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  77 <li class="toc-logo"><a href="./"><img src="assets/images/Breedbase_HighRes.png"></a></li>
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  79 <li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Introduction</a></li>
  80 <li class="chapter" data-level="1" data-path="basic-website-usage.html"><a href="basic-website-usage.html"><i class="fa fa-check"></i><b>1</b> Basic Website Usage</a>
  81 <ul>
  82 <li class="chapter" data-level="1.1" data-path="basic-website-usage.html"><a href="basic-website-usage.html#creating-a-user-account"><i class="fa fa-check"></i><b>1.1</b> Creating a User Account</a>
  83 <ul>
  84 <li class="chapter" data-level="1.1.1" data-path="basic-website-usage.html"><a href="basic-website-usage.html#verifying-first-that-you-do-not-already-have-an-account"><i class="fa fa-check"></i><b>1.1.1</b> Verifying first that you do not already have an account</a></li>
  85 <li class="chapter" data-level="1.1.2" data-path="basic-website-usage.html"><a href="basic-website-usage.html#creating-a-user-account-1"><i class="fa fa-check"></i><b>1.1.2</b> Creating a user account</a></li>
  86 </ul></li>
  87 <li class="chapter" data-level="1.2" data-path="basic-website-usage.html"><a href="basic-website-usage.html#managing-your-account"><i class="fa fa-check"></i><b>1.2</b> Managing your Account</a>
  88 <ul>
  89 <li class="chapter" data-level="1.2.1" data-path="basic-website-usage.html"><a href="basic-website-usage.html#login"><i class="fa fa-check"></i><b>1.2.1</b> Login</a></li>
  90 <li class="chapter" data-level="1.2.2" data-path="basic-website-usage.html"><a href="basic-website-usage.html#editing-account-settings"><i class="fa fa-check"></i><b>1.2.2</b> Editing Account Settings</a></li>
  91 <li class="chapter" data-level="1.2.3" data-path="basic-website-usage.html"><a href="basic-website-usage.html#changing-your-account-status-from-user-to-submitter"><i class="fa fa-check"></i><b>1.2.3</b> Changing Your Account Status: From “User” to “Submitter”</a></li>
  92 <li class="chapter" data-level="1.2.4" data-path="basic-website-usage.html"><a href="basic-website-usage.html#submitting-feedback-on-an-sgn-database"><i class="fa fa-check"></i><b>1.2.4</b> Submitting Feedback on an SGN Database</a></li>
  93 </ul></li>
  94 <li class="chapter" data-level="1.3" data-path="basic-website-usage.html"><a href="basic-website-usage.html#menu-layout"><i class="fa fa-check"></i><b>1.3</b> Menu Layout</a>
  95 <ul>
  96 <li class="chapter" data-level="1.3.1" data-path="basic-website-usage.html"><a href="basic-website-usage.html#menu-options"><i class="fa fa-check"></i><b>1.3.1</b> Menu Options</a></li>
  97 </ul></li>
  98 <li class="chapter" data-level="1.4" data-path="basic-website-usage.html"><a href="basic-website-usage.html#working-with-lists"><i class="fa fa-check"></i><b>1.4</b> Working with Lists</a>
  99 <ul>
 100 <li class="chapter" data-level="1.4.1" data-path="basic-website-usage.html"><a href="basic-website-usage.html#creating-lists"><i class="fa fa-check"></i><b>1.4.1</b> Creating lists</a></li>
 101 <li class="chapter" data-level="1.4.2" data-path="basic-website-usage.html"><a href="basic-website-usage.html#viewing-and-editing-lists"><i class="fa fa-check"></i><b>1.4.2</b> Viewing and editing lists</a></li>
 102 </ul></li>
 103 <li class="chapter" data-level="1.5" data-path="basic-website-usage.html"><a href="basic-website-usage.html#user-permissions"><i class="fa fa-check"></i><b>1.5</b> User Permissions</a></li>
 104 </ul></li>
 105 <li class="chapter" data-level="2" data-path="searching-the-database.html"><a href="searching-the-database.html"><i class="fa fa-check"></i><b>2</b> Searching the Database</a>
 106 <ul>
 107 <li class="chapter" data-level="2.1" data-path="searching-the-database.html"><a href="searching-the-database.html#search-wizard"><i class="fa fa-check"></i><b>2.1</b> The Search Wizard</a>
 108 <ul>
 109 <li class="chapter" data-level="2.1.1" data-path="searching-the-database.html"><a href="searching-the-database.html#how-the-search-wizard-works"><i class="fa fa-check"></i><b>2.1.1</b> How the Search Wizard Works</a></li>
 110 <li class="chapter" data-level="2.1.2" data-path="searching-the-database.html"><a href="searching-the-database.html#how-to-use-retrieved-data"><i class="fa fa-check"></i><b>2.1.2</b> How to use retrieved data</a></li>
 111 <li class="chapter" data-level="2.1.3" data-path="searching-the-database.html"><a href="searching-the-database.html#updating-the-wizard"><i class="fa fa-check"></i><b>2.1.3</b> Updating the Wizard</a></li>
 112 </ul></li>
 113 <li class="chapter" data-level="2.2" data-path="searching-the-database.html"><a href="searching-the-database.html#accessions-and-plot-search"><i class="fa fa-check"></i><b>2.2</b> Accessions and Plot Search</a></li>
 114 <li class="chapter" data-level="2.3" data-path="searching-the-database.html"><a href="searching-the-database.html#trials-search"><i class="fa fa-check"></i><b>2.3</b> Trials Search</a></li>
 115 <li class="chapter" data-level="2.4" data-path="searching-the-database.html"><a href="searching-the-database.html#trait-search"><i class="fa fa-check"></i><b>2.4</b> Trait Search</a></li>
 116 <li class="chapter" data-level="2.5" data-path="searching-the-database.html"><a href="searching-the-database.html#ontology-browser"><i class="fa fa-check"></i><b>2.5</b> Ontology Browser</a></li>
 117 <li class="chapter" data-level="2.6" data-path="searching-the-database.html"><a href="searching-the-database.html#search-seedlots"><i class="fa fa-check"></i><b>2.6</b> Search Seedlots</a></li>
 118 </ul></li>
 119 <li class="chapter" data-level="3" data-path="managing-user-roles.html"><a href="managing-user-roles.html"><i class="fa fa-check"></i><b>3</b> Managing User Roles</a>
 120 <ul>
