 -435
- sciml/regress2.py +217 -0
- {sciml-0.0.9.dist-info → sciml-0.0.10.dist-info}/LICENSE +21 -21
- {sciml-0.0.9.dist-info → sciml-0.0.10.dist-info}/METADATA +13 -13
- sciml-0.0.10.dist-info/RECORD +11 -0
- {sciml-0.0.9.dist-info → sciml-0.0.10.dist-info}/WHEEL +1 -1
- sciml/utils.py +0 -46
- sciml-0.0.9.dist-info/RECORD +0 -9
- {sciml-0.0.9.dist-info → sciml-0.0.10.dist-info}/top_level.txt +0 -0
sciml/regress2.py
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# Model type I and II regression, including RMA (reduced major axis regression)
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"""
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Credit: UMaine MISC Lab; emmanuel.boss@maine.edu
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http://misclab.umeoce.maine.edu/
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https://github.com/OceanOptics
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------------------------------------------------------------------------------
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MIT License
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Copyright (c) [year] [fullname]
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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"""
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import statsmodels.api as sm
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import numpy as np
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def regress2(_x, _y, _method_type_1 = "ordinary least square",
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_method_type_2 = "reduced major axis",
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_weight_x = [], _weight_y = [], _need_intercept = True):
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# Regression Type II based on statsmodels
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# Type II regressions are recommended if there is variability on both x and y
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# It's computing the linear regression type I for (x,y) and (y,x)
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# and then average relationship with one of the type II methods
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#
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# INPUT:
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# _x <np.array>
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# _y <np.array>
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# _method_type_1 <str> method to use for regression type I:
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# ordinary least square or OLS <default>
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# weighted least square or WLS
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# robust linear model or RLM
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# _method_type_2 <str> method to use for regression type II:
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# major axis
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# reduced major axis <default> (also known as geometric mean)
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# arithmetic mean
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# _need_intercept <bool>
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# True <default> add a constant to relation (y = a x + b)
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# False force relation by 0 (y = a x)
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# _weight_x <np.array> containing the weigth of x
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# _weigth_y <np.array> containing the weigth of y
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#
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# OUTPUT:
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# slope
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# intercept
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# r
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# std_slope
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# std_intercept
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# predict
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#
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# REQUIRE:
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# numpy
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# statsmodels
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#
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# The code is based on the matlab function of MBARI.
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# AUTHOR: Nils Haentjens
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# REFERENCE: https://www.mbari.org/products/research-software/matlab-scripts-linear-regressions/
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# Check input
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if _method_type_2 != "reduced major axis" and _method_type_1 != "ordinary least square":
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raise ValueError("'" + _method_type_2 + "' only supports '" + _method_type_1 + "' method as type 1.")
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# Set x, y depending on intercept requirement
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if _need_intercept:
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x_intercept = sm.add_constant(_x)
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y_intercept = sm.add_constant(_y)
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# Compute Regression Type I (if type II requires it)
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if (_method_type_2 == "reduced major axis" or
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_method_type_2 == "geometric mean"):
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if _method_type_1 == "OLS" or _method_type_1 == "ordinary least square":
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if _need_intercept:
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[intercept_a, slope_a] = sm.OLS(_y, x_intercept).fit().params
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[intercept_b, slope_b] = sm.OLS(_x, y_intercept).fit().params
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else:
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slope_a = sm.OLS(_y, _x).fit().params
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slope_b = sm.OLS(_x, _y).fit().params
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elif _method_type_1 == "WLS" or _method_type_1 == "weighted least square":
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if _need_intercept:
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[intercept_a, slope_a] = sm.WLS(
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_y, x_intercept, weights=1. / _weight_y).fit().params
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[intercept_b, slope_b] = sm.WLS(
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_x, y_intercept, weights=1. / _weight_x).fit().params
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else:
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slope_a = sm.WLS(_y, _x, weights=1. / _weight_y).fit().params
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slope_b = sm.WLS(_x, _y, weights=1. / _weight_x).fit().params
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elif _method_type_1 == "RLM" or _method_type_1 == "robust linear model":
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if _need_intercept:
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[intercept_a, slope_a] = sm.RLM(_y, x_intercept).fit().params
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[intercept_b, slope_b] = sm.RLM(_x, y_intercept).fit().params
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else:
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slope_a = sm.RLM(_y, _x).fit().params
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slope_b = sm.RLM(_x, _y).fit().params
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else:
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raise ValueError("Invalid literal for _method_type_1: " + _method_type_1)
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# Compute Regression Type II
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if (_method_type_2 == "reduced major axis" or
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_method_type_2 == "geometric mean"):
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# Transpose coefficients
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if _need_intercept:
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intercept_b = -intercept_b / slope_b
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slope_b = 1 / slope_b
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# Check if correlated in same direction
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if np.sign(slope_a) != np.sign(slope_b):
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raise RuntimeError('Type I regressions of opposite sign.')
