{
  "_id": "6a2759c324555f66ed53134a",
  "Package": "grayleafspotr",
  "Title": "Quantitative Analysis of Gray Leaf Spot Colonies from Plate\nImages",
  "Version": "0.99.2",
  "Authors@R": "person(\ngiven = \"Rohan\",\nfamily = \"R\",\nemail = \"phonics-tiffs1i@icloud.com\",\nrole = c(\"aut\", \"cre\", \"cph\")\n)",
  "Description": "Quantitative phenotyping of gray leaf spot (Cercospora\nzeae-maydis) fungal colonies grown on petri dishes. The package\nsegments colonies from time-lapse plate photographs using a\nbundled SmallUNet deep-learning model, extracts morphometric\nand texture features (area, eccentricity, crack coverage,\nradial profile), and provides tidy result objects together with\ntemplate ggplot2 visualisations. Python dependencies are\nmanaged automatically through basilisk; no manual environment\nsetup is required.",
  "License": "Apache License (>= 2.0) | file LICENSE",
  "URL": "https://rotsl.github.io/grayleafspotr,\nhttps://github.com/rotsl/grayleafspotr",
  "BugReports": "https://github.com/rotsl/grayleafspotr/issues",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "biocViews": "Software, Preprocessing, Visualization, Classification,\nFeatureExtraction",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "libpng-dev python3 libx11-dev",
  "Repository": "https://rotsl.r-universe.dev",
  "Date/Publication": "2026-06-08 23:55:24 UTC",
  "RemoteUrl": "https://github.com/rotsl/grayleafspotr",
  "RemoteRef": "HEAD",
  "RemoteSha": "6a87fafd1c3440832e512ea536277003ab055cda",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-09 00:05:22 UTC",
    "User": "root"
  },
  "Author": "Rohan R [aut, cre, cph]",
  "Maintainer": "Rohan R <phonics-tiffs1i@icloud.com>",
  "MD5sum": "098e39c3735db9f660391eb757468b4d",
  "_user": "rotsl",
  "_type": "src",
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  "_created": "2026-06-09T00:05:22.000Z",
  "_published": "2026-06-09T00:09:39.051Z",
  "_distro": "noble",
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    "author": "rotsl <wot25kir.nbi@gmail.com>",
    "committer": "rotsl <wot25kir.nbi@gmail.com>",
    "message": "Add devel branch to workflow triggers\n\nExtend push and pull_request triggers in BiocCheck and R-CMD-check\nworkflows\n",
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    "description": "Me try idea. Idea from wires, robots, biology brain stuff, number machine. Sometimes idea punch back. Me punch again",
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  "_updates": [
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    "preprocessing",
    "visualization",
    "classification",
    "featureextraction",
    "biological-data-analysis",
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    "huggingface",
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    "extra/citation.json",
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    "example_grayleafspot_results",
    "grayleafspot_analyze",
    "grayleafspot_download_model",
    "grayleafspot_python_available",
    "grayleafspot_python_executable",
    "grayleafspot_run",
    "launch_grayleafspotr",
    "plot_colony_expansion",
    "plot_feature_heatmap",
    "plot_growth_roughness",
    "plot_radial_growth_area",
    "plot_radial_profile",
    "plot_shape_vs_stress",
    "plot_stress_remodeling",
    "plot_texture_organization",
    "read_grayleafspot_results",
    "write_grayleafspot_results"
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    {
      "page": "as_grayleafspot_growth_data",
      "title": "Coerce a grayleafspot run object to a tidy data frame",
      "topics": [
        "as_grayleafspot_growth_data"
      ]
    },
    {
      "page": "example_grayleafspot_results",
      "title": "Load the built-in example grayleafspot run",
      "topics": [
        "example_grayleafspot_results"
      ]
    },
    {
      "page": "grayleafspot_analyze",
      "title": "Analyze plate images with the SmallUNet pipeline",
      "topics": [
        "grayleafspot_analyze"
      ]
    },
    {
      "page": "grayleafspot_download_model",
      "title": "Download the SmallUNet segmentation model",
      "topics": [
        "grayleafspot_download_model"
      ]
    },
    {
      "page": "grayleafspot_python_available",
      "title": "Check whether the Python ML dependencies are available",
      "topics": [
        "grayleafspot_python_available"
      ]
    },
    {
      "page": "grayleafspot_python_executable",
      "title": "Return the Python executable used by the grayleafspot pipeline",
      "topics": [
        "grayleafspot_python_executable"
      ]
    },
    {
      "page": "grayleafspot_run",
      "title": "Run the gray leaf spot pipeline — simplified entry point",
      "topics": [
        "grayleafspot_run"
      ]
    },
    {
      "page": "launch_grayleafspotr",
      "title": "Launch the grayleafspotr Shiny app",
      "topics": [
        "launch_grayleafspotr"
      ]
    },
    {
      "page": "plot_colony_expansion",
      "title": "Plot colony expansion over time",
      "topics": [
        "plot_colony_expansion"
      ]
    },
    {
      "page": "plot_feature_heatmap",
      "title": "Pearson correlation heatmap of numeric morphology features",
      "topics": [
        "plot_feature_heatmap"
      ]
    },
    {
      "page": "plot_growth_roughness",
      "title": "Plot relative growth rate and edge roughness",
      "topics": [
        "plot_growth_roughness"
      ]
    },
    {
      "page": "plot_radial_growth_area",
      "title": "Plot radial growth rate and colony area by plate over time",
      "topics": [
        "plot_radial_growth_area"
      ]
    },
    {
      "page": "plot_radial_profile",
      "title": "Plot the radial intensity profile from the first image in a run",
      "topics": [
        "plot_radial_profile"
      ]
    },
    {
      "page": "plot_shape_vs_stress",
      "title": "Scatter plot of colony shape vs crack stress",
      "topics": [
        "plot_shape_vs_stress"
      ]
    },
    {
      "page": "plot_stress_remodeling",
      "title": "Plot crack coverage and crack count over time",
      "topics": [
        "plot_stress_remodeling"
      ]
    },
    {
      "page": "plot_texture_organization",
      "title": "Plot texture entropy and center-to-edge intensity delta over time",
      "topics": [
        "plot_texture_organization"
      ]
    },
    {
      "page": "read_grayleafspot_results",
      "title": "Read a saved grayleafspot run from disk",
      "topics": [
        "read_grayleafspot_results"
      ]
    },
    {
      "page": "write_grayleafspot_results",
      "title": "Write grayleafspot results to disk",
      "topics": [
        "write_grayleafspot_results"
      ]
    }
  ],
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