 121 <li class="chapter" data-level="3.1" data-path="managing-user-roles.html"><a href="managing-user-roles.html#what-are-user-roles"><i class="fa fa-check"></i><b>3.1</b> What are User Roles?</a></li>
 122 <li class="chapter" data-level="3.2" data-path="managing-user-roles.html"><a href="managing-user-roles.html#the-manage-user-roles-page"><i class="fa fa-check"></i><b>3.2</b> The Manage User Roles page</a></li>
 123 </ul></li>
 124 <li class="chapter" data-level="4" data-path="managing-breeding-programs.html"><a href="managing-breeding-programs.html"><i class="fa fa-check"></i><b>4</b> Managing Breeding Programs</a></li>
 125 <li class="chapter" data-level="5" data-path="managing-locations.html"><a href="managing-locations.html"><i class="fa fa-check"></i><b>5</b> Managing Locations</a></li>
 126 <li class="chapter" data-level="6" data-path="managing-accessions.html"><a href="managing-accessions.html"><i class="fa fa-check"></i><b>6</b> Managing Accessions</a>
 127 <ul>
 128 <li class="chapter" data-level="6.1" data-path="managing-accessions.html"><a href="managing-accessions.html#add-accessions-using-a-list"><i class="fa fa-check"></i><b>6.1</b> Add Accessions Using A List</a></li>
 129 <li class="chapter" data-level="6.2" data-path="managing-accessions.html"><a href="managing-accessions.html#uploading-accessions-and-accessions-info-from-a-file"><i class="fa fa-check"></i><b>6.2</b> Uploading Accessions and Accession’s Info From A File</a></li>
 130 <li class="chapter" data-level="6.3" data-path="managing-accessions.html"><a href="managing-accessions.html#email-alert-for-accession-upload"><i class="fa fa-check"></i><b>6.3</b> Email alert for accession upload</a></li>
 131 <li class="chapter" data-level="6.4" data-path="managing-accessions.html"><a href="managing-accessions.html#add-parentage-pedigree-information-to-accessions"><i class="fa fa-check"></i><b>6.4</b> Add Parentage (Pedigree) Information to Accessions</a></li>
 132 <li class="chapter" data-level="6.5" data-path="managing-accessions.html"><a href="managing-accessions.html#working-with-grafts"><i class="fa fa-check"></i><b>6.5</b> Working with grafts</a></li>
 133 <li class="chapter" data-level="6.6" data-path="managing-accessions.html"><a href="managing-accessions.html#bulk-renaming-of-accessions"><i class="fa fa-check"></i><b>6.6</b> Bulk renaming of accessions</a></li>
 134 </ul></li>
 135 <li class="chapter" data-level="7" data-path="managing-seed-lots.html"><a href="managing-seed-lots.html"><i class="fa fa-check"></i><b>7</b> Managing Seed Lots</a>
 136 <ul>
 137 <li class="chapter" data-level="7.1" data-path="managing-seed-lots.html"><a href="managing-seed-lots.html#add-new-seedlots"><i class="fa fa-check"></i><b>7.1</b> Add New Seedlot(s)</a></li>
 138 <li class="chapter" data-level="7.2" data-path="managing-seed-lots.html"><a href="managing-seed-lots.html#seedlot-transactions"><i class="fa fa-check"></i><b>7.2</b> Seedlot Transactions</a></li>
 139 <li class="chapter" data-level="7.3" data-path="managing-seed-lots.html"><a href="managing-seed-lots.html#seed-inventory"><i class="fa fa-check"></i><b>7.3</b> Seed Inventory</a></li>
 140 <li class="chapter" data-level="7.4" data-path="managing-seed-lots.html"><a href="managing-seed-lots.html#find-seedlots-for-a-list-of-accessions"><i class="fa fa-check"></i><b>7.4</b> Find Seedlots For a List of Accessions</a></li>
 141 <li class="chapter" data-level="7.5" data-path="managing-seed-lots.html"><a href="managing-seed-lots.html#create-a-seedlot-for-an-accession-or-cross"><i class="fa fa-check"></i><b>7.5</b> Create a seedlot for an Accession or Cross</a></li>
 142 <li class="chapter" data-level="7.6" data-path="managing-seed-lots.html"><a href="managing-seed-lots.html#add-quality-data-to-a-seedlot"><i class="fa fa-check"></i><b>7.6</b> Add quality data to a seedlot</a></li>
 143 <li class="chapter" data-level="7.7" data-path="managing-seed-lots.html"><a href="managing-seed-lots.html#seedlot-maintenance-events"><i class="fa fa-check"></i><b>7.7</b> Seedlot Maintenance Events</a>
 144 <ul>
 145 <li class="chapter" data-level="7.7.1" data-path="managing-seed-lots.html"><a href="managing-seed-lots.html#setup"><i class="fa fa-check"></i><b>7.7.1</b> Setup</a></li>
 146 <li class="chapter" data-level="7.7.2" data-path="managing-seed-lots.html"><a href="managing-seed-lots.html#adding-events"><i class="fa fa-check"></i><b>7.7.2</b> Adding Events</a></li>
 147 <li class="chapter" data-level="7.7.3" data-path="managing-seed-lots.html"><a href="managing-seed-lots.html#displaying-events"><i class="fa fa-check"></i><b>7.7.3</b> Displaying Events</a></li>
 148 <li class="chapter" data-level="7.7.4" data-path="managing-seed-lots.html"><a href="managing-seed-lots.html#downloading-events"><i class="fa fa-check"></i><b>7.7.4</b> Downloading Events</a></li>
 149 </ul></li>
 150 <li class="chapter" data-level="7.8" data-path="managing-seed-lots.html"><a href="managing-seed-lots.html#deleting-seedlots"><i class="fa fa-check"></i><b>7.8</b> Deleting Seedlots</a></li>
 151 </ul></li>
 152 <li class="chapter" data-level="8" data-path="managing-populations.html"><a href="managing-populations.html"><i class="fa fa-check"></i><b>8</b> Managing Populations</a></li>
 153 <li class="chapter" data-level="9" data-path="managing-crosses.html"><a href="managing-crosses.html"><i class="fa fa-check"></i><b>9</b> Managing Crosses</a>
 154 <ul>
 155 <li class="chapter" data-level="9.1" data-path="managing-crosses.html"><a href="managing-crosses.html#crossing-experiment"><i class="fa fa-check"></i><b>9.1</b> Crossing Experiment</a>
 156 <ul>
 157 <li class="chapter" data-level="9.1.1" data-path="managing-crosses.html"><a href="managing-crosses.html#add-new-crossing-experiment"><i class="fa fa-check"></i><b>9.1.1</b> Add New Crossing Experiment</a></li>
 158 </ul></li>