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# Compute Reduced Major Axis Slope
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slope = np.sign(slope_a) * np.sqrt(slope_a * slope_b)
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if _need_intercept:
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# Compute Intercept (use mean for least square)
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if _method_type_1 == "OLS" or _method_type_1 == "ordinary least square":
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intercept = np.mean(_y) - slope * np.mean(_x)
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else:
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intercept = np.median(_y) - slope * np.median(_x)
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else:
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intercept = 0
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# Compute r
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r = np.sign(slope_a) * np.sqrt(slope_a / slope_b)
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# Compute predicted values
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predict = slope * _x + intercept
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# Compute standard deviation of the slope and the intercept
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n = len(_x)
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diff = _y - predict
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Sx2 = np.sum(np.multiply(_x, _x))
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den = n * Sx2 - np.sum(_x) ** 2
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s2 = np.sum(np.multiply(diff, diff)) / (n - 2)
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std_slope = np.sqrt(n * s2 / den)
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if _need_intercept:
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std_intercept = np.sqrt(Sx2 * s2 / den)
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else:
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std_intercept = 0
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elif (_method_type_2 == "Pearson's major axis" or
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_method_type_2 == "major axis"):
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if not _need_intercept:
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raise ValueError("Invalid value for _need_intercept: " + str(_need_intercept))
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xm = np.mean(_x)
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ym = np.mean(_y)
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xp = _x - xm
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yp = _y - ym
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sumx2 = np.sum(np.multiply(xp, xp))
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sumy2 = np.sum(np.multiply(yp, yp))
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sumxy = np.sum(np.multiply(xp, yp))
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slope = ((sumy2 - sumx2 + np.sqrt((sumy2 - sumx2)**2 + 4 * sumxy**2)) /
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(2 * sumxy))
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intercept = ym - slope * xm
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# Compute r
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r = sumxy / np.sqrt(sumx2 * sumy2)
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# Compute standard deviation of the slope and the intercept
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n = len(_x)
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std_slope = (slope / r) * np.sqrt((1 - r ** 2) / n)
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sigx = np.sqrt(sumx2 / (n - 1))
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sigy = np.sqrt(sumy2 / (n - 1))
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std_i1 = (sigy - sigx * slope) ** 2
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std_i2 = (2 * sigx * sigy) + ((xm ** 2 * slope * (1 + r)) / r ** 2)
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std_intercept = np.sqrt((std_i1 + ((1 - r) * slope * std_i2)) / n)
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# Compute predicted values
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predict = slope * _x + intercept
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elif _method_type_2 == "arithmetic mean":
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if not _need_intercept:
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raise ValueError("Invalid value for _need_intercept: " + str(_need_intercept))
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n = len(_x)
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sg = np.floor(n / 2)
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# Sort x and y in order of x
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sorted_index = sorted(range(len(_x)), key=lambda i: _x[i])
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x_w = np.array([_x[i] for i in sorted_index])
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y_w = np.array([_y[i] for i in sorted_index])
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x1 = x_w[1:sg + 1]
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x2 = x_w[sg:n]
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y1 = y_w[1:sg + 1]
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y2 = y_w[sg:n]
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x1m = np.mean(x1)
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x2m = np.mean(x2)
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y1m = np.mean(y1)
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y2m = np.mean(y2)
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xm = (x1m + x2m) / 2
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ym = (y1m + y2m) / 2
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slope = (x2m - x1m) / (y2m - y1m)
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intercept = ym - xm * slope
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# r (to verify)
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r = []
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# Compute predicted values
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predict = slope * _x + intercept
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# Compute standard deviation of the slope and the intercept
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std_slope = []
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std_intercept = []
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# Return all that
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return {"slope": float(slope), "intercept": intercept, "r": r,
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"std_slope": std_slope, "std_intercept": std_intercept,
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"predict": predict}
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# if __name__ == '__main__':
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# x = np.linspace(0, 10, 100)
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# # Add random error on y
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# e = np.random.normal(size=len(x))
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# y = x + e
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# results = regress2(x, y, _method_type_2="reduced major axis",
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# _need_intercept=False)
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# # print(results)
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MIT License
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Copyright (c) 2021 Zhu
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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MIT License
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Copyright (c) 2021 Zhu
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Metadata-Version: 2.1
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Name: sciml
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Version: 0.0.
