Metadata-Version: 2.1
Name: scikit-diveMove
Version: 0.1.3
Summary: Python interface to R package diveMove
Home-page: https://github.com/spluque/scikit-diveMove
Author: Sebastian Luque
Author-email: spluque@gmail.com
License: AGPLv3
Download-URL: https://github.com/spluque/scikit-diveMove
Description: 
        `scikit-diveMove` is a Python interface to R package `diveMove`_ for
        scientific data analysis, with a focus on diving behaviour analysis.  It
        has utilities to represent, visualize, filter, analyse, and summarize
        time-depth recorder (TDR) data.  Miscellaneous functions for handling
        location data are also provided.  `scikit-diveMove` communicates with a
        single `R` instance for access to low-level tools of package `diveMove`.
        
        .. _diveMove: https://github.com/spluque/diveMove
        
        The table below shows which features of `diveMove` are accessible from
        `scikit-diveMove`:
        
        +----------------------------------+--------------------------+--------------------------------+
        |                  `diveMove`      |`scikit-diveMove`         |Notes                           |
        +---------------+------------------+                          |                                |
        |Functionality  |Functions/Methods |                          |                                |
        +===============+==================+==========================+================================+
        |Movement       |``austFilter``    |                          |Under consideration.            |
        |               |``rmsDistFilter`` |                          |                                |
        |               |``grpSpeedFilter``|                          |                                |
        |               |``distSpeed``     |                          |                                |
        |               |``readLocs``      |                          |                                |
        +---------------+------------------+--------------------------+--------------------------------+
        |Bout analysis  |``boutfreqs``     |``BoutsNLS`` ``BoutsMLE`` |Fully implemented in Python.    |
        |               |``boutinit``      |                          |                                |
        |               |``bouts2.nlsFUN`` |                          |                                |
        |               |``bouts2.nls``    |                          |                                |
        |               |``bouts3.nlsFUN`` |                          |                                |
        |               |``bouts3.nls``    |                          |                                |
        |               |``bouts2.mleFUN`` |                          |                                |
        |               |``bouts2.ll``     |                          |                                |
        |               |``bouts2.LL``     |                          |                                |
        |               |``bouts.mle``     |                          |                                |
        |               |``labelBouts``    |                          |                                |
        |               |``plotBouts``     |                          |                                |
        |               |``plotBouts2.cdf``|                          |                                |
        |               |``bec2``          |                          |                                |
        |               |``bec3``          |                          |                                |
        +---------------+------------------+--------------------------+--------------------------------+
        |Dive analysis  |``readTDR``       |``TDR.__init__``          |Fully implemented.  Single      |
        |               |``createTDR``     |``TDRSource.__init__``    |``TDR`` class for data with or  |
        |               |                  |                          |without speed measurements.     |
        +---------------+------------------+--------------------------+--------------------------------+
        |               |``calibrateDepth``|``TDR.calibrate``         |Fully implemented               |
        |               |                  |``TDR.zoc``               |                                |
        |               |                  |``TDR.detect_wet``        |                                |
        |               |                  |``TDR.detect_dives``      |                                |
        |               |                  |``TDR.detect_dive_phases``|                                |
        +---------------+------------------+--------------------------+--------------------------------+
        |               |``calibrateSpeed``|``TDR.calibrate_speed``   |New implementation of the       |
        |               |``rqPlot``        |                          |algorithm entirely in Python.   |
        |               |                  |                          |The procedure generates the plot|
        |               |                  |                          |concurrently.                   |
        +---------------+------------------+--------------------------+--------------------------------+
        |               |``diveStats``     |``TDR.dive_stats``        |Fully implemented               |
        |               |``stampDive``     |``TDR.time_budget``       |                                |
        |               |``timeBudget``    |``TDR.stamp_dives``       |                                |
        +---------------+------------------+--------------------------+--------------------------------+
        |               |``plotTDR``       |``TDR.plot``              |Fully implemented.              |
        |               |``plotDiveModel`` |``TDR.plot_zoc_filters``  |Interactivity is the default, as|
        |               |``plotZOC``       |``TDR.plot_phases``       |standard `matplotlib`.          |
        |               |                  |``TDR.plot_dive_model``   |                                |
        +---------------+------------------+--------------------------+--------------------------------+
        |               |``getTDR``        |``TDR.tdr``               |Fully implemented.              |
        |               |``getDepth``      |``TDR.get_depth``         |``getCCData`` deemed redundant, |
        |               |``getSpeed``      |``TDR.get_speed``         |as the columns can be accessed  |
        |               |``getTime``       |``TDR.tdr.index``         |directly from the ``TDR.tdr``   |
        |               |``getCCData``     |``TDR.src_file``          |attribute.                      |
        |               |``getDtime``      |``TDR.dtime``             |                                |
        |               |``getFileName``   |                          |                                |
        +---------------+------------------+--------------------------+--------------------------------+
        |               |``getDAct``       |``TDR.get_wet_activity``  |Fully implemented               |
        |               |``getDPhaseLab``  |``TDR.get_dives_details`` |                                |
        |               |``getDiveDeriv``  |``TDR.get_dive_deriv``    |                                |
        |               |``getDiveModel``  |                          |                                |
        |               |``getGAct``       |                          |                                |
        +---------------+------------------+--------------------------+--------------------------------+
        |               |``extractDive``   |                          |Fully implemented               |
        +---------------+------------------+--------------------------+--------------------------------+
        
        
        Installation
        ============
        
        Type the following at a terminal command line:
        
        .. code-block:: sh
        
           pip install scikit-kinematics
        
        Or install from source tree by typing the following at the command line:
        
        .. code-block:: sh
        
           python setup.py install
        
        The documentation can also be installed as described in `Documentation`_.
        
        Once installed, `skdiveMove` can be easily imported as: ::
        
          import skdiveMove as skdive
        
        
        Dependencies
        ------------
        
        `skdiveMove` depends primarily on ``R`` package `diveMove`, which must be
        installed and available to the user running Python.  If needed, install
        `diveMove` at the ``R`` prompt:
        
        .. code-block:: R
        
           install.packages("diveMove")
        
        Required Python packages are listed in the `requirements
        <requirements.txt>`_ file.
        
        
        Documentation
        =============
        
        Available at: https://spluque.github.io/scikit-diveMove
        
        Alternatively, installing the package as follows:
        
        .. code-block:: sh
        
           pip install -e .["docs"]
        
        allows the documentation to be built locally (choosing the desired target
        {"html", "pdf", etc.}):
        
        .. code-block:: sh
        
           make -C docs/ html
        
        The `html` tree is at `docs/build/html`.
        
Keywords: animal behaviour,biology,behavioural ecology,diving,diving behaviour
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 3
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Affero General Public License v3
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.6
Description-Content-Type: text/x-rst
Provides-Extra: dev
Provides-Extra: docs