 159 <li class="chapter" data-level="9.2" data-path="managing-crosses.html"><a href="managing-crosses.html#cross"><i class="fa fa-check"></i><b>9.2</b> Cross</a>
 160 <ul>
 161 <li class="chapter" data-level="9.2.1" data-path="managing-crosses.html"><a href="managing-crosses.html#add-new-crosses"><i class="fa fa-check"></i><b>9.2.1</b> Add New Crosses</a></li>
 162 <li class="chapter" data-level="9.2.2" data-path="managing-crosses.html"><a href="managing-crosses.html#update-crosses-by-uploading"><i class="fa fa-check"></i><b>9.2.2</b> Update Crosses by Uploading</a></li>
 163 </ul></li>
 164 <li class="chapter" data-level="9.3" data-path="managing-crosses.html"><a href="managing-crosses.html#cross-wishlist"><i class="fa fa-check"></i><b>9.3</b> Cross Wishlist</a>
 165 <ul>
 166 <li class="chapter" data-level="9.3.1" data-path="managing-crosses.html"><a href="managing-crosses.html#create-a-cross-wishlist"><i class="fa fa-check"></i><b>9.3.1</b> Create a Cross Wishlist</a></li>
 167 </ul></li>
 168 <li class="chapter" data-level="9.4" data-path="managing-crosses.html"><a href="managing-crosses.html#crossing-experiment-detail-page"><i class="fa fa-check"></i><b>9.4</b> Crossing Experiment Detail Page</a></li>
 169 <li class="chapter" data-level="9.5" data-path="managing-crosses.html"><a href="managing-crosses.html#cross-detail-page"><i class="fa fa-check"></i><b>9.5</b> Cross Detail Page</a></li>
 170 </ul></li>
 171 <li class="chapter" data-level="10" data-path="managing-field-trials.html"><a href="managing-field-trials.html"><i class="fa fa-check"></i><b>10</b> Managing Field Trials</a>
 172 <ul>
 173 <li class="chapter" data-level="10.1" data-path="managing-field-trials.html"><a href="managing-field-trials.html#trial-detail-page"><i class="fa fa-check"></i><b>10.1</b> Trial Detail Page</a></li>
 174 <li class="chapter" data-level="10.2" data-path="managing-field-trials.html"><a href="managing-field-trials.html#adding-trials"><i class="fa fa-check"></i><b>10.2</b> Adding Trials</a>
 175 <ul>
 176 <li class="chapter" data-level="10.2.1" data-path="managing-field-trials.html"><a href="managing-field-trials.html#prerequisites"><i class="fa fa-check"></i><b>10.2.1</b> Prerequisites</a></li>
 177 <li class="chapter" data-level="10.2.2" data-path="managing-field-trials.html"><a href="managing-field-trials.html#adding-a-trial-by-using-add-trial-form"><i class="fa fa-check"></i><b>10.2.2</b> Adding a trial by using “Add Trial” form</a></li>
 178 <li class="chapter" data-level="10.2.3" data-path="managing-field-trials.html"><a href="managing-field-trials.html#adding-a-trial-from-an-uploaded-file"><i class="fa fa-check"></i><b>10.2.3</b> Adding a trial from an uploaded file</a></li>
 179 <li class="chapter" data-level="10.2.4" data-path="managing-field-trials.html"><a href="managing-field-trials.html#multi-location-trials"><i class="fa fa-check"></i><b>10.2.4</b> Multi-location trials</a></li>
 180 <li class="chapter" data-level="10.2.5" data-path="managing-field-trials.html"><a href="managing-field-trials.html#email-alert-for-multiple-trial-design-upload"><i class="fa fa-check"></i><b>10.2.5</b> Email alert for multiple trial design upload</a></li>
 181 <li class="chapter" data-level="10.2.6" data-path="managing-field-trials.html"><a href="managing-field-trials.html#viewing-plot-layout-and-trait-heatmap"><i class="fa fa-check"></i><b>10.2.6</b> Viewing Plot Layout and Trait HeatMap</a></li>
 182 <li class="chapter" data-level="10.2.7" data-path="managing-field-trials.html"><a href="managing-field-trials.html#adding-additional-information-in-the-trial-detail-page"><i class="fa fa-check"></i><b>10.2.7</b> Adding additional information in the “Trial Detail” page</a></li>
 183 <li class="chapter" data-level="10.2.8" data-path="managing-field-trials.html"><a href="managing-field-trials.html#downloading-the-trial-layout-from-the-trial-detail-page"><i class="fa fa-check"></i><b>10.2.8</b> Downloading the Trial Layout from the “Trial Detail” page</a></li>
 184 <li class="chapter" data-level="10.2.9" data-path="managing-field-trials.html"><a href="managing-field-trials.html#adding-plant-entries-to-your-trial"><i class="fa fa-check"></i><b>10.2.9</b> Adding Plant Entries To Your Trial</a></li>
 185 <li class="chapter" data-level="10.2.10" data-path="managing-field-trials.html"><a href="managing-field-trials.html#adding-tissue-sample-entries-to-your-trial"><i class="fa fa-check"></i><b>10.2.10</b> Adding Tissue Sample Entries To Your Trial</a></li>
 186 <li class="chapter" data-level="10.2.11" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-gps-coordinates-for-plots"><i class="fa fa-check"></i><b>10.2.11</b> Uploading GPS Coordinates For Plots</a></li>
 187 <li class="chapter" data-level="10.2.12" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-additional-files-to-trial"><i class="fa fa-check"></i><b>10.2.12</b> Uploading Additional Files To Trial</a></li>
 188 <li class="chapter" data-level="10.2.13" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.2.13</b> Deleting Trial Data</a></li>
 189 </ul></li>
 190 </ul></li>
 191 <li class="chapter" data-level="11" data-path="managing-genotyping-plates.html"><a href="managing-genotyping-plates.html"><i class="fa fa-check"></i><b>11</b> Managing Genotyping Plates</a>
 192 <ul>
 193 <li class="chapter" data-level="11.1" data-path="managing-genotyping-plates.html"><a href="managing-genotyping-plates.html#adding-a-new-genotyping-plate"><i class="fa fa-check"></i><b>11.1</b> Adding a New Genotyping Plate</a></li>
 194 <li class="chapter" data-level="11.2" data-path="managing-genotyping-plates.html"><a href="managing-genotyping-plates.html#genotyping-plate-detail-page"><i class="fa fa-check"></i><b>11.2</b> Genotyping Plate Detail Page</a></li>
 195 </ul></li>
