pycodamath 1.1.1__tar.gz

pycodamath-1.1.1/LICENSE

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+Copyright (c) 2018 The Python Packaging Authority
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pycodamath-1.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: pycodamath
+Version: 1.1.1
+Summary: Compositional data (CoDa) analysis tools for Python
+Author-email: Christian Brinch <cbri@food.dtu.dk>
+License: MIT
+Project-URL: Homepage, https://bitbucket.org/genomicepidemiology/pycodamath
+Project-URL: Bug Tracker, https://bitbucket.org/genomicepidemiology/pycodamath/issues
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: adjustText>=0.7.3
+Requires-Dist: matplotlib>=3.1.1
+Requires-Dist: numpy>=1.17.2
+Requires-Dist: pandas>=0.25.1
+Requires-Dist: python-ternary>=1.0.6
+Requires-Dist: scipy>=1.3.1
+Requires-Dist: webcolors>=1.13
+Dynamic: license-file
+
+#  pyCoDaMath
+
+[![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/)
+
+
+pyCoDaMath provides compositional data (CoDa) analysis tools for Python
+
+- **Source code:** https://bitbucket.org/genomicepidemiology/pycodamath
+
+## Getting Started
+
+This package extends the Pandas dataframe object with various CoDa tools. It also provides a set of plotting functions for CoDa figures.
+
+### Installation
+
+Clone the git repo to your local hard drive:
+
+    git clone https://bitbucket.org/genomicepidemiology/pycodamath.git
+
+Enter the directory and install:
+
+    pip install .
+
+### Usage
+
+The pyCoDaMath module is loaded as
+
+    import pycodamath
+
+At this point, in order to get CLR values from a Pandas DataFrame `df`, do
+
+    df.coda.clr()
+
+
+## Documentation
+
+### CLR transformation - point estimate
+    df.coda.clr()
+
+Returns centered logratio coefficients. If the dataframe contains zeros, values
+will be replaced by the Aitchison mean point estimate.
+
+### CLR transformation - standard deviation
+    df.coda.clr_std(n_samples=5000)
+
+Returns the standard deviation of `n_samples` random draws in CLR space.
+
+**Parameters**
+
+- n_samples (int) - Number of random draws from a Dirichlet distribution.
+
+
+### ALR transformation - point estimate
+    df.coda.alr(part=None)
+
+Returns additive logratio values. If `part` is None, the last part of the composition is used as the denominator.
+
+**Parameters**
+
+- part (str) - Name of the part to use as denominator.
+
+
+### ALR transformation - standard deviation
+    df.coda.alr_std(part=None, n_samples=5000)
+
+Returns the standard deviation of `n_samples` random draws in ALR space.
+
+**Parameters**
+
+- part (str) - Name of the part to use as denominator.
+- n_samples (int) - Number of random draws from a Dirichlet distribution.
+
+
+### ILR transformation - point estimate
+    df.coda.ilr(psi=None)
+
+Returns isometric logratio values. If no basis is given, a default sequential binary partition basis is used.
+
+**Parameters**
+
+- psi (array_like) - Orthonormal basis. If None, the default SBP basis is used.
+
+
+### ILR inverse transformation
+    df.coda.ilr_inv(psi=None)
+
+Returns the composition corresponding to a set of ILR coordinates. The same basis used for the forward transform must be supplied.
+
+**Parameters**
+
+- psi (array_like) - Orthonormal basis. If None, the default SBP basis is used.
+
+
+### Aitchison point estimate
+    df.coda.aitchison_mean(alpha=1.0)
+
+Returns the Bayesian point estimate based on the Dirichlet concentration parameter alpha.
+Use values between 0.5 (sparse prior) and 1.0 (flat prior).
+
+**Parameters**
+
+- alpha (float) - Dirichlet concentration parameter. Defaults to 1.0.
+
+
+### Bayesian zero replacement
+    df.coda.zero_replacement(n_samples=5000)
+
+Returns a count table with zero values replaced by finite values using Bayesian inference.
+
+**Parameters**
+
+- n_samples (int) - Number of random draws from a Dirichlet distribution.
+
+
+### Closure
+    df.coda.closure(N)
+
+Applies closure to constant N to the composition.
+
+**Parameters**
+
+- N (float) - Closure constant.
+
+
+### Variance matrix
+    df.coda.varmatrix(nmp=False)
+
+Returns the total variation matrix of a composition. For large datasets, variance is
+estimated from at most 500 rows.
+
+**Parameters**
+
+- nmp (bool) - If True, return a numpy array instead of a DataFrame. Defaults to False.
+
+
+### Total variance
+    df.coda.totvar()
+
+Returns the total variance of a set of compositions, computed as the sum of the
