Skip to content

Commit

Permalink
Deploying to gh-pages from @ 51b8de8 🚀
Browse files Browse the repository at this point in the history
  • Loading branch information
ehwenk committed Nov 27, 2023
1 parent fb97b85 commit 1593207
Show file tree
Hide file tree
Showing 37 changed files with 1,382 additions and 2,003 deletions.
178 changes: 86 additions & 92 deletions AusTraits_tutorial.html

Large diffs are not rendered by default.

79 changes: 37 additions & 42 deletions adding_data_brief.html

Large diffs are not rendered by default.

92 changes: 43 additions & 49 deletions adding_data_long.html

Large diffs are not rendered by default.

68 changes: 31 additions & 37 deletions austraits_database.html

Large diffs are not rendered by default.

98 changes: 46 additions & 52 deletions austraits_package.html

Large diffs are not rendered by default.

74 changes: 34 additions & 40 deletions check_dataset_functions.html

Large diffs are not rendered by default.

52 changes: 23 additions & 29 deletions create_dictionary.html
Original file line number Diff line number Diff line change
Expand Up @@ -211,19 +211,13 @@
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./adding_data_brief.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Adding datasets (brief)</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./custom_R_code.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Adding custom_R_code</span></span></a>
<span class="menu-text"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Adding datasets, an introduction</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./publishing.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Publishing</span></span></a>
<span class="menu-text"><span class="chapter-number">15</span>&nbsp; <span class="chapter-title">Publishing</span></span></a>
</div>
</li>
</ul>
Expand All @@ -240,67 +234,67 @@
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./tutorial_datasets.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Tutorial: Adding datasets</span></span></a>
<span class="menu-text"><span class="chapter-number">16</span>&nbsp; <span class="chapter-title">Tutorial: Adding datasets</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./tutorial_dataset_1.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Tutorial 1: Adding a simple dataset</span></span></a>
<span class="menu-text"><span class="chapter-number">17</span>&nbsp; <span class="chapter-title">Tutorial 1: Adding a simple dataset</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./tutorial_dataset_2.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">19</span>&nbsp; <span class="chapter-title">Tutorial 2: Adding a more complex dataset</span></span></a>
<span class="menu-text"><span class="chapter-number">18</span>&nbsp; <span class="chapter-title">Tutorial 2: Adding a more complex dataset</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./tutorial_dataset_3.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">20</span>&nbsp; <span class="chapter-title">Tutorial 3: Adding contexts and complex units</span></span></a>
<span class="menu-text"><span class="chapter-number">19</span>&nbsp; <span class="chapter-title">Tutorial 3: Adding contexts and complex units</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./tutorial_dataset_4.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">21</span>&nbsp; <span class="chapter-title">Tutorial 4: Additional complexities</span></span></a>
<span class="menu-text"><span class="chapter-number">20</span>&nbsp; <span class="chapter-title">Tutorial 4: Additional complexities</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./tutorial_dataset_5.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">22</span>&nbsp; <span class="chapter-title">Tutorial 5: Multiple columns for a trait</span></span></a>
<span class="menu-text"><span class="chapter-number">21</span>&nbsp; <span class="chapter-title">Tutorial 5: Multiple columns for a trait</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./tutorial_dataset_6.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">23</span>&nbsp; <span class="chapter-title">Tutorial 6: Data with repeat measurements</span></span></a>
<span class="menu-text"><span class="chapter-number">22</span>&nbsp; <span class="chapter-title">Tutorial 6: Data with repeat measurements</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./tutorial_dataset_7.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">24</span>&nbsp; <span class="chapter-title">Tutorial 7: Adding long format dataset</span></span></a>
<span class="menu-text"><span class="chapter-number">23</span>&nbsp; <span class="chapter-title">Tutorial 7: Adding long format dataset</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./adding_data_long.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">25</span>&nbsp; <span class="chapter-title">Adding datasets</span></span></a>
<span class="menu-text"><span class="chapter-number">24</span>&nbsp; <span class="chapter-title">Adding datasets, a lengthy guide</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./check_dataset_functions.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">26</span>&nbsp; <span class="chapter-title">Check data quality functions</span></span></a>
<span class="menu-text"><span class="chapter-number">25</span>&nbsp; <span class="chapter-title">Check data quality functions</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./data_common_issues.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">27</span>&nbsp; <span class="chapter-title">Common issues</span></span></a>
<span class="menu-text"><span class="chapter-number">26</span>&nbsp; <span class="chapter-title">Common issues</span></span></a>
</div>
</li>
</ul>
Expand All @@ -317,31 +311,31 @@
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./austraits_database.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">28</span>&nbsp; <span class="chapter-title">AusTraits, Australia’s Plant Trait Database</span></span></a>
<span class="menu-text"><span class="chapter-number">27</span>&nbsp; <span class="chapter-title">AusTraits, Australia’s Plant Trait Database</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./AusTraits_tutorial.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">AusTraits tutorial</span></span></a>
<span class="menu-text"><span class="chapter-number">28</span>&nbsp; <span class="chapter-title">AusTraits tutorial</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./traits_and_climate_example.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">30</span>&nbsp; <span class="chapter-title">Combining trait values and climate data</span></span></a>
<span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Analysis example: Using AusTraits for trait-climate analyses</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./spatial_data_example.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">31</span>&nbsp; <span class="chapter-title">Tutorial: Using AusTraits with spatial data</span></span></a>
<span class="menu-text"><span class="chapter-number">30</span>&nbsp; <span class="chapter-title">Analysis example: Using AusTraits with spatial data</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./austraits_package.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">32</span>&nbsp; <span class="chapter-title">The <code>austraits</code> package</span></span></a>
<span class="menu-text"><span class="chapter-number">31</span>&nbsp; <span class="chapter-title">The <code>austraits</code> package</span></span></a>
</div>
</li>
</ul>
Expand All @@ -358,13 +352,13 @@
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./help.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">33</span>&nbsp; <span class="chapter-title">Getting help</span></span></a>
<span class="menu-text"><span class="chapter-number">32</span>&nbsp; <span class="chapter-title">Getting help</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./debugging.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">34</span>&nbsp; <span class="chapter-title">Debugging</span></span></a>
<span class="menu-text"><span class="chapter-number">33</span>&nbsp; <span class="chapter-title">Debugging</span></span></a>
</div>
</li>
</ul>
Expand Down Expand Up @@ -421,7 +415,7 @@ <h1 class="title"><span class="chapter-number">13</span>&nbsp; <span class="chap
</header>