 196 <li class="chapter" data-level="12" data-path="using-fieldbook-app.html"><a href="using-fieldbook-app.html"><i class="fa fa-check"></i><b>12</b> Using Field Book App</a>
 197 <ul>
 198 <li class="chapter" data-level="12.1" data-path="using-fieldbook-app.html"><a href="using-fieldbook-app.html#a-typical-workflow"><i class="fa fa-check"></i><b>12.1</b> A typical workflow</a></li>
 199 <li class="chapter" data-level="12.2" data-path="using-fieldbook-app.html"><a href="using-fieldbook-app.html#creating-layout-files"><i class="fa fa-check"></i><b>12.2</b> Creating Field Layout Files for the Field Book App</a>
 200 <ul>
 201 <li class="chapter" data-level="12.2.1" data-path="using-fieldbook-app.html"><a href="using-fieldbook-app.html#creating-field-layout-files-by-using-field-book-tools-page."><i class="fa fa-check"></i><b>12.2.1</b> Creating “Field Layout Files” by using “Field Book Tools” page.</a></li>
 202 <li class="chapter" data-level="12.2.2" data-path="using-fieldbook-app.html"><a href="using-fieldbook-app.html#creating-field-layout-files-by-using-trial-detail-page."><i class="fa fa-check"></i><b>12.2.2</b> Creating “Field Layout Files” by using “Trial Detail” page.</a></li>
 203 </ul></li>
 204 <li class="chapter" data-level="12.3" data-path="using-fieldbook-app.html"><a href="using-fieldbook-app.html#creating-trait-files"><i class="fa fa-check"></i><b>12.3</b> Creating Trait Files for the Field Book App</a>
 205 <ul>
 206 <li class="chapter" data-level="12.3.1" data-path="using-fieldbook-app.html"><a href="using-fieldbook-app.html#creating-a-trait-list"><i class="fa fa-check"></i><b>12.3.1</b> Creating a Trait List</a></li>
 207 <li class="chapter" data-level="12.3.2" data-path="using-fieldbook-app.html"><a href="using-fieldbook-app.html#creating-a-trait-file"><i class="fa fa-check"></i><b>12.3.2</b> Creating a Trait File</a></li>
 208 </ul></li>
 209 <li class="chapter" data-level="12.4" data-path="using-fieldbook-app.html"><a href="using-fieldbook-app.html#transferring-files-from-your-computer-to-android-tablet"><i class="fa fa-check"></i><b>12.4</b> Transferring Files from Your Computer to Android Tablet</a>
 210 <ul>
 211 <li class="chapter" data-level="12.4.1" data-path="using-fieldbook-app.html"><a href="using-fieldbook-app.html#files-on-your-computer"><i class="fa fa-check"></i><b>12.4.1</b> Files on your computer</a></li>
 212 <li class="chapter" data-level="12.4.2" data-path="using-fieldbook-app.html"><a href="using-fieldbook-app.html#files-on-your-android-tablet"><i class="fa fa-check"></i><b>12.4.2</b> Files on your Android tablet</a></li>
 213 </ul></li>
 214 <li class="chapter" data-level="12.5" data-path="using-fieldbook-app.html"><a href="using-fieldbook-app.html#setting-up-field-book-app-for-data-collection"><i class="fa fa-check"></i><b>12.5</b> Setting up “Field Book App” for data collection</a></li>
 215 <li class="chapter" data-level="12.6" data-path="using-fieldbook-app.html"><a href="using-fieldbook-app.html#exporting-files-from-field-book-app"><i class="fa fa-check"></i><b>12.6</b> Exporting Files from Field Book App</a></li>
 216 <li class="chapter" data-level="12.7" data-path="using-fieldbook-app.html"><a href="using-fieldbook-app.html#uploading-pheno-files"><i class="fa fa-check"></i><b>12.7</b> Uploading Phenotype Files to an SGN database</a></li>
 217 </ul></li>
 218 <li class="chapter" data-level="13" data-path="managing-phenotypic-data.html"><a href="managing-phenotypic-data.html"><i class="fa fa-check"></i><b>13</b> Managing Phenotypic Data</a>
 219 <ul>
 220 <li class="chapter" data-level="13.1" data-path="managing-phenotypic-data.html"><a href="managing-phenotypic-data.html#uploading-fieldbook-phenotypes"><i class="fa fa-check"></i><b>13.1</b> Uploading Fieldbook Phenotypes</a>
 221 <ul>
 222 <li class="chapter" data-level="13.1.1" data-path="managing-phenotypic-data.html"><a href="managing-phenotypic-data.html#export-field-book-database-file"><i class="fa fa-check"></i><b>13.1.1</b> Export Field Book Database File</a></li>
 223 <li class="chapter" data-level="13.1.2" data-path="managing-phenotypic-data.html"><a href="managing-phenotypic-data.html#upload-field-book-database-file"><i class="fa fa-check"></i><b>13.1.2</b> Upload Field Book Database File</a></li>
 224 </ul></li>
 225 <li class="chapter" data-level="13.2" data-path="managing-phenotypic-data.html"><a href="managing-phenotypic-data.html#uploading-spreadsheet-phenotypes"><i class="fa fa-check"></i><b>13.2</b> Uploading Spreadsheet Phenotypes</a>
 226 <ul>
 227 <li class="chapter" data-level="13.2.1" data-path="managing-phenotypic-data.html"><a href="managing-phenotypic-data.html#generating-spreadsheet-file"><i class="fa fa-check"></i><b>13.2.1</b> Generating Spreadsheet File</a></li>
 228 <li class="chapter" data-level="13.2.2" data-path="managing-phenotypic-data.html"><a href="managing-phenotypic-data.html#uploading-spreadsheet-file"><i class="fa fa-check"></i><b>13.2.2</b> Uploading Spreadsheet File</a></li>
 229 </ul></li>
 230 </ul></li>
 231 <li class="chapter" data-level="14" data-path="managing-barcodes.html"><a href="managing-barcodes.html"><i class="fa fa-check"></i><b>14</b> Managing Barcodes</a></li>
 232 <li class="chapter" data-level="15" data-path="using-the-label-designer.html"><a href="using-the-label-designer.html"><i class="fa fa-check"></i><b>15</b> Using the Label Designer</a>
 233 <ul>
 234 <li class="chapter" data-level="15.0.1" data-path="using-the-label-designer.html"><a href="using-the-label-designer.html#first-select-a-datasource"><i class="fa fa-check"></i><b>15.0.1</b> First Select a Datasource</a></li>
 235 <li class="chapter" data-level="15.0.2" data-path="using-the-label-designer.html"><a href="using-the-label-designer.html#set-page-and-label-size"><i class="fa fa-check"></i><b>15.0.2</b> Set Page and Label Size</a></li>