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Summary: draw and basic calculations/conversions
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Home-page: https://github.com/soonyenju/sciml
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Author: Songyan Zhu
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Author-email: zhusy93@gmail.com
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License: MIT Licence
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Keywords: Scientific machine learning wrappers
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Platform: any
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License-File: LICENSE
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coming soon
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Metadata-Version: 2.1
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Name: sciml
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Version: 0.0.10
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Summary: draw and basic calculations/conversions
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Home-page: https://github.com/soonyenju/sciml
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Author: Songyan Zhu
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Author-email: zhusy93@gmail.com
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License: MIT Licence
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Keywords: Scientific machine learning wrappers
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Platform: any
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License-File: LICENSE
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coming soon
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sciml/__init__.py,sha256=BqRVu5DbfbnxksBXhe4gH_uulPdqTjSaSO1LvGkc37Q,79
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sciml/ccc.py,sha256=AE1l46hvh18_Q9_BQufMjsGF9-JfsTw2hrT1CbgBHE8,1210
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sciml/metrics.py,sha256=ICEeH6jwmpdx9jxwYSzB_YTvbyBq9AEUYqkZiVS1ZGs,3577
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sciml/models.py,sha256=qc2LgdpSkq9kGMnLKZTnyuwzytCu6R8hyU5i6PaI7Qw,10345
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sciml/pipelines.py,sha256=NGBwl5vA0Uq5GO-VtIow_k42K7HoVwxPQrkW-jINflY,8381
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sciml/regress2.py,sha256=GSZ4IqmyF9u3PGOhHIKV0Rb_C2pI8eJ3jGJBa1IrEXM,8978
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sciml-0.0.10.dist-info/LICENSE,sha256=dX4jBmkgQPWc_TfYkXtKQzVIgZQWFuHZ8vQjV4sEeV4,1060
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sciml-0.0.10.dist-info/METADATA,sha256=iMcI6kpM6IX2oBhx9JwmI77JiX2bZPWI93dHta_jkCM,314
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sciml-0.0.10.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
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sciml-0.0.10.dist-info/top_level.txt,sha256=dS_7aBCZFKQE3myPy5sh4USjQZCZyGg382-YxUUYcdw,6
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sciml-0.0.10.dist-info/RECORD,,
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sciml/utils.py
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import numpy as np
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import pandas as pd
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from sklearn.model_selection import ShuffleSplit
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from sklearn.model_selection import train_test_split
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# randomly select sites
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def random_select(ds, count, num, random_state = 0):
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np.random.seed(random_state)
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idxs = np.random.choice(np.delete(np.arange(len(ds)), count), num, replace = False)
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return np.sort(idxs)
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def split(Xs, ys, return_index = False, test_size = 0.33, random_state = 42):
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if return_index:
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sss = ShuffleSplit(n_splits=1, test_size = test_size, random_state = random_state)
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sss.get_n_splits(Xs, ys)
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train_index, test_index = next(sss.split(Xs, ys))
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return (train_index, test_index)
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else:
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X_train, X_test, y_train, y_test = train_test_split(
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Xs, ys,
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test_size = test_size,
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random_state = random_state
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)
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return (X_train, X_test, y_train, y_test)
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def split_cut(Xs, ys, test_ratio = 0.33):
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assert ys.ndim == 2, 'ys must be 2D!'
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assert len(Xs) == len(ys), 'Xs and ys should be equally long!'
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assert type(Xs) == type(ys), 'Xs and ys should be the same data type!'
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if not type(Xs) in [pd.core.frame.DataFrame, np.ndarray]: raise Exception('Only accept numpy ndarray or pandas dataframe')
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anchor = int(np.floor(len(ys) * (1 - test_ratio)))
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if type(Xs) == pd.core.frame.DataFrame:
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X_train = Xs.iloc[0: anchor, :]
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X_test = Xs.iloc[anchor::, :]
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y_train = ys.iloc[0: anchor, :]
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y_test = ys.iloc[anchor::, :]
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else:
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X_train = Xs[0: anchor, :]
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X_test = Xs[anchor::, :]
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y_train = ys[0: anchor, :]
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y_test = ys[anchor::, :]
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assert len(X_train) + len(X_test) == len(Xs), 'The sum of train and test lengths must equal to Xs/ys!'
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return (X_train, X_test, y_train, y_test)
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sciml-0.0.9.dist-info/RECORD
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sciml/__init__.py,sha256=wtdlXERN2ik7NT_TQxFdd2gdodBY9vSU1ClSdeJnLm4,59
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sciml/models.py,sha256=BjbliW-KNfzbNdGNgM7nBdJ2SF2z21qCoAvug_v0FEg,10574
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sciml/pipelines.py,sha256=ReNEkQbdFn04D5G2tbxcA7jdSwACy8SnmZ8bFZI_oqE,15702
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sciml/utils.py,sha256=qCdABaTUu3K0R269jI7D_8SO6AqEjphg03CzdxCJR2k,1876
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sciml-0.0.9.dist-info/LICENSE,sha256=hcunSTJmVgRcUNOa1rKl8axtY3Jsy2B4wXDYtQsrAt0,1081
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sciml-0.0.9.dist-info/METADATA,sha256=S5hG3pP3x4yDPe8AJOKn4R-fIuvL-DL1GSKqGqiImSw,326
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sciml-0.0.9.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
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sciml-0.0.9.dist-info/top_level.txt,sha256=dS_7aBCZFKQE3myPy5sh4USjQZCZyGg382-YxUUYcdw,6
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sciml-0.0.9.dist-info/RECORD,,
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File without changes
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