+variance matrix divided by twice the number of parts.
+
+
+### Geometric mean
+    df.coda.gmean()
+
+Returns the geometric mean of a set of compositions as percentages.
+
+
+### Power transformation
+    df.coda.power(alpha)
+
+Applies compositional scalar multiplication (power transformation).
+
+**Parameters**
+
+- alpha (float) - Scalar multiplier.
+
+
+### Perturbation
+    df.coda.perturbation(comp)
+
+Applies a compositional perturbation (Aitchison addition) with another composition.
+
+**Parameters**
+
+- comp (array_like) - Composition to perturb with.
+
+
+### Scaling
+    df.coda.scale()
+
+Scales the composition by the reciprocal of the square root of the total variance.
+
+
+### Centering
+    df.coda.center()
+
+Centers the composition by perturbing with the reciprocal of the geometric mean.
+
+
+---
+
+## Plotting functions
+
+### Ternary diagram
+    pycodamath.plot.ternary(data, descr=None, center=False, conf=False)
+
+Plots a ternary diagram from a three-part composition closed to 100.
+
+**Parameters**
+
+- data (DataFrame) - Three-part compositional data, closed to 100.
+- descr (Series) - Optional grouping variable; if provided, points are coloured by group.
+- center (bool) - If True, the composition is centred before plotting. Defaults to False.
+- conf (bool) - If True, a 95% confidence ellipse is overlaid. Defaults to False.
+
+
+### Scree plot
+    pycodamath.pca.scree_plot(axis, eig_val)
+
+Plots a scree plot of explained variance from singular values.
+
+**Parameters**
+
+- axis - A Matplotlib axes object.
+- eig_val (array_like) - Singular values from SVD.
+
+
+### PCA biplot
+    class pycodamath.pca.Biplot(data, axis=None, default=True)
+
+Creates a PCA biplot based on a centered log-ratio transformation of the data.
+
+**Parameters**
+
+- data (DataFrame) - Compositional count data to analyse.
+- axis - A Matplotlib axes object. If None, a new figure is created.
+- default (bool) - If True, loadings and scores are plotted immediately. Defaults to True.
+
+The following methods are available for customising the biplot:
+
+- `plotloadings(cutoff=0, scale=None, labels=None, cluster=False)` — plot loading arrows.
+  Set `cutoff` (as a fraction of the maximum loading length) to suppress short loadings.
+  Set `cluster=True` to reduce the number of loadings by hierarchical clustering; the
+  resulting cluster legend is accessible as `biplot.clusterlegend`.
+- `plotloadinglabels(labels=None, loadings=None, cutoff=0)` — add text labels to loadings.
+- `adjustloadinglabels()` — shift loading labels to reduce overlap.
+- `plotscores(group=None, palette=None, legend=True, labels=None)` — plot sample scores
+  as points, optionally coloured by group.
+- `plotscorelabels(labels=None)` — add text labels to the scores.
+- `plotellipses(group, palette=None, legend=False)` — plot 90% confidence ellipses for
+  each group (requires at least 3 samples per group).
+- `plotcentroids(group, palette=None, legend=False)` — plot the centroid of each group.
+- `plothulls(group, palette=None, legend=True)` — plot convex hulls around each group
+  (requires at least 3 samples per group).
+- `plotcontours(group, palette=None, legend=True, plot_outliers=True, percent_outliers=0.1, linewidth=2.2)` — plot kernel density contours for each group. Samples outside the outermost contour are optionally shown as individual points.
+- `labeloutliers(group, conf=3.0)` — label samples more than `conf` standard deviations
+  from their group centroid.
+- `displaylegend(loc=2)` — display the group legend at Matplotlib legend location `loc`.
+- `removepatches()` — remove loading arrows and hull polygons from the plot.
+- `removescores()` — remove score points from the plot.
+- `removelabels()` — remove text labels from the plot.
+- `removecontours()` — remove contour fills from the plot.
+
+The keyword `labels` is a list of label names. If `labels` is None, all labels are plotted.
+
+The keyword `group` is a Pandas Series with an index matching the data index.
+
+The keyword `palette` is a dict mapping each unique group value to a colour.
+
+**Example**
+
+    import pycodamath as coda
+    import pandas as pd
+    data = pd.read_csv('example/kilauea_iki_chem.csv')
+    mypca = coda.pca.Biplot(data)
+    mypca.removelabels()
+    mypca.plotloadings(cluster=True)
+    print(mypca.clusterlegend)
+    mypca.removelabels()
+    mypca.plotloadings(labels=['FeO', 'Al2O3', 'CaO'], cluster=False)
+    mypca.adjustloadinglabels()

