{
  "_id": "6a0f5f4aacfb0bcc41c5b39c",
  "Package": "statgenHTP",
  "Title": "High Throughput Phenotyping (HTP) Data Analysis",
  "Version": "1.0.9.2",
  "Date": "2026-05-21",
  "Authors@R": "c(person(given = \"Emilie J\",\nfamily = \"Millet\",\nrole = \"aut\",\nemail = \"emilie.millet@wur.nl\",\ncomment = c(ORCID = \"0000-0002-2913-4892\")),\nperson(given = \"Maria Xose\",\nfamily = \"Rodriguez Alvarez\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-1329-9238\")),\nperson(given = \"Diana Marcela\",\nfamily = \"Perez Valencia\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-9053-2929\")),\nperson(given = \"Isabelle\",\nfamily = \"Sanchez\",\nrole = \"aut\"),\nperson(given = \"Nadine\",\nfamily = \"Hilgert\",\nrole = \"aut\"),\nperson(given = \"Bart-Jan\",\nfamily = \"van Rossum\",\nrole = c(\"aut\", \"cre\"),\nemail = \"bart-jan.vanrossum@wur.nl\",\ncomment = c(ORCID = \"0000-0002-8673-2514\")),\nperson(given = \"Fred\",\nfamily = \"van Eeuwijk\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-3672-2921\")),\nperson(given = \"Martin\",\nfamily = \"Boer\",\nrole = \"aut\"))",
  "Description": "Phenotypic analysis of data coming from high throughput\nphenotyping (HTP) platforms, including different types of\noutlier detection, spatial analysis, and parameter estimation.\nThe package is being developed within the EPPN2020 project\n(<https://cordis.europa.eu/project/id/731013>). Some functions\nhave been created to be used in conjunction with the R package\n'asreml' for the 'ASReml' software, which can be obtained upon\npurchase from 'VSN' international\n(<https://vsni.co.uk/software/asreml-r/>).",
  "License": "GPL",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "URL": "https://biometris.github.io/statgenHTP/index.html,\nhttps://github.com/Biometris/statgenHTP/",
  "BugReports": "https://github.com/Biometris/statgenHTP/issues",
  "Config/roxygen2/version": "8.0.0",
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  "Repository": "https://biometris.r-universe.dev",
  "Date/Publication": "2026-05-21 13:22:30 UTC",
  "RemoteUrl": "https://github.com/biometris/statgenhtp",
  "RemoteRef": "HEAD",
  "RemoteSha": "ccfa98ed3845240fa3c9940cd09a165baaaaa26b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-21 14:08:06 UTC",
    "User": "root"
  },
  "Author": "Emilie J Millet [aut] (ORCID: <https://orcid.org/0000-0002-2913-4892>),\nMaria Xose Rodriguez Alvarez [aut] (ORCID:\n<https://orcid.org/0000-0002-1329-9238>),\nDiana Marcela Perez Valencia [aut] (ORCID:\n<https://orcid.org/0000-0002-9053-2929>),\nIsabelle Sanchez [aut],\nNadine Hilgert [aut],\nBart-Jan van Rossum [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-8673-2514>),\nFred van Eeuwijk [aut] (ORCID: <https://orcid.org/0000-0003-3672-2921>),\nMartin Boer [aut]",
  "Maintainer": "Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>",
  "MD5sum": "f780f4d39219a778bf1821c7e2832edb",
  "_user": "biometris",
  "_type": "src",
  "_file": "statgenHTP_1.0.9.2.tar.gz",
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  "_created": "2026-05-21T14:08:06.000Z",
  "_published": "2026-05-21T19:38:50.714Z",
  "_distro": "noble",
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    "author": "Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>",
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  "_topics": [
    "genetics",
    "high-troughput-phenotyping"
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    "name": "Wageningen Universtiy & Research, Biometris",
    "description": "Biometris develops statistical and mathematical methods for the quantification of biological processes and processes in our living environment."
