{"@type": "dcat:Dataset", "accessLevel": "public", "bureauCode": ["005:18"], "contactPoint": {"fn": "Read, Quentin D.", "hasEmail": "mailto:quentin.read@usda.gov"}, "description": "<p dir=\"ltr\">This dataset contains all raw data and R statistical software code needed to reproduce the data processing, statistical model fitting, and data/model visualizations presented in the associated manuscript, titled \u201cDistribution of <i>Pseudomonas amygdali</i> pv. <i>loropetali</i> in the twig phylloplane of <i>Loropetalum chinense</i> shrubs in ornamental plant nurseries.\u201d</p><p dir=\"ltr\">The manuscript describes a survey done across six ornamental plant nurseries to assess the prevalence of galling symptoms in loropetalum plants caused by the bacterium <i>Pseudomonas amygdali </i>pv. <i>loropetali </i>(PAL), and the abundance of the PAL bacterium. The presence of symptoms was assessed, and the abundance of PAL estimated with a PAL-specific qPCR method, on twigs at three height strata on each plant. In the associated analysis notebook, we present a spatial analysis of the symptom prevalence (Moran\u2019s <i>I </i>and logistic regression), and a Gamma generalized linear mixed model comparing PAL abundance across nurseries, height strata, and galled versus gall-free plants. Significant differences in PAL number were found between nurseries, between strata, and between galled and gall-free plants. The raw data are provided here in .csv format, and the R statistical software code in an RMarkdown notebook, with .Rmd source code and rendered .html output.</p><h2>Included files</h2><ul><li><b>PALqantitData.csv</b>: Copy numbers obtained from the PAL qPCR.</li><li><b>PALplantData_withcoords.csv</b>: Spatial locations (row and column coordinates) of surveyed plants.</li><li><b>SymptSpatial.csv</b>: Row and column coordinates and field symptom rating of surveyed plants.</li><li><b>Loropetalum_PAL_qPCR_analysis.Rmd</b>: RMarkdown notebook containing all R statistical software code to import and process data, fit statistical models, create maps, and create graphs and tables of raw data and model output.</li><li><b>Loropetalum_PAL_qPCR_analysis.html</b>: Rendered output of .Rmd notebook</li><li><b>column_metadata.pdf</b>: Description of columns in .csv files.</li></ul><p><br></p>", "distribution": [{"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/56607011", "format": "csv", "mediaType": "text/csv", "title": "PALplantData_withcoords.csv"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/56607014", "format": "csv", "mediaType": "text/csv", "title": "PALqantitData.csv"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/56607017", "format": "csv", "mediaType": "text/csv", "title": "SymptSpatial.csv"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/56607023", "format": "Rmd", "mediaType": "text/plain", "title": "Loropetalum_PAL_qPCR_analysis.Rmd"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/56607026", "format": "html", "mediaType": "text/html", "title": "Loropetalum_PAL_qPCR_analysis.html"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/56607029", "format": "pdf", "mediaType": "application/pdf", "title": "column_metadata.pdf"}], "identifier": "10.15482/USDA.ADC/29647553.v1", "keyword": ["Loropetalum chinense", "Pseudomonas amygdali pv. loropetali", "galls", "horticulture", "nursery", "ornamental plants", "qPCR", "source code"], "license": "https://creativecommons.org/publicdomain/zero/1.0/", "modified": "2026-07-17", "programCode": ["005:040"], "publisher": {"@type": "org:Organization", "name": "Agricultural Research Service"}, "temporal": "2023-01-01/2024-12-31", "title": "Data and code from: Distribution of <i>Pseudomonas amygdali</i> pv. <i>loropetali</i> in the twig phylloplane of <i>Loropetalum chinense</i> shrubs in ornamental plant nurseries"}