 236 <li class="chapter" data-level="15.0.3" data-path="using-the-label-designer.html"><a href="using-the-label-designer.html#design-your-label"><i class="fa fa-check"></i><b>15.0.3</b> Design Your Label</a></li>
 237 <li class="chapter" data-level="15.0.4" data-path="using-the-label-designer.html"><a href="using-the-label-designer.html#adjust-formatting-save-and-download"><i class="fa fa-check"></i><b>15.0.4</b> Adjust Formatting, Save, and Download</a></li>
 238 </ul></li>
 239 <li class="chapter" data-level="16" data-path="managing-downloads.html"><a href="managing-downloads.html"><i class="fa fa-check"></i><b>16</b> Managing Downloads</a></li>
 240 <li class="chapter" data-level="17" data-path="managing-odk-data-collection.html"><a href="managing-odk-data-collection.html"><i class="fa fa-check"></i><b>17</b> Managing ODK Data Collection</a>
 241 <ul>
 242 <li class="chapter" data-level="17.1" data-path="managing-odk-data-collection.html"><a href="managing-odk-data-collection.html#ona-crossing-information"><i class="fa fa-check"></i><b>17.1</b> ONA Crossing Information</a>
 243 <ul>
 244 <li class="chapter" data-level="17.1.1" data-path="managing-odk-data-collection.html"><a href="managing-odk-data-collection.html#managing-ona-crossing-information"><i class="fa fa-check"></i><b>17.1.1</b> Managing ONA Crossing Information</a></li>
 245 <li class="chapter" data-level="17.1.2" data-path="managing-odk-data-collection.html"><a href="managing-odk-data-collection.html#reviewing-plant-status"><i class="fa fa-check"></i><b>17.1.2</b> Reviewing Plant Status</a></li>
 246 <li class="chapter" data-level="17.1.3" data-path="managing-odk-data-collection.html"><a href="managing-odk-data-collection.html#graphical-summary-for-performed-crosses"><i class="fa fa-check"></i><b>17.1.3</b> Graphical Summary For Performed Crosses</a></li>
 247 <li class="chapter" data-level="17.1.4" data-path="managing-odk-data-collection.html"><a href="managing-odk-data-collection.html#summary-information-for-performed-crosses"><i class="fa fa-check"></i><b>17.1.4</b> Summary Information For Performed Crosses</a></li>
 248 </ul></li>
 249 </ul></li>
 250 <li class="chapter" data-level="18" data-path="managing-tissue-samples.html"><a href="managing-tissue-samples.html"><i class="fa fa-check"></i><b>18</b> Managing Tissue Samples</a>
 251 <ul>
 252 <li class="chapter" data-level="18.1" data-path="managing-tissue-samples.html"><a href="managing-tissue-samples.html#tissue-samples-from-field-trials"><i class="fa fa-check"></i><b>18.1</b> Tissue samples from field trials</a></li>
 253 <li class="chapter" data-level="18.2" data-path="managing-tissue-samples.html"><a href="managing-tissue-samples.html#genotyping-plate-tissue-samples-96-or-384-well-plates"><i class="fa fa-check"></i><b>18.2</b> Genotyping Plate Tissue Samples (96 or 384 well plates)</a></li>
 254 </ul></li>
 255 <li class="chapter" data-level="19" data-path="managing-observation-variables.html"><a href="managing-observation-variables.html"><i class="fa fa-check"></i><b>19</b> Managing Observation Variables</a>
 256 <ul>
 257 <li class="chapter" data-level="19.1" data-path="managing-observation-variables.html"><a href="managing-observation-variables.html#managing-observation-variables-with-traits-methods-and-scales"><i class="fa fa-check"></i><b>19.1</b> Managing Observation Variables with Traits, Methods, and Scales</a></li>
 258 </ul></li>
 259 <li class="chapter" data-level="20" data-path="managing-image-data.html"><a href="managing-image-data.html"><i class="fa fa-check"></i><b>20</b> Managing Image Data</a>
 260 <ul>
 261 <li class="chapter" data-level="20.1" data-path="managing-image-data.html"><a href="managing-image-data.html#image-phenotyping-dashboard"><i class="fa fa-check"></i><b>20.1</b> Image-Phenotyping Dashboard</a></li>
 262 <li class="chapter" data-level="20.2" data-path="managing-image-data.html"><a href="managing-image-data.html#image-input"><i class="fa fa-check"></i><b>20.2</b> Image Input</a></li>
 263 <li class="chapter" data-level="20.3" data-path="managing-image-data.html"><a href="managing-image-data.html#standard-process"><i class="fa fa-check"></i><b>20.3</b> Standard Process</a></li>
 264 <li class="chapter" data-level="20.4" data-path="managing-image-data.html"><a href="managing-image-data.html#ground-control-points"><i class="fa fa-check"></i><b>20.4</b> Ground Control Points</a></li>
 265 </ul></li>
 266 <li class="chapter" data-level="21" data-path="managing-vcf-data.html"><a href="managing-vcf-data.html"><i class="fa fa-check"></i><b>21</b> Managing VCF Data</a>
 267 <ul>
 268 <li class="chapter" data-level="21.1" data-path="managing-vcf-data.html"><a href="managing-vcf-data.html#uploading-vcf-data"><i class="fa fa-check"></i><b>21.1</b> Uploading VCF Data</a></li>
 269 <li class="chapter" data-level="21.2" data-path="managing-vcf-data.html"><a href="managing-vcf-data.html#searching-and-downloading-vcf-data"><i class="fa fa-check"></i><b>21.2</b> Searching and Downloading VCF Data</a></li>
 270 <li class="chapter" data-level="21.3" data-path="managing-vcf-data.html"><a href="managing-vcf-data.html#searching-protocols"><i class="fa fa-check"></i><b>21.3</b> Searching Protocols</a></li>
 271 <li class="chapter" data-level="21.4" data-path="managing-vcf-data.html"><a href="managing-vcf-data.html#detail-pages-and-deletion"><i class="fa fa-check"></i><b>21.4</b> Detail Pages and Deletion</a></li>
 272 </ul></li>
 273 <li class="chapter" data-level="22" data-path="managing-spectral-data.html"><a href="managing-spectral-data.html"><i class="fa fa-check"></i><b>22</b> Managing Spectral Data</a>
 274 <ul>
 275 <li class="chapter" data-level="22.1" data-path="managing-spectral-data.html"><a href="managing-spectral-data.html#upload-spectral-data"><i class="fa fa-check"></i><b>22.1</b> Upload Spectral Data</a></li>