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  "_devurl": "https://github.com/biometris/statgenhtp",
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  "_homeurl": "https://github.com/biometris/statgenhtp",
  "_realowner": "biometris",
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  "_releases": [
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  "_exports": [
    "countValid",
    "countValidPlot",
    "createTimePoints",
    "detectSerieOut",
    "detectSingleOut",
    "detectSingleOutMaize",
    "estimateSplineParameters",
    "fitModels",
    "fitSpline",
    "fitSplineHDM",
    "getCorrected",
    "getEffDims",
    "getGenoPred",
    "getHerit",
    "getTimePoints",
    "getVar",
    "removeSerieOut",
    "removeSingleOut",
    "removeTimePoints"
  ],
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      "name": "noCorrectedRoot",
      "title": "Root data corrected for outliers for single observations.",
      "object": "noCorrectedRoot",
      "class": [
        "data.frame"
      ],
      "fields": [
        "timePoint",
        "Date",
        "thermalTime",
        "Exp",
        "genotype",
        "Tank",
        "plotId",
        "rowId",
        "colId",
        "tipPos_y"
      ],
      "rows": 15934,
      "table": true,
      "tojson": true
    },
    {
      "name": "PhenoarchDat1",
      "title": "Greenhouse data for a maize experiment in the PhenoArch platform.",
      "object": "PhenoarchDat1",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Date",
        "pos",
        "Genotype",
        "Scenario",
        "population",
        "Row",
        "Col",
        "Biomass",
        "LeafArea",
        "PlantHeight",
        "LeafCount",
        "phyllocron"
      ],
      "rows": 40573,
      "table": true,
      "tojson": true
    },
    {
      "name": "PhenovatorDat1",
      "title": "Growth chamber data for an Arabidopsis experiment in the Phenovator platform.",
      "object": "PhenovatorDat1",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Genotype",
        "Basin",
        "Image_pos",
        "Replicate",
        "x",
        "y",
        "Sowing_Position",
        "timepoints",
        "EffpsII",
        "pos"
      ],
      "rows": 103839,
      "table": true,
      "tojson": true
    },
    {
      "name": "RootDat1",
      "title": "Greenhouse data for an experiment in the RootPhAir platform.",
      "object": "RootDat1",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Exp",
        "thermalTime",
        "Genotype",
        "plantId",
        "Tank",
        "Strip",
        "Pos",
        "tipPos_x",
        "tipPos_y",
        "Time"
      ],
      "rows": 16275,
      "table": true,
      "tojson": true
    },
    {
      "name": "spatCorrectedArch",
      "title": "Maize data corrected for spatial trends.",
      "object": "spatCorrectedArch",
      "class": [
        "data.frame"
      ],
      "fields": [
        "timeNumber",
        "timePoint",
        "LeafArea_corr",
        "LeafArea",
        "wt",
        "genotype",
        "geno.decomp",
        "rowId",
        "colId",
        "plotId"
      ],
      "rows": 40573,
      "table": true,
      "tojson": true
    },
    {
      "name": "spatCorrectedVator",
      "title": "Arabidopsis data corrected for spatial trends.",
      "object": "spatCorrectedVator",
      "class": [
        "data.frame"
      ],
      "fields": [
        "timeNumber",
        "timePoint",
        "EffpsII_corr",
        "EffpsII",
        "wt",
        "genotype",
        "check",
        "repId",
        "Image_pos",
        "rowId",
        "colId",
        "plotId",
        "timeNumHour"
      ],
      "rows": 103801,
      "table": true,
      "tojson": true
    },
    {
      "name": "spatPredArch",
      "title": "Maize data, genotypic predictions.",
      "object": "spatPredArch",
      "class": [
        "data.frame"
      ],
      "fields": [
        "timeNumber",
        "timePoint",
        "geno.decomp",
        "genotype",
        "predicted.values",
        "standard.errors"
      ],
      "rows": 5940,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "as.data.frame.TP",
      "title": "Coerce TP object to data.frame",
      "concept": [
        "functions for data preparation"
      ],
      "topics": [
        "as.data.frame.TP"
      ]
    },
    {
      "page": "countValid",
      "title": "Count valid observations per time point for a given trait",
      "topics": [
        "countValid"
      ]
    },
    {
      "page": "countValidPlot",
      "title": "Count valid observations per plotId for a given trait",
      "topics": [
        "countValidPlot"
      ]
    },
    {
      "page": "createTimePoints",
      "title": "Create an object of class TP",
      "concept": [
        "functions for data preparation"
      ],
      "topics": [
        "createTimePoints"
      ]
    },
    {
      "page": "detectSerieOut",
      "title": "Detect outliers for series of observations",
      "concept": [
        "functions for detecting outliers for series of observations"
      ],
      "topics": [
        "detectSerieOut"
      ]
    },
    {
      "page": "detectSingleOut",
      "title": "Detect outliers for single observations",
      "concept": [
        "functions for detecting outliers for single observations"
      ],
      "topics": [
        "detectSingleOut"
      ]
    },
    {
      "page": "detectSingleOutMaize",
      "title": "detectSingleOutMaize",
      "concept": [
        "functions for detecting outliers for single observations"
      ],
      "topics": [
        "detectSingleOutMaize"
      ]
    },
    {
      "page": "estimateSplineParameters",