<p>All with data within a trait database must be including in an accompanying trait dictionary.</p>
<p>Following the ETS <a href="https://doi.org/10.1111/2041-210X.13288">Ecological Trait-data Standard</a>:</p>
<p>Following the Ecological Trait-data Standard, <a href="https://doi.org/10.1111/2041-210X.13288">ETS</a>:</p>
<ul>
<li><p>all traits must have a label and definition</p></li>
<li><p>all traits must be defined as being either <code>type: numeric</code> or <code>type: categorical</code></p></li>
Expand All @@ -431,7 +425,7 @@ <h1 class="title"><span class="chapter-number">13</span>&nbsp; <span class="chap
<p>Examples are available <a href="dictionary.html">here</a>, while the complete AusTraits dictionary is available <a href="https://github.com/traitecoevo/austraits.build/tree/develop/config">here</a>.</p>
<p>The trait dictionary is compiled in a simple yml format, allowing trait definitions to be easily added and edited.</p>
<p>Creating a trait dictionary that allows a database to build is quick; it simply requires filling in a brief definition and the required units/range/trait value fields. However, drafting meaningful, reusable trait definitions and categorical trait values requires complete, explicit definitions to eliminate confusion between trait concepts. The definitions and trait values should be agreed upon by the broader research community to allow the database to be reused by other researchers and supported by the research community.</p>
<p>For instance, to achieve these broader goals, the trait dictionary used for the AusTraits database has been formalised into a standalone output, the AusTraits Plant Dictionary (APD), available in both machine-readable and humman-friendly outputs through the <a href="https://w3id.org/APD">w3id.org/APD</a> namespace. The traits included in the APD have undergone a rigorous internal and external review process to ensure the trait concepts and their definitions are complete and robust.</p>
<p>For instance, to achieve these broader goals, the trait dictionary used for the AusTraits database has been formalised into a standalone output, the AusTraits Plant Dictionary (APD), available in both machine-readable and humman-friendly outputs through the <a href="https://w3id.org/APD">w3id.org/APD</a> namespace. The traits included in the APD have undergone a rigorous internal and external review process to ensure the trait concepts and their definitions are complete and robust, as described in the <a href="doi.org/10.1101/2023.06.16.545047">The AusTraits Plant Dictionary paper</a>.</p>



Expand Down Expand Up @@ -677,7 +671,7 @@ <h1 class="title"><span class="chapter-number">13</span>&nbsp; <span class="chap
</div>
<div class="nav-page nav-page-next">
<a href="./adding_data_brief.html" class="pagination-link">
<span class="nav-page-text"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Adding datasets (brief)</span></span> <i class="bi bi-arrow-right-short"></i>
<span class="nav-page-text"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Adding datasets, an introduction</span></span> <i class="bi bi-arrow-right-short"></i>
</a>
</div>
</nav>
Expand Down
Loading

0 comments on commit 1593207

Please sign in to comment.