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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -50,7 +50,7 @@ The Soil Water Processes Lab at Kansas State University combines a range of expe

## Community Guidelines
### Contributing
To contribute to the software, please first fork the repository and create your own branch from `master`. Ensure your code adheres to our established standards and includes appropriate test coverage. Then, submit a pull request with a clear and detailed description of your changes.
To contribute to the software, please first fork the repository and create your own branch from `main`. Ensure your code adheres to our established code structure and includes appropriate test/examples coverage. CRNPy source code is located in the `/src/crnpy/` folder, and tests implemented using `pytest` are stored in the `/src/tests/` folder. Submit a pull request with a clear and detailed description of your changes to include them in the main repository.

### Reporting Issues
If you encounter any issues or problems with the software, please report them on our [issues page](https://github.com/soilwater/crnpy/issues). Include a detailed description of the issue, steps to reproduce the problem, any error messages you received, and details about your operating system and software version.
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2 changes: 1 addition & 1 deletion docs/index.md
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Expand Up @@ -51,7 +51,7 @@ The Soil Water Processes Lab at Kansas State University combines a range of expe
## Community Guidelines

### Contributing
To contribute to the software, please first fork the repository and create your own branch from `master`. Ensure your code adheres to our established standards and includes appropriate test coverage. Then, submit a pull request with a clear and detailed description of your changes.
To contribute to the software, please first fork the repository and create your own branch from `main`. Ensure your code adheres to our established code structure and includes appropriate test/examples coverage. CRNPy source code is located in the `/src/crnpy/` folder, and tests implemented using `pytest` are stored in the `/src/tests/` folder. Submit a pull request with a clear and detailed description of your changes to include them in the main repository.

### Reporting Issues
If you encounter any issues or problems with the software, please report them on our [issues page](https://github.com/soilwater/crnpy/issues). Include a detailed description of the issue, steps to reproduce the problem, any error messages you received, and details about your operating system and software version.
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10 changes: 5 additions & 5 deletions site/correction_routines/index.html
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Expand Up @@ -612,7 +612,7 @@ <h3 id="incoming-neutron-flux">Incoming neutron flux</h3>
</table>
<div class="admonition info">
<p class="admonition-title">Implementation</p>
<p>See <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.cutoff_rigidity">crnpy.crnpy.cutoff_rigidity</a>, <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.find_neutron_monitor">crnpy.crnpy.find_neutron_monitor</a>, <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.get_incoming_neutron_flux">crnpy.crnpy.get_incoming_neutron_flux</a>, <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.interpolate_incoming_flux">crnpy.crnpy.interpolate_incoming_flux</a> and <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.incoming_flux_correction">crnpy.crnpy.incoming_flux_correction</a> documentation for the implementation details.</p>
<p>See <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.cutoff_rigidity">crnpy.crnpy.cutoff_rigidity</a>, <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.find_neutron_monitor">crnpy.crnpy.find_neutron_monitor</a>, <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.get_incoming_neutron_flux">crnpy.crnpy.get_incoming_neutron_flux</a>, <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.interpolate_incoming_flux">crnpy.crnpy.interpolate_incoming_flux</a> and [crnpy.crnpy.incoming_flux_correction][] documentation for the implementation details.</p>
</div>
<h3 id="atmospheric-corrections">Atmospheric corrections</h3>
<p>The CRNPy library also provides functions for correcting raw neutron counts for atmospheric pressure, air humidity, and air temperature (Andreasen et al., 2017; Rosolem et al., 2013).</p>
Expand Down Expand Up @@ -648,7 +648,7 @@ <h3 id="atmospheric-corrections">Atmospheric corrections</h3>
</table>
<div class="admonition info">
<p class="admonition-title">Implementation</p>
<p>See <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.humidity_correction">crnpy.crnpy.humidity_correction</a> and <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.pressure_correction">crnpy.crnpy.pressure_correction</a> documentation for the implementation details.</p>
<p>See [crnpy.crnpy.humidity_correction][] and [crnpy.crnpy.pressure_correction][] documentation for the implementation details.</p>
</div>
<h3 id="biomass-correction">Biomass correction</h3>
<p>The library provides a function for correcting neutron counts for the effects of above-ground biomass by combining an approach for estimating biomass water equivalent (BWE) from in-situ biomass samples and the BWE correction factor (Baatz et al., 2015).</p>
Expand All @@ -675,7 +675,7 @@ <h3 id="biomass-correction">Biomass correction</h3>
</table>
<div class="admonition info">
<p class="admonition-title">Implementation</p>
<p>See <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.bwe_correction">crnpy.crnpy.bwe_correction</a> and <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.biomass_to_bwe">crnpy.crnpy.biomass_to_bwe</a> documentation for the implementation details.</p>
<p>See [crnpy.crnpy.bwe_correction][] and <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.biomass_to_bwe">crnpy.crnpy.biomass_to_bwe</a> documentation for the implementation details.</p>
</div>
<h3 id="road-correction">Road correction</h3>
<p>The lCRNPY library includes functions to correct for the effect of roads during rover surveys which account for the field soil water content and the road water content following the approach proposed by Schrön et al., (2018).</p>
Expand Down Expand Up @@ -705,13 +705,13 @@ <h3 id="road-correction">Road correction</h3>
</table>
<div class="admonition info">
<p class="admonition-title">Implementation</p>
<p>See <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.road_correction">crnpy.crnpy.road_correction</a> documentation for the implementation details.</p>
<p>See [crnpy.crnpy.road_correction][] documentation for the implementation details.</p>
</div>
<h3 id="additional-corrections">Additional corrections</h3>
<p>Other correction routines includes corrections for soil lattice water and total soil carbon that are known to affect the attentuation of epithermal cosmic-ray neutrons. A function to estimate the soil lattice water content based on clay content and soil organic carbon content was developed using soil samples collected across the state of Kansas.</p>
<div class="admonition info">
<p class="admonition-title">Implementation</p>
<p>See <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.estimate_lattice_water">crnpy.crnpy.estimate_lattice_water</a> and <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.counts_to_vwc">crnpy.crnpy.counts_to_vwc</a> documentation for the implementation details.</p>
<p>See [crnpy.crnpy.estimate_lattice_water][] and <a class="autorefs autorefs-internal" href="../reference/#crnpy.crnpy.counts_to_vwc">crnpy.crnpy.counts_to_vwc</a> documentation for the implementation details.</p>
</div>
<div class="admonition note">
<p class="admonition-title">References</p>
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95 changes: 95 additions & 0 deletions site/index.html
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</label>
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>