 276 <li class="chapter" data-level="22.2" data-path="managing-spectral-data.html"><a href="managing-spectral-data.html#evaluate-and-remove-outliers"><i class="fa fa-check"></i><b>22.2</b> Evaluate and Remove Outliers</a></li>
 277 <li class="chapter" data-level="22.3" data-path="managing-spectral-data.html"><a href="managing-spectral-data.html#plot-spectra"><i class="fa fa-check"></i><b>22.3</b> Plot Spectra</a></li>
 278 <li class="chapter" data-level="22.4" data-path="managing-spectral-data.html"><a href="managing-spectral-data.html#aggregate-spectra"><i class="fa fa-check"></i><b>22.4</b> Aggregate Spectra</a></li>
 279 <li class="chapter" data-level="22.5" data-path="managing-spectral-data.html"><a href="managing-spectral-data.html#references"><i class="fa fa-check"></i><b>22.5</b> References</a></li>
 280 </ul></li>
 281 <li class="chapter" data-level="23" data-path="managing-sequence-metadata.html"><a href="managing-sequence-metadata.html"><i class="fa fa-check"></i><b>23</b> Managing Sequence Metadata</a>
 282 <ul>
 283 <li class="chapter" data-level="23.1" data-path="managing-sequence-metadata.html"><a href="managing-sequence-metadata.html#what-is-sequence-metadata"><i class="fa fa-check"></i><b>23.1</b> What is Sequence Metadata?</a></li>
 284 <li class="chapter" data-level="23.2" data-path="managing-sequence-metadata.html"><a href="managing-sequence-metadata.html#loading-sequence-metadata"><i class="fa fa-check"></i><b>23.2</b> Loading Sequence Metadata</a></li>
 285 <li class="chapter" data-level="23.3" data-path="managing-sequence-metadata.html"><a href="managing-sequence-metadata.html#searching-sequence-metadata"><i class="fa fa-check"></i><b>23.3</b> Searching Sequence Metadata</a>
 286 <ul>
 287 <li class="chapter" data-level="23.3.1" data-path="managing-sequence-metadata.html"><a href="managing-sequence-metadata.html#basic-search"><i class="fa fa-check"></i><b>23.3.1</b> Basic Search</a></li>
 288 <li class="chapter" data-level="23.3.2" data-path="managing-sequence-metadata.html"><a href="managing-sequence-metadata.html#advanced-search"><i class="fa fa-check"></i><b>23.3.2</b> Advanced Search</a></li>
 289 </ul></li>
 290 <li class="chapter" data-level="23.4" data-path="managing-sequence-metadata.html"><a href="managing-sequence-metadata.html#marker-integration"><i class="fa fa-check"></i><b>23.4</b> Marker Integration</a></li>
 291 <li class="chapter" data-level="23.5" data-path="managing-sequence-metadata.html"><a href="managing-sequence-metadata.html#sequence-metadata-api"><i class="fa fa-check"></i><b>23.5</b> Sequence Metadata API</a></li>
 292 </ul></li>
 293 <li class="chapter" data-level="24" data-path="managing-outliers-in-dataset.html"><a href="managing-outliers-in-dataset.html"><i class="fa fa-check"></i><b>24</b> Managing Outliers in Dataset</a>
 294 <ul>
 295 <li class="chapter" data-level="24.1" data-path="managing-outliers-in-dataset.html"><a href="managing-outliers-in-dataset.html#what-is-outliers-functionality-in-dataset"><i class="fa fa-check"></i><b>24.1</b> What is Outliers Functionality in Dataset ?</a></li>
 296 <li class="chapter" data-level="24.2" data-path="managing-outliers-in-dataset.html"><a href="managing-outliers-in-dataset.html#accessing-trait-visualization"><i class="fa fa-check"></i><b>24.2</b> Accessing Trait Visualization</a></li>
 297 <li class="chapter" data-level="24.3" data-path="managing-outliers-in-dataset.html"><a href="managing-outliers-in-dataset.html#interpreting-visual-elements"><i class="fa fa-check"></i><b>24.3</b> Interpreting Visual Elements</a></li>
 298 <li class="chapter" data-level="24.4" data-path="managing-outliers-in-dataset.html"><a href="managing-outliers-in-dataset.html#choosing-cut-off-values"><i class="fa fa-check"></i><b>24.4</b> Choosing Cut-Off Values</a></li>
 299 <li class="chapter" data-level="24.5" data-path="managing-outliers-in-dataset.html"><a href="managing-outliers-in-dataset.html#setting-deviation-multiplier"><i class="fa fa-check"></i><b>24.5</b> Setting Deviation Multiplier</a></li>
 300 <li class="chapter" data-level="24.6" data-path="managing-outliers-in-dataset.html"><a href="managing-outliers-in-dataset.html#utilizing-graph-controls"><i class="fa fa-check"></i><b>24.6</b> Utilizing Graph Controls</a></li>
 301 </ul></li>
 302 <li class="chapter" data-level="25" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html"><i class="fa fa-check"></i><b>25</b> Data Analysis Tools</a>
 303 <ul>
 304 <li class="chapter" data-level="25.1" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#selection-index"><i class="fa fa-check"></i><b>25.1</b> Selection Index</a></li>
 305 <li class="chapter" data-level="25.2" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-selection"><i class="fa fa-check"></i><b>25.2</b> Genomic Selection</a>
 306 <ul>
 307 <li class="chapter" data-level="25.2.1" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#method-1"><i class="fa fa-check"></i><b>25.2.1</b> Building a Model - Method 1:</a></li>
 308 <li class="chapter" data-level="25.2.2" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#method-2"><i class="fa fa-check"></i><b>25.2.2</b> Building a Model - Method 2</a></li>
 309 <li class="chapter" data-level="25.2.3" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#building-a-model---method-3"><i class="fa fa-check"></i><b>25.2.3</b> Building a Model - Method 3</a></li>
 310 </ul></li>
 311 <li class="chapter" data-level="25.3" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genome-browsing"><i class="fa fa-check"></i><b>25.3</b> Genome Browsing</a>
 312 <ul>
 313 <li class="chapter" data-level="25.3.1" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#browsing-genotype-data-by-accession"><i class="fa fa-check"></i><b>25.3.1</b> Browsing Genotype data by Accession</a></li>