      "title": "Extract estimates from fitted splines.",
      "concept": [
        "functions for spline parameter estimation"
      ],
      "topics": [
        "estimateSplineParameters"
      ]
    },
    {
      "page": "fitModels",
      "title": "Fit spatial models per time point",
      "concept": [
        "functions for spatial modeling"
      ],
      "topics": [
        "fitModels"
      ]
    },
    {
      "page": "fitSpline",
      "title": "Fit Splines",
      "concept": [
        "functions for fitting splines"
      ],
      "topics": [
        "fitSpline"
      ]
    },
    {
      "page": "fitSplineHDM",
      "title": "Fit P-Spline Hierarchical Curve Data Models",
      "concept": [
        "functions for fitting hierarchical curve data models"
      ],
      "topics": [
        "fitSplineHDM"
      ]
    },
    {
      "page": "getCorrected",
      "title": "Extract corrected phenotypic values",
      "concept": [
        "functions for spatial modeling"
      ],
      "topics": [
        "getCorrected"
      ]
    },
    {
      "page": "getEffDims",
      "title": "Extract effective dimensions",
      "concept": [
        "functions for spatial modeling"
      ],
      "topics": [
        "getEffDims"
      ]
    },
    {
      "page": "getGenoPred",
      "title": "Extract predicted genotypic values",
      "concept": [
        "functions for spatial modeling"
      ],
      "topics": [
        "getGenoPred"
      ]
    },
    {
      "page": "getHerit",
      "title": "Extract heritabilities",
      "concept": [
        "functions for spatial modeling"
      ],
      "topics": [
        "getHerit"
      ]
    },
    {
      "page": "getTimePoints",
      "title": "Extract time points",
      "concept": [
        "functions for data preparation"
      ],
      "topics": [
        "getTimePoints"
      ]
    },
    {
      "page": "getVar",
      "title": "Extract variances",
      "concept": [
        "functions for spatial modeling"
      ],
      "topics": [
        "getVar"
      ]
    },
    {
      "page": "noCorrectedRoot",
      "title": "Root data corrected for outliers for single observations.",
      "topics": [
        "noCorrectedRoot"
      ]
    },
    {
      "page": "PhenoarchDat1",
      "title": "Greenhouse data for a maize experiment in the PhenoArch platform.",
      "topics": [
        "PhenoarchDat1"
      ]
    },
    {
      "page": "PhenovatorDat1",
      "title": "Growth chamber data for an Arabidopsis experiment in the Phenovator platform.",
      "topics": [
        "PhenovatorDat1"
      ]
    },
    {
      "page": "plot.fitMod",
      "title": "Plot function for class fitMod",
      "concept": [
        "functions for spatial modeling"
      ],
      "topics": [
        "plot.fitMod"
      ]
    },
    {
      "page": "plot.HTPSpline",
      "title": "Plot the results of a fitted spline.",
      "concept": [
        "functions for fitting splines"
      ],
      "topics": [
        "plot.HTPSpline"
      ]
    },
    {
      "page": "plot.psHDM",
      "title": "Plot function for class psHDM",
      "concept": [
        "functions for fitting hierarchical curve data models"
      ],
      "topics": [
        "plot.psHDM"
      ]
    },
    {
      "page": "plot.serieOut",
      "title": "Plot outliers for series of observations",
      "concept": [
        "functions for detecting outliers for series of observations"
      ],
      "topics": [
        "plot.serieOut"
      ]
    },
    {
      "page": "plot.singleOut",
      "title": "Plot outliers for single observations",
      "concept": [
        "functions for detecting outliers for single observations"
      ],
      "topics": [
        "plot.singleOut"
      ]
    },
    {
      "page": "plot.splineEst",
      "title": "Plot the results of estimated spline parameters.",
      "concept": [
        "functions for spline parameter estimation"
      ],
      "topics": [
        "plot.splineEst"
      ]
    },
    {
      "page": "plot.TP",
      "title": "Plot function for class TP",
      "concept": [
        "functions for data preparation"
      ],
      "topics": [
        "plot.TP"
      ]
    },
    {
      "page": "predict.psHDM",
      "title": "Predict the P-Splines Hierarchical Curve Data Model",
      "concept": [
        "functions for fitting hierarchical curve data models"
      ],
      "topics": [
        "predict.psHDM"
      ]
    },
    {
      "page": "removeSerieOut",
      "title": "Replace outliers for series of observations by NA",
      "concept": [
        "functions for detecting outliers for series of observations"
      ],
      "topics": [
        "removeSerieOut"
      ]
    },
    {
      "page": "removeSingleOut",
      "title": "Replace outliers for single observations by NA",
      "concept": [
        "functions for detecting outliers for single observations"
      ],
      "topics": [
        "removeSingleOut"
      ]
    },
    {
      "page": "removeTimePoints",
      "title": "Remove time points from an object of class TP",
      "concept": [
        "functions for data preparation"
      ],
      "topics": [
        "removeTimePoints"
      ]
    },
    {
      "page": "RootDat1",
      "title": "Greenhouse data for an experiment in the RootPhAir platform.",
      "topics": [
        "RootDat1"
      ]
    },
    {
      "page": "spatCorrectedArch",
      "title": "Maize data corrected for spatial trends.",
      "topics": [
        "spatCorrectedArch"
      ]
    },
    {
      "page": "spatCorrectedVator",
      "title": "Arabidopsis data corrected for spatial trends.",
      "topics": [
        "spatCorrectedVator"
      ]
    },
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