<li class="md-nav__item">
<a href="#statement-of-need" class="md-nav__link">
Statement of Need
</a>

</li>

<li class="md-nav__item">
<a href="#key-features" class="md-nav__link">
Key Features
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Authors
</a>

</li>

<li class="md-nav__item">
<a href="#community-guidelines" class="md-nav__link">
Community Guidelines
</a>

<nav class="md-nav" aria-label="Community Guidelines">
<ul class="md-nav__list">

<li class="md-nav__item">
<a href="#contributing" class="md-nav__link">
Contributing
</a>

</li>

<li class="md-nav__item">
<a href="#reporting-issues" class="md-nav__link">
Reporting Issues
</a>

</li>

<li class="md-nav__item">
<a href="#seeking-support" class="md-nav__link">
Seeking Support
</a>

</li>

</ul>
</nav>

</li>

</ul>
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</label>
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>

<li class="md-nav__item">
<a href="#statement-of-need" class="md-nav__link">
Statement of Need
</a>

</li>

<li class="md-nav__item">
<a href="#key-features" class="md-nav__link">
Key Features
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Authors
</a>

</li>

<li class="md-nav__item">
<a href="#community-guidelines" class="md-nav__link">
Community Guidelines
</a>

<nav class="md-nav" aria-label="Community Guidelines">
<ul class="md-nav__list">

<li class="md-nav__item">
<a href="#contributing" class="md-nav__link">
Contributing
</a>

</li>

<li class="md-nav__item">
<a href="#reporting-issues" class="md-nav__link">
Reporting Issues
</a>

</li>

<li class="md-nav__item">
<a href="#seeking-support" class="md-nav__link">
Seeking Support
</a>

