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Data and code from: Evaluation, release, and utilization of soybean lines for improved resistance to Phomopsis seed decay and enhanced seed quality
This dataset contains all raw data (CSV) and R software code (RMarkdown notebook) required to reproduce the analyses, figures, and tables presented in the associated manuscript. The study is a comparison of Phomopsis seed decay (PSD) infection rates among different soybean genotypes, with data from an early and late maturity group test in each of five years, 2019-2023. The data consist of binary PSD presence-absence observations on five seeds per plate per genotype, with multiple replicate plates in each test. The statistical analysis is a binomial generalized linear mixed model. Probabilities of infections and their confidence intervals are estimated and compared among genotypes within each test, and code to generate figures and tables follows.The following files are included:Li_PSD_2019_2023_clean.csv: Primary data filedata_dictionary.csv: Description of columns in primary data filePSD_compareentries_code_supplement.Rmd: RMarkdown notebook with R code to analyze data; a HTML file with the same name is the rendered output of the notebookearly_and_late_contrast_tables.xlsx: Output of analysis, pairwise contrasts between genotypesearly_and_late_mean_tables.xlsx: Output of analysis, estimated infection probabilities for each genotype
Resources
6 resources available
-
Li_PSD_2019_2023_clean.csv
CSV -
data_dictionary.csv
CSV -
PSD_compareentries_code_supplement.Rmd
RMD -
PSD_compareentries_code_supplement.html
HTML -
early_and_late_contrast_tables.xlsx
XLSX -
early_and_late_mean_tables.xlsx
XLSX
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Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| accrualPeriodicity | R/P1Y |
| bureauCode |
[ "005:18" ] |
| contactPoint |
{ "fn": "Read, Quentin D.", "hasEmail": "mailto:quentin.read@usda.gov" } |
| description | <p dir="ltr">This dataset contains all raw data (CSV) and R software code (RMarkdown notebook) required to reproduce the analyses, figures, and tables presented in the associated manuscript. The study is a comparison of Phomopsis seed decay (PSD) infection rates among different soybean genotypes, with data from an early and late maturity group test in each of five years, 2019-2023. The data consist of binary PSD presence-absence observations on five seeds per plate per genotype, with multiple replicate plates in each test. The statistical analysis is a binomial generalized linear mixed model. Probabilities of infections and their confidence intervals are estimated and compared among genotypes within each test, and code to generate figures and tables follows.</p><p dir="ltr">The following files are included:</p><p><br></p><ul><li>Li_PSD_2019_2023_clean.csv: Primary data file</li><li>data_dictionary.csv: Description of columns in primary data file</li><li>PSD_compareentries_code_supplement.Rmd: RMarkdown notebook with R code to analyze data; a HTML file with the same name is the rendered output of the notebook</li><li>early_and_late_contrast_tables.xlsx: Output of analysis, pairwise contrasts between genotypes</li><li>early_and_late_mean_tables.xlsx: Output of analysis, estimated infection probabilities for each genotype</li></ul><p></p> |
| distribution |
[ { "@type": "dcat:Distribution", "title": "Li_PSD_2019_2023_clean.csv", "format": "csv", "mediaType": "text/csv", "downloadURL": "https://ndownloader.figshare.com/files/64140148" }, { "@type": "dcat:Distribution", "title": "data_dictionary.csv", "format": "csv", "mediaType": "text/csv", "downloadURL": "https://ndownloader.figshare.com/files/64140151" }, { "@type": "dcat:Distribution", "title": "PSD_compareentries_code_supplement.Rmd", "format": "Rmd", "mediaType": "text/plain", "downloadURL": "https://ndownloader.figshare.com/files/64140154" }, { "@type": "dcat:Distribution", "title": "PSD_compareentries_code_supplement.html", "format": "html", "mediaType": "text/html", "downloadURL": "https://ndownloader.figshare.com/files/64140157" }, { "@type": "dcat:Distribution", "title": "early_and_late_contrast_tables.xlsx", "format": "xlsx", "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "downloadURL": "https://ndownloader.figshare.com/files/64140334" }, { "@type": "dcat:Distribution", "title": "early_and_late_mean_tables.xlsx", "format": "xlsx", "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "downloadURL": "https://ndownloader.figshare.com/files/64140337" } ] |
| identifier | 10.15482/USDA.ADC/32091706.v2 |
| keyword |
[ "Diaporthe longicolla", "Glycine max", "PSD", "Phomopsis", "Phomopsis longicolla", "Phomopsis seed decay", "evaluation", "resistance", "source code", "soybean", "soybean disease", "soybean disease resistance" ] |
| license | https://creativecommons.org/publicdomain/zero/1.0/ |
| modified | 2026-07-14 |
| programCode |
[ "005:040" ] |
| publisher |
{ "name": "Agricultural Research Service", "@type": "org:Organization" } |
| temporal | 2019-01-01/2023-12-31 |
| title | Data and code from: Evaluation, release, and utilization of soybean lines for improved resistance to Phomopsis seed decay and enhanced seed quality |