pycodamath-1.1.1/README.md

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+#  pyCoDaMath
+
+[![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/)
+
+
+pyCoDaMath provides compositional data (CoDa) analysis tools for Python
+
+- **Source code:** https://bitbucket.org/genomicepidemiology/pycodamath
+
+## Getting Started
+
+This package extends the Pandas dataframe object with various CoDa tools. It also provides a set of plotting functions for CoDa figures.
+
+### Installation
+
+Clone the git repo to your local hard drive:
+
+    git clone https://bitbucket.org/genomicepidemiology/pycodamath.git
+
+Enter the directory and install:
+
+    pip install .
+
+### Usage
+
+The pyCoDaMath module is loaded as
+
+    import pycodamath
+
+At this point, in order to get CLR values from a Pandas DataFrame `df`, do
+
+    df.coda.clr()
+
+
+## Documentation
+
+### CLR transformation - point estimate
+    df.coda.clr()
+
+Returns centered logratio coefficients. If the dataframe contains zeros, values
+will be replaced by the Aitchison mean point estimate.
+
+### CLR transformation - standard deviation
+    df.coda.clr_std(n_samples=5000)
+
+Returns the standard deviation of `n_samples` random draws in CLR space.
+
+**Parameters**
+
+- n_samples (int) - Number of random draws from a Dirichlet distribution.
+
+
+### ALR transformation - point estimate
+    df.coda.alr(part=None)
+
+Returns additive logratio values. If `part` is None, the last part of the composition is used as the denominator.
+
+**Parameters**
+
+- part (str) - Name of the part to use as denominator.
+
+
+### ALR transformation - standard deviation
+    df.coda.alr_std(part=None, n_samples=5000)
+
+Returns the standard deviation of `n_samples` random draws in ALR space.
+
+**Parameters**
+
+- part (str) - Name of the part to use as denominator.
+- n_samples (int) - Number of random draws from a Dirichlet distribution.
+
+
+### ILR transformation - point estimate
+    df.coda.ilr(psi=None)
+
+Returns isometric logratio values. If no basis is given, a default sequential binary partition basis is used.
+
+**Parameters**
+
+- psi (array_like) - Orthonormal basis. If None, the default SBP basis is used.
+
+
+### ILR inverse transformation
+    df.coda.ilr_inv(psi=None)
+
+Returns the composition corresponding to a set of ILR coordinates. The same basis used for the forward transform must be supplied.
+
+**Parameters**
+
+- psi (array_like) - Orthonormal basis. If None, the default SBP basis is used.
+
+
+### Aitchison point estimate
+    df.coda.aitchison_mean(alpha=1.0)
+
+Returns the Bayesian point estimate based on the Dirichlet concentration parameter alpha.
+Use values between 0.5 (sparse prior) and 1.0 (flat prior).
+
+**Parameters**
+
+- alpha (float) - Dirichlet concentration parameter. Defaults to 1.0.
+
+
+### Bayesian zero replacement
+    df.coda.zero_replacement(n_samples=5000)
+
+Returns a count table with zero values replaced by finite values using Bayesian inference.
+
+**Parameters**
+
+- n_samples (int) - Number of random draws from a Dirichlet distribution.
+
+
+### Closure
+    df.coda.closure(N)
+
+Applies closure to constant N to the composition.
+
+**Parameters**
+
+- N (float) - Closure constant.
+
+
+### Variance matrix
+    df.coda.varmatrix(nmp=False)
+
+Returns the total variation matrix of a composition. For large datasets, variance is
+estimated from at most 500 rows.
+
+**Parameters**
+
+- nmp (bool) - If True, return a numpy array instead of a DataFrame. Defaults to False.
+
+
+### Total variance
+    df.coda.totvar()
+
+Returns the total variance of a set of compositions, computed as the sum of the
+variance matrix divided by twice the number of parts.
+
+
+### Geometric mean
+    df.coda.gmean()
+
+Returns the geometric mean of a set of compositions as percentages.
+
+
+### Power transformation
+    df.coda.power(alpha)
+
+Applies compositional scalar multiplication (power transformation).
+
+**Parameters**
+
+- alpha (float) - Scalar multiplier.
+
+
+### Perturbation
+    df.coda.perturbation(comp)
+
+Applies a compositional perturbation (Aitchison addition) with another composition.
+
+**Parameters**
+
+- comp (array_like) - Composition to perturb with.
+
+
+### Scaling
+    df.coda.scale()
+
+Scales the composition by the reciprocal of the square root of the total variance.
+
+
+### Centering
+    df.coda.center()
+
+Centers the composition by perturbing with the reciprocal of the geometric mean.
+
+
+---
+
+## Plotting functions
+
+### Ternary diagram
+    pycodamath.plot.ternary(data, descr=None, center=False, conf=False)
+
+Plots a ternary diagram from a three-part composition closed to 100.
+
+**Parameters**
+
+- data (DataFrame) - Three-part compositional data, closed to 100.
+- descr (Series) - Optional grouping variable; if provided, points are coloured by group.
+- center (bool) - If True, the composition is centred before plotting. Defaults to False.
+- conf (bool) - If True, a 95% confidence ellipse is overlaid. Defaults to False.
+
+
+### Scree plot
+    pycodamath.pca.scree_plot(axis, eig_val)
+
+Plots a scree plot of explained variance from singular values.
+
+**Parameters**
+
+- axis - A Matplotlib axes object.
+- eig_val (array_like) - Singular values from SVD.
+
+
+### PCA biplot
+    class pycodamath.pca.Biplot(data, axis=None, default=True)
+
+Creates a PCA biplot based on a centered log-ratio transformation of the data.
+
+**Parameters**
+
+- data (DataFrame) - Compositional count data to analyse.
+- axis - A Matplotlib axes object. If None, a new figure is created.
+- default (bool) - If True, loadings and scores are plotted immediately. Defaults to True.
+
+The following methods are available for customising the biplot:
+
+- `plotloadings(cutoff=0, scale=None, labels=None, cluster=False)` — plot loading arrows.
+  Set `cutoff` (as a fraction of the maximum loading length) to suppress short loadings.
+  Set `cluster=True` to reduce the number of loadings by hierarchical clustering; the
+  resulting cluster legend is accessible as `biplot.clusterlegend`.
+- `plotloadinglabels(labels=None, loadings=None, cutoff=0)` — add text labels to loadings.
+- `adjustloadinglabels()` — shift loading labels to reduce overlap.
+- `plotscores(group=None, palette=None, legend=True, labels=None)` — plot sample scores
+  as points, optionally coloured by group.
+- `plotscorelabels(labels=None)` — add text labels to the scores.
+- `plotellipses(group, palette=None, legend=False)` — plot 90% confidence ellipses for
+  each group (requires at least 3 samples per group).
+- `plotcentroids(group, palette=None, legend=False)` — plot the centroid of each group.
+- `plothulls(group, palette=None, legend=True)` — plot convex hulls around each group
+  (requires at least 3 samples per group).
+- `plotcontours(group, palette=None, legend=True, plot_outliers=True, percent_outliers=0.1, linewidth=2.2)` — plot kernel density contours for each group. Samples outside the outermost contour are optionally shown as individual points.
+- `labeloutliers(group, conf=3.0)` — label samples more than `conf` standard deviations
+  from their group centroid.
+- `displaylegend(loc=2)` — display the group legend at Matplotlib legend location `loc`.
+- `removepatches()` — remove loading arrows and hull polygons from the plot.
+- `removescores()` — remove score points from the plot.
+- `removelabels()` — remove text labels from the plot.
+- `removecontours()` — remove contour fills from the plot.
+
+The keyword `labels` is a list of label names. If `labels` is None, all labels are plotted.
+
+The keyword `group` is a Pandas Series with an index matching the data index.
+
+The keyword `palette` is a dict mapping each unique group value to a colour.
+
+**Example**
+
+    import pycodamath as coda
+    import pandas as pd
+    data = pd.read_csv('example/kilauea_iki_chem.csv')
+    mypca = coda.pca.Biplot(data)
+    mypca.removelabels()
+    mypca.plotloadings(cluster=True)
+    print(mypca.clusterlegend)
+    mypca.removelabels()
+    mypca.plotloadings(labels=['FeO', 'Al2O3', 'CaO'], cluster=False)
+    mypca.adjustloadinglabels()