</li>

</ul>
</nav>

</li>

</ul>
Expand Down Expand Up @@ -507,6 +589,8 @@ <h1 id="cosmic-ray-neutron-python-crnpy-library">Cosmic-Ray Neutron Python (CRNP
<a href="https://github.com/soilwater/crnpy"><img alt="GitHub commits since latest release (by SemVer including pre-releases)" src="https://img.shields.io/github/commits-since/soilwater/crnpy/latest/main" /></a></p>
<p>Welcome to the homepage of the CRNPy (Cosmic-Ray Neutron Python) library, an open-source Python library designed for the processing and conversion of raw neutron counts from cosmic-ray neutron probes (CRNP) into soil moisture data.</p>
<p>This library has been developed with the intent of providing a comprehensive yet easy-to-use workflow for processing raw data from a variety of CRNP, encompassing multiple manufacturers and models.</p>
<h2 id="statement-of-need">Statement of Need</h2>
<p>CRNPs are a valuable tool for non-invasive soil moisture estimation at the hectometer scale (e.g., typical agricultural fields), filling the gap between point-level sensors and large-scale (i.e., several kilometers) remote sensors onboard orbiting satellites. However, cleaning, processing, and analyzing CRNP data involves multiple corrections and filtering steps spread across multiple peer-reviewed manuscripts. CRNPy simplifies these steps by providing a complete, user-friendly, and well-documented library with minimal dependencies that includes examples to convert raw CRNP data into soil moisture. The library is designed to be accessible to both researchers and instrument manufacturers. Unlike other similar libraries, CRNPy does not require any specific naming convention for the input data or large external data sources, or reanalysis data.</p>
<h2 id="key-features">Key Features</h2>
<ul>
<li>
Expand All @@ -521,6 +605,10 @@ <h2 id="installation">Installation</h2>
<p><code>pip install crnpy</code></p>
<p>from the Jupyter notebook, type:</p>
<p><code>!pip install crnpy</code></p>
<p>Ideally dependencies should be installed automatically. If not, you can install them manually by typing:</p>
<p><code>pip install -r requirements.txt</code></p>
<p>The CRNPy library is compatible with Python 3.7 and above.
See <a href="https://github.com/soilwater/crnpy/blob/main/requirements.txt">requirements.txt</a> for a list of dependencies.</p>
<h2 id="authors">Authors</h2>
<p>The CRNPy library was developed at the Kansas State University Soil Water Processes Lab by:</p>
<ul>
Expand All @@ -532,6 +620,13 @@ <h2 id="authors">Authors</h2>
</li>
</ul>
<p>The Soil Water Processes Lab at Kansas State University combines a range of experimental and computational approaches to tackle pressing issues in soil and water research. The development of the CRNPy library is a step forward to creating reproducible data processing workflows across the scientific community using cosmic-ray neutrons probes for soil moisture sensing. </p>
<h2 id="community-guidelines">Community Guidelines</h2>
<h3 id="contributing">Contributing</h3>
<p>To contribute to the software, please first fork the repository and create your own branch from <code>main</code>. Ensure your code adheres to our established code structure and includes appropriate test/examples coverage. CRNPy source code is located in the <code>/src/crnpy/</code> folder, and tests implemented using <code>pytest</code> are stored in the <code>/src/tests/</code> folder. Submit a pull request with a clear and detailed description of your changes to include them in the main repository.</p>
<h3 id="reporting-issues">Reporting Issues</h3>
<p>If you encounter any issues or problems with the software, please report them on our <a href="https://github.com/soilwater/crnpy/issues">issues page</a>. Include a detailed description of the issue, steps to reproduce the problem, any error messages you received, and details about your operating system and software version.</p>
<h3 id="seeking-support">Seeking Support</h3>
<p>If you need support, please first refer to the documentation. If you still require assistance, post a question on the <a href="https://github.com/soilwater/crnpy/issues">issues page</a> with the <code>question</code> tag. For private inquiries, you can reach us via email at jperaza@ksu.edu or andrespatrignani@ksu.edu.</p>



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# Project: CRNPy Documentation
# Version: 0.0.0
# The remainder of this file is compressed using zlib.
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