qdiv 4.0.0__py3-none-any.whl

qdiv/__init__.py

@@ -0,0 +1,47 @@
+"""
+qdiv: Microbial diversity analysis with Hill numbers
+====================================================
+
+This package provides tools for diversity analysis, including:
+
+- **Data structures**: Easily filter and manipulate abundance tables, taxonomic data, and phylogenetic trees.
+- **Diversity calculations**: Compute alpha and beta diversity metrics, focusing on the Hill number framework.
+- **Statistics**: Perform multivariate tests and generate null models.
+- **Visualization**: Create plots for ordinations, diversity metrics, and relative abundance.
+
+Subpackages
+-----------
+.. autosummary::
+    :toctree: _autosummary
+
+    qdiv.sequences
+    qdiv.stats
+    qdiv.diversity
+    qdiv.plot
+    qdiv.model
+
+"""
+
+__version__ = "4.0.0"
+__author__ = "Oskar Modin"
+__docformat__ = "restructuredtext"
+
+# Public API imports
+from .data_object import MicrobiomeData
+from .citations import citations
+from . import sequences
+from . import stats
+from . import diversity
+from . import plot
+from . import model
+
+__all__ = [
+    "MicrobiomeData",
+    "citations",
+    "sequences",
+    "stats",
+    "diversity",
+    "plot",
+    "model"
+]
+

qdiv/citations.py

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+def citations(f="all") -> None:
+    """
+    Function to show key references that were important for developing qdiv.
+
+    Parameters
+    ----------
+    f : str, optional
+        Define for which function references will be displayed. The default is "all".
+
+    Returns
+    -------
+    None.
+    """
+    
+    if f == "all" or f == "qdiv":
+        print("qdiv package:")
+        print("Modin, O. https://github.com/omvatten/qdiv")
+    if f == "all" or f in ["diversity.naive_alpha", "diversity.naive_beta", "diversity.naive_multi_beta", "naive"]:
+        print("\nNaive diversity:")
+        print("Hill, M. O. (1973). Ecology 54(2): 427-432.")
+        print("Jost, L. (2006). OIKOS 113(2): 363-375.")
+        print("Jost, L. (2007). Ecology 88(10): 2427-2439.")
+    if f == "all" or f in ["diversity.phyl_alpha", "diversity.phyl_beta", "diversity.phyl_multi_beta", "phyl"]:
+        print("\nPhylogenetic diversity:")
+        print("Chao, A., C.-H. Chiu and L. Jost (2010). Philosophical Transactions of the Royal Society B: Biological Sciences 365(1558): 3599-3609.")
+        print("Chiu, C. H., L. Jost and A. Chao (2014). Ecological Monographs 84(1): 21-44.")
+    if f == "all" or f in ["diversity.func_alpha", "diversity.func_beta", "diversity.func_multi_beta", "func"]:
+        print("\nFunctional diversity:")
+        print("Chiu, C. H. and A. Chao (2014). PLoS One 9(7): e100014.")
+    if f == "all" or f in ["diversity.evenness", "diversity.dissimilarity_by_feature", "plot.dissimilarity_contributions"]:
+        print("\nEvenness:")
+        print("Chao, A. and C. Ricotta (2019). Ecology 100(12): e02852.")
+    if f == "all" or f in ["model.rcq"]:
+        print("\nRCq null model:")
+        print("Raup, D. M. and R. E. Crick (1979). Journal of Paleontology 53(5): 1213-1227.")
+        print("Chase, J. M., N. J. B. Kraft, K. G. Smith, M. Vellend and B. D. Inouye (2011). Ecosphere 2(2): 24.")
+        print("Stegen, J. C., X. Lin, J. K. Fredrickson, X. Chen, D. W. Kennedy, C. J. Murray, M. L. Rockhold and A. Konopka (2013). ISME Journal 7(11): 2069-2079.")
+        print("Modin, O., R. Liébana, S. Saheb-Alam, B.-M. Wilén, C. Suarez, M. Hermansson and F. Persson (2020). Microbiome 8, 132, DOI: 10.1186/s40168-020-00909-7")
+    if f == "all" or f in ["model.nriq", "model.ntiq"]:
+        print("\nNRI and NTI:")
+        print("Webb, C. O., D. D. Ackerly, M. A. McPeek and M. J. Donoghue (2002). Annual Review of Ecology and Systematics 33(1): 475-505.")
+    if f == "all" or f in ["model.beta_nriq", "model.beta_ntiq"]:
+        print("\nbeta NRI and beta NTI:")
+        print("Fine, P. V. A. and S. W. Kembel (2011). Ecography 34: 552-565.")
+    if f == "all" or f in ["stats.mantel"]:
+        print("\nMantel test:")
+        print("Mantel, N. (1967). Cancer Research 27(2): 209-220.")
+    if f == "all" or f in ["stats.permanova"]:
+        print("\nPermanova test:")
+        print("Anderson, M. (2001). Austral Ecology 26(1): 32-46.")