{"@type": "dcat:Dataset", "accessLevel": "public", "bureauCode": ["005:18"], "contactPoint": {"fn": "Read, Quentin", "hasEmail": "mailto:quentin.read@usda.gov"}, "description": "<p>This dataset contains all data and code necessary to reproduce the analysis described under the heading \"Experiment 3\" in the manuscript:</p>\n<p>Taliercio, E., Eickholt, D., Read, Q. D., Carter, T., Waldeck, N., & Fallen, B. (2023). Parental choice and seed size impact the uprightness of progeny from interspecific <em>Glycine</em> hybridizations. <em>Crop Science</em>. <a href=\"https://doi.org/10.1002/csc2.21015\">https://doi.org/10.1002/csc2.21015</a></p>\n<p>The attached files are:</p>\n<ul>\n<li>\n<p><code>G_max_G_soja_seedweight_seedcolor_analysis.Rmd</code>: RMarkdown notebook containing all analysis code. The CSV data files should be placed in a subdirectory called data within the working directory from which the notebook is rendered.</p>\n</li>\n<li>\n<p><code>G_max_G_soja_seedweight_seedcolor_analysis.html</code>: Rendered HTML output from RMarkdown notebook, including figures, tables, and explanatory text.</p>\n</li>\n<li>\n<p><code>counts_seedwt.csv</code>: CSV file containing the number of progeny selected and average 100-seed weight data for each combination of cross, size class, and replicate. Columns are:</p>\n<ul>\n<li><strong>F3_location:</strong> text identifier of F3 nursery location, either <code>\"CLA\"</code> or <code>\"FF\"</code></li>\n<li><strong>plot:</strong> numeric ID of plot</li>\n<li><strong>pop:</strong> numeric ID of population</li>\n<li><strong>max:</strong> name of G. max parent</li>\n<li><strong>soja:</strong> name of G. soja parent</li>\n<li><strong>F2_location:</strong> text identifier of F2 nursery location, either <code>\"Caswell\"</code> or <code>\"Hugo\"</code></li>\n<li><strong>n_planted:</strong> number of seeds planted (raw)</li>\n<li><strong>n_selected:</strong> number of progeny selected</li>\n<li><strong>size_ordered:</strong> seed size class, to be converted to an ordered factor</li>\n<li><strong>size_combined:</strong> seed size class aggregated to fewer unique levels</li>\n<li><strong>ave_100sw:</strong> average 100-seed weight for the given size class</li>\n<li><strong>n_planted_trials:</strong> number of seeds planted rounded to nearest integer</li>\n</ul>\n</li>\n<li>\n<p><code>seedcolor.csv</code>: CSV file with additional data on number of seeds of each color by population. Columns are:</p>\n<ul>\n<li><strong>cross:</strong> text identifier of cross</li>\n<li><strong>line:</strong> text identifier of line</li>\n<li><strong>light:</strong> number of light seeds</li>\n<li><strong>mid:</strong> number of mid-green seeds</li>\n<li><strong>brown:</strong> number of brown seeds</li>\n<li><strong>dark:</strong> number of dark or black seeds</li>\n<li><strong>population:</strong> identifier of population type (F2 derived or selected)</li>\n<li><strong>max:</strong> name of <em>G. max</em> parent</li>\n<li><strong>n_total:</strong> sum of the light, mid, brown, and dark columns</li>\n<li><strong>soja:</strong> name of <em>G. soja</em> parent</li>\n</ul>\n</li>\n</ul>\n<p>The data processing and analysis pipeline in the RMarkdown notebook includes:</p>\n<ul>\n<li>Importing the data (slightly cleaned version is provided)</li>\n<li>Creating boxplots of proportion selected by cross, nursery location, and size class</li>\n<li>Fitting logistic GLMM to estimate the probability of selection as a function of parent, 100-seed weight, and their interactions</li>\n<li>Extracting and plotting random effect estimates from model</li>\n<li>Calculating and plotting estimated marginal means from model</li>\n<li>Taking contrasts between pairs of estimated marginal means and trends</li>\n<li>Calculating Bayes Factors associated with the contrasts</li>\n<li>Generating figures and tables for all above results</li>\n<li>Additional seed color analysis: importing data (slightly cleaned version is provided)</li>\n<li>Additional seed color analysis: drawing exploratory bar plot</li>\n<li>Additional seed color analysis: fitting multinomial GLM modeling the proportion of seeds with each color as a function of population</li>\n<li>Additional seed color analysis: generating expected value predictions from GLM and taking contrasts</li>\n<li>Additional seed color analysis: creating figures and tables for model results</li>\n</ul>\n<p>This research was funded by CRIS 6070-21220-069-00D, United Soybean Board Project # 2333-203-0101, and falls under National Program NP301.</p>\n<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: RMarkdown document with all analysis code.</p> <p>File Name: G_max_G_soja_seedweight_seedcolor_analysis.Rmd</p></li><br><li><p>Resource Title: Rendered HTML version of notebook.</p> <p>File Name: G_max_G_soja_seedweight_seedcolor_analysis.html</p></li><br><li><p>Resource Title: Progeny counts and seed weight data.</p> <p>File Name: counts_seedwt.csv</p></li><br><li><p>Resource Title: Seed color counts data.</p> <p>File Name: seedcolor.csv</p></li></ul>", "distribution": [{"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/44532833", "format": "Rmd", "mediaType": "text/plain", "title": "G_max_G_soja_seedweight_seedcolor_analysis.Rmd"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/44532836", "format": "html", "mediaType": "text/html", "title": "G_max_G_soja_seedweight_seedcolor_analysis.html"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/44532848", "format": "csv", "mediaType": "text/plain", "title": "counts_seedwt.csv"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/44532854", "format": "csv", "mediaType": "text/plain", "title": "seedcolor.csv"}], "identifier": "10.15482/USDA.ADC/1528604", "keyword": ["Glycine max", "Glycine soja", "soybean", "seed size", "uprightness", "hybrids", "plant breeding", "response to selection", "NP301", "data.gov", "ARS"], "license": "https://www.usa.gov/publicdomain/label/1.0/", "modified": "2025-11-21", "programCode": ["005:040"], "publisher": {"@type": "org:Organization", "name": "Agricultural Research Service"}, "spatial": "{\"type\": \"MultiPoint\", \"coordinates\": [[-77.58, 35.26], [-77.79, 35.95], [-78.46, 35.65], [-67, 18.45]]}", "temporal": "2013-01-01/2021-12-31", "title": "Data and code from: The Impacts of Parental Choice and Intrapopulation Selection for Seed Size on the Uprightness of Progeny Derived from Interspecific Hybridization between Glycine max and Glycine soja"}