 314 <li class="chapter" data-level="25.3.2" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#browsing-genotype-data-by-trial"><i class="fa fa-check"></i><b>25.3.2</b> Browsing Genotype data by Trial</a></li>
 315 </ul></li>
 316 <li class="chapter" data-level="25.4" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#principal-component-analysis-pca"><i class="fa fa-check"></i><b>25.4</b> Principal Component Analysis (PCA)</a></li>
 317 <li class="chapter" data-level="25.5" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#anova"><i class="fa fa-check"></i><b>25.5</b> ANOVA</a></li>
 318 <li class="chapter" data-level="25.6" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#clustering-k-means-hierarchical"><i class="fa fa-check"></i><b>25.6</b> Clustering (K-Means, Hierarchical)</a></li>
 319 <li class="chapter" data-level="25.7" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genetic-gain"><i class="fa fa-check"></i><b>25.7</b> Genetic Gain</a></li>
 320 <li class="chapter" data-level="25.8" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#kinship-and-inbreeding-coefficients"><i class="fa fa-check"></i><b>25.8</b> Kinship and Inbreeding Coefficients</a></li>
 321 <li class="chapter" data-level="25.9" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#creating-crossing-groups"><i class="fa fa-check"></i><b>25.9</b> Creating Crossing Groups</a></li>
 322 <li class="chapter" data-level="25.10" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#search-wizard-genomic-relationship-matrix-grm-download"><i class="fa fa-check"></i><b>25.10</b> Search Wizard Genomic Relationship Matrix (GRM) Download</a></li>
 323 <li class="chapter" data-level="25.11" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#search-wizard-genome-wide-association-study-gwas"><i class="fa fa-check"></i><b>25.11</b> Search Wizard Genome Wide Association Study (GWAS)</a></li>
 324 <li class="chapter" data-level="25.12" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#spectral-analysis"><i class="fa fa-check"></i><b>25.12</b> Spectral Analysis</a>
 325 <ul>
 326 <li class="chapter" data-level="25.12.1" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#dataset-selection"><i class="fa fa-check"></i><b>25.12.1</b> Dataset selection</a></li>
 327 <li class="chapter" data-level="25.12.2" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#cross-validation"><i class="fa fa-check"></i><b>25.12.2</b> Cross-validation</a></li>
 328 <li class="chapter" data-level="25.12.3" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#preprocessing"><i class="fa fa-check"></i><b>25.12.3</b> Preprocessing</a></li>
 329 <li class="chapter" data-level="25.12.4" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#algorithms"><i class="fa fa-check"></i><b>25.12.4</b> Algorithms</a></li>
 330 <li class="chapter" data-level="25.12.5" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#output-common-model-summary-statistics"><i class="fa fa-check"></i><b>25.12.5</b> Output: common model summary statistics</a></li>
 331 <li class="chapter" data-level="25.12.6" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#export-model-for-later-use"><i class="fa fa-check"></i><b>25.12.6</b> Export model for later use</a></li>
 332 <li class="chapter" data-level="25.12.7" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#predict-phenotypes-from-an-exported-model-routine-use"><i class="fa fa-check"></i><b>25.12.7</b> Predict phenotypes from an exported model (routine use)</a></li>
 333 <li class="chapter" data-level="25.12.8" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#faq"><i class="fa fa-check"></i><b>25.12.8</b> FAQ</a></li>
 334 </ul></li>
 335 <li class="chapter" data-level="25.13" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#general-mixed-model-tool"><i class="fa fa-check"></i><b>25.13</b> General Mixed Model Tool</a></li>
 336 <li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gcpc"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GCPC)</a></li>
 337 </ul></li>
 338 <li class="divider"></li>
 339 <li><a href="https://bookdown.org/" target="blank">Published with bookdown</a></li>
 340 </ul>
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 349             <i class="fa fa-circle-o-notch fa-spin"></i><a href="./">User Manual of Breedbase</a>
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 356             <section class="normal" id="section-">
 357 <div id="managing-spectral-data" class="section level1 hasAnchor" number="22">
 358 <h1><span class="header-section-number">Chapter 22</span> Managing Spectral Data<a href="managing-spectral-data.html#managing-spectral-data" class="anchor-section" aria-label="Anchor link to header"></a></h1>
 359 <p>Breedbase has implemented a flexible spectral data storage protocol that handles spectral data irrespective of the source spectrometer. Spectral data storage and analysis in Breedbase makes use of the R package <em>waves</em> for outlier identification, plotting, sample aggregation, and prediction model training.</p>
 360 <p><img src="assets/images/waves_breedbase_schema.png" width="95%" style="display: block; margin: auto;" /></p>
 361 <hr />
 362 <div id="upload-spectral-data" class="section level2 hasAnchor" number="22.1">
 363 <h2><span class="header-section-number">22.1</span> Upload Spectral Data<a href="managing-spectral-data.html#upload-spectral-data" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 364 <p>Spectral data can be added as a CSV file that includes metadata in the leftmost columns followed by one column per spectral measurement to the right. Rows represent a single scan or sample, each with a unique ID that must match to a Breedbase observationUnitName. Future data transfer using <a href="https://brapi.org">BrAPI</a> will allow for interoperability with data collection software.</p>
