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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

Published by Agricultural Research Service | Department of Agriculture | Catalog Last Checked: August 03, 2026 at 05:01 PM | Dataset Last Updated: July 17, 2026
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 “Distribution of Pseudomonas amygdali pv. loropetali in the twig phylloplane of Loropetalum chinense shrubs in ornamental plant nurseries.”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 Pseudomonas amygdali pv. loropetali (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’s 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.Included filesPALqantitData.csv: Copy numbers obtained from the PAL qPCR.PALplantData_withcoords.csv: Spatial locations (row and column coordinates) of surveyed plants.SymptSpatial.csv: Row and column coordinates and field symptom rating of surveyed plants.Loropetalum_PAL_qPCR_analysis.Rmd: 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.Loropetalum_PAL_qPCR_analysis.html: Rendered output of .Rmd notebookcolumn_metadata.pdf: Description of columns in .csv files.

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Complete Metadata
@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 “Distribution of <i>Pseudomonas amygdali</i> pv. <i>loropetali</i> in the twig phylloplane of <i>Loropetalum chinense</i> shrubs in ornamental plant nurseries.”</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’s <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",
    "title": "PALplantData_withcoords.csv",
    "format": "csv",
    "mediaType": "text/csv",
    "downloadURL": "https://ndownloader.figshare.com/files/56607011"
  },
  {
    "@type": "dcat:Distribution",
    "title": "PALqantitData.csv",
    "format": "csv",
    "mediaType": "text/csv",
    "downloadURL": "https://ndownloader.figshare.com/files/56607014"
  },
  {
    "@type": "dcat:Distribution",
    "title": "SymptSpatial.csv",
    "format": "csv",
    "mediaType": "text/csv",
    "downloadURL": "https://ndownloader.figshare.com/files/56607017"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Loropetalum_PAL_qPCR_analysis.Rmd",
    "format": "Rmd",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/56607023"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Loropetalum_PAL_qPCR_analysis.html",
    "format": "html",
    "mediaType": "text/html",
    "downloadURL": "https://ndownloader.figshare.com/files/56607026"
  },
  {
    "@type": "dcat:Distribution",
    "title": "column_metadata.pdf",
    "format": "pdf",
    "mediaType": "application/pdf",
    "downloadURL": "https://ndownloader.figshare.com/files/56607029"
  }
]
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 
{
  "name": "Agricultural Research Service",
  "@type": "org:Organization"
}
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

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