pycodamath-1.1.1/pyproject.toml

@@ -0,0 +1,43 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pycodamath"
+version = "1.1.1"
+authors = [
+  { name="Christian Brinch", email="cbri@food.dtu.dk" },
+]
+description = "Compositional data (CoDa) analysis tools for Python"
+readme = "README.md"
+license = { text = "MIT" }
+requires-python = ">=3.8"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering",
+]
+dependencies = [
+    "adjustText>=0.7.3",
+    "matplotlib>=3.1.1",
+    "numpy>=1.17.2",
+    "pandas>=0.25.1",
+    "python-ternary>=1.0.6",
+    "scipy>=1.3.1",
+    "webcolors>=1.13",
+]
+
+[project.urls]
+"Homepage" = "https://bitbucket.org/genomicepidemiology/pycodamath"
+"Bug Tracker" = "https://bitbucket.org/genomicepidemiology/pycodamath/issues"
+
+[tool.setuptools.packages.find]
+where = ["src"]

pycodamath-1.1.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

pycodamath-1.1.1/src/pycodamath/__init__.py

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+'''
+    pyCoDa init script
+'''
+
+__title__ = "pyCoDaMath"
+__author__ = "Christian Brinch"
+__email__ = "cbri@food.dtu.dk"
+__copyright__ = "Copyright 2019 C. Brinch"
+__version__ = 1.0
+__all__ = ['pycoda', 'extra', 'plot', 'pca']
+
+from . import pycoda, pca, entropy
+pycoda.init()
+entropy.init()