 365 <p>To upload a spectral dataset, navigate to the ‘Manage NIRS Data’ page by selecting ‘NIRS’ in the ‘Manage’ menu and click the blue ‘Upload NIRS’ button. This will open an upload workflow. A link to the required file format and an example .csv file can be found by clicking in the light blue info box in this workflow. Another example of the file format is shown below.</p>
 366 <ul>
 367 <li><strong>id</strong>: Optional identifier for each NIRS read. The id must be an integer.</li>
 368 <li><strong>sampling_id</strong>: Optional identifier for each sample. Strings are allowed.</li>
 369 <li><strong>sampling_date</strong>: Optional field. The format allowed is: YYYY-MM-DD.</li>
 370 <li><strong>observationunit_name</strong>: Required field that matches existing data in the database. It can be the plot name, subplots, plant name, or tissue sample, depending how your trial is designed.</li>
 371 <li><strong>device_id</strong>: Optional field to identify your device. Strings are allowed.</li>
 372 <li><strong>device_type</strong>: Required field. It is possible upload data for a single device type. They can be: SCiO, QST, Foss6500, BunchiN500, or LinkSquare.</li>
 373 <li><strong>comments</strong>: Optional field for general comments.
 374 All other columns are required wavelengths. You can add how many columns you want upload – there is no limit.</li>
 375 </ul>
 376 <p><img src="assets/images/manage_NIRS_main_display.png" width="95%" style="display: block; margin: auto;" /></p>
 377 <p><img src="assets/images/upload_NIRS_example_format.png" width="95%" style="display: block; margin: auto;" /></p>
 378 </div>
 379 <div id="evaluate-and-remove-outliers" class="section level2 hasAnchor" number="22.2">
 380 <h2><span class="header-section-number">22.2</span> Evaluate and Remove Outliers<a href="managing-spectral-data.html#evaluate-and-remove-outliers" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 381 <p>Spectral calibration models can be heavily affected by the presence of outliers, whether they come from spectrometer spectral artifacts or user errors. Mahalanobis distance (Mahalanobis, 1936) is a measure of the distance between a single observation and a larger distribution and is commonly used in the identification of outliers in a multivariate space (Des Maesschalck et al, 2000). The <em>FilterSpectra()</em> function in the R package <a href="https://CRAN.R-project.org/package=waves"><em>waves</em></a> calculates the Mahalanobis distance of each observation in a given spectral matrix using the <em>stats::mahalanobis()</em> function. Observations are identified as outliers if the squared distance is greater than the 95th percentile of a <span class="math inline">\(\chi\)</span><sup>2</sup>-distribution with <em>p</em> degrees of freedom, where <em>p</em> is the number of columns (wavelengths) in the spectral matrix (Johnson and Wichern, 2007). In Breedbase, this procedure is applied on a per-dataset basis on upload and outliers are given binary tags “Outlier.”</p>
 382 </div>
 383 <div id="plot-spectra" class="section level2 hasAnchor" number="22.3">
 384 <h2><span class="header-section-number">22.3</span> Plot Spectra<a href="managing-spectral-data.html#plot-spectra" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 385 <p>After outlier identification, a plot is generated using the <em>PlotSpectra()</em> function in <a href="https://CRAN.R-project.org/package=waves"><em>waves</em></a>. This function uses the filtered spectra and <em>ggplot2::ggplot()</em> to create a line plot with outliers highlighted by color. A list of rows identified as outliers are shown beneath the plot. Plots are saved as .png files and linked to the original input datasets. Plot image files can be downloaded via the “Download Plot” button in the upload workflow.</p>
 386 <p><img src="assets/images/upload_NIRS_plot_example.png" width="95%" style="display: block; margin: auto;" /></p>
 387 </div>
 388 <div id="aggregate-spectra" class="section level2 hasAnchor" number="22.4">
 389 <h2><span class="header-section-number">22.4</span> Aggregate Spectra<a href="managing-spectral-data.html#aggregate-spectra" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 390 <p>To obtain a stable and reliable spectral profile, most spectrometer manufacturers recommend that multiple spectral scans are captured for each sample. While some spectrometers aggregate these scans internally, many do not, requiring the user to do so before analysis can take place. Breedbase handles these cases upon data upload following filtering steps by calling the <em>AggregateSpectra()</em> function from <a href="https://CRAN.R-project.org/package=waves"><em>waves</em></a>, saving the aggregated scans for future access through the search wizard feature. Scans are aggregated by sample mean (e.g. plot-level basis) according to the provided observationUnitName field. After aggregation, the user exits the upload workflow and the raw data file is saved in the upload archive.</p>
 391 </div>
 392 <div id="references" class="section level2 hasAnchor" number="22.5">
 393 <h2><span class="header-section-number">22.5</span> References<a href="managing-spectral-data.html#references" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 394 <ul>
 395 <li>De Maesschalck, R., Jouan-Rimbaud, D., and Massart, D. L. (2000). The Mahalanobis distance. Chemom. Intell. Lab. Syst. 50(1): 1-18.</li>
 396 <li>Johnson, R. A. &amp; Wichern, D. W. (2007). Applied Multivariate Statistical Analysis (6th Edition). p 773.</li>
 397 <li>Mahalanobis, P. C. (1936). On the generalized distance in statistics. National Institute of Science of India.</li>
 398 </ul>
 399 <p><a href="data-analysis-tools.html#spectral-analysis"><strong>Analysis tool documentation</strong></a></p>
 400
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