{
  "_id": "6a1bfb0a1d7bb097a0a27d18",
  "Package": "TIMP",
  "Title": "Fitting Separable Nonlinear Models in Spectroscopy and\nMicroscopy",
  "Version": "1.13.6",
  "Authors@R": "c(\nperson(\"Katharine M.\", \"Mullen\", role = \"aut\",\ncomment = \"Original package creator\"),\nperson(\"Joris\", \"Snellenburg\", , \"j.snellenburg@vu.nl\", role = c(\"cre\", \"ctb\"),\ncomment = c(ORCID = \"0000-0002-1428-0221\")),\nperson(\"Sergey P.\", \"Laptenok\", role = \"ctb\"),\nperson(\"David\", \"Nicolaides\", role = \"ctb\"),\nperson(\"Ivo H.M.\", \"van Stokkum\", , \"i.h.m.van.stokkum@vu.nl\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-6143-2021\"))\n)",
  "Description": "A problem solving environment (PSE) for fitting separable\nnonlinear models to measurements arising in physics and\nchemistry experiments, as described by Mullen & van Stokkum\n(2007) <doi:10.18637/jss.v018.i03> for its use in fitting time\nresolved spectroscopy data, and as described by Laptenok et al.\n(2007) <doi:10.18637/jss.v018.i08> for its use in fitting\nFluorescence Lifetime Imaging Microscopy (FLIM) data, in the\nstudy of Förster Resonance Energy Transfer (FRET).  `TIMP` also\nserves as the computation backend for the `GloTarAn` software,\na graphical user interface for the package, as described in\nSnellenburg et al. (2012) <doi:10.18637/jss.v049.i03>.",
  "License": "GPL (>= 2)",
  "URL": "https://github.com/glotaran/TIMP",
  "BugReports": "https://github.com/glotaran/TIMP/issues",
  "Encoding": "UTF-8",
  "Language": "en-US",
  "RoxygenNote": "7.2.3",
  "Repository": "https://glotaran.r-universe.dev",
  "Date/Publication": "2023-02-10 20:06:36 UTC",
  "RemoteUrl": "https://github.com/glotaran/timp",
  "RemoteRef": "HEAD",
  "RemoteSha": "7d7be69d0cc50a8925d3d505694f1cf6b197929b",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-31 09:04:29 UTC",
    "User": "root"
  },
  "Author": "Katharine M. Mullen [aut] (Original package creator),\nJoris Snellenburg [cre, ctb] (ORCID:\n<https://orcid.org/0000-0002-1428-0221>),\nSergey P. Laptenok [ctb],\nDavid Nicolaides [ctb],\nIvo H.M. van Stokkum [aut] (ORCID:\n<https://orcid.org/0000-0002-6143-2021>)",
  "Maintainer": "Joris Snellenburg <j.snellenburg@vu.nl>",
  "MD5sum": "edf7235e9a079d6a8e7971e20d6ff434",
  "_user": "glotaran",
  "_type": "src",
  "_file": "TIMP_1.13.6.tar.gz",
  "_fileid": "5f3f9bafc94259f2b5e05709b32b143ff41aabc423823d8ffb6b644ce000af8e",
  "_filesize": 1369367,
  "_sha256": "5f3f9bafc94259f2b5e05709b32b143ff41aabc423823d8ffb6b644ce000af8e",
  "_created": "2026-05-31T09:04:29.000Z",
  "_published": "2026-05-31T09:10:34.204Z",
  "_distro": "noble",
  "_jobs": [
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  "_buildurl": "https://github.com/r-universe/glotaran/actions/runs/26708377459",
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  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/glotaran/timp",
  "_commit": {
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    "author": "Joris Snellenburg <jsnel@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "📚 Add package statistics to README (#16)\n\nAdd package statistics to README\n\n### Change summary\n\n- 📚 Add package statistics (download and citation count) to README\n\n### Checklist\n\n- [x] ✔️ Passing the tests (mandatory for all PR's)\n- [x] 📚 Adds documentation of the feature",
    "time": 1676059596
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  "_maintainer": {
    "name": "Joris Snellenburg",
    "email": "j.snellenburg@vu.nl",
    "login": "jsnel",
    "orcid": "0000-0002-1428-0221",
    "twitter": "@jsnellenburg",
    "description": "Blazingly curious, tech enthusiast, devops aficionado, @glotaran guardian, and proud father-of-two.",
    "uuid": 3616369
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "fields",
      "version": ">= 4.1",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "R",
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    {
      "package": "colorspace",
      "role": "Imports"
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    {
      "package": "deSolve",
      "role": "Imports"
    },
    {
      "package": "gclus",
      "role": "Imports"
    },
    {
      "package": "gplots",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
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    {
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      "role": "Imports"
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    {
      "package": "minpack.lm",
      "version": ">= 1.1-1",
      "role": "Imports"
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      "role": "Imports"
    },
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      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    }
  ],
  "_owner": "glotaran",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "parameter-estimation"
  ],
  "_stars": 3,
  "_contributors": [
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      "user": "jsnel",
      "count": 44,
      "uuid": 3616369
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  "_userbio": {
    "uuid": 10042353,
    "type": "organization",
    "name": "GloTarAn",
    "description": "Modeling frameworks for global and target analysis (GloTarAn)"
  },
  "_downloads": {
    "count": 239,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TIMP"
  },
  "_mentions": 14,
  "_devurl": "https://github.com/glotaran/timp",
  "_searchresults": 15,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/TIMP.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/glotaran/timp",
  "_realowner": "glotaran",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.2",
      "date": "2007-05-01"
    },
    {
      "version": "1.3",
      "date": "2007-07-23"
    },
    {
      "version": "1.4",
      "date": "2007-10-04"
    },
    {
      "version": "1.5",
      "date": "2008-01-29"
    },
    {
      "version": "1.6",
      "date": "2008-04-27"
    },
    {
      "version": "1.7",
      "date": "2008-08-22"
    },
    {
      "version": "1.8",
      "date": "2008-10-13"
    },
    {
      "version": "1.9",
      "date": "2010-02-11"
    },
    {
      "version": "1.10",
      "date": "2010-08-24"
    },
    {
      "version": "1.10.1",
      "date": "2011-04-24"
    },
    {
      "version": "1.10.2",
      "date": "2012-07-22"
    },
    {
      "version": "1.10.3",
      "date": "2013-09-30"
    },
    {
      "version": "1.11.0",
      "date": "2014-01-25"
    },
    {
      "version": "1.12.0",
      "date": "2014-12-02"
    },
    {
      "version": "1.12.1",
      "date": "2014-12-11"
    },
    {
      "version": "1.13.0",
      "date": "2015-10-19"
    },
    {
      "version": "1.13.1",
      "date": "2019-01-28"
    },
    {
      "version": "1.13.2",
      "date": "2019-03-15"
    },
    {
      "version": "1.13.6",
      "date": "2022-12-12"
    }
  ],
  "_exports": [
    "addDscal",
    "addPrel",
    "addPrelCl",
    "amp",
    "applyWeightingModel",
    "barplot3",
    "baseCorlambda",
    "baseCortime",
    "baseIRF",
    "calcB",
    "calcC",
    "calcCirf",
    "calcD",
    "calcEbspline",
    "calcEhiergaus",
    "compCoh",
    "compModel",
    "compModelMass",
    "compOsc",
    "convGausExp",
    "dat",
    "diffAdd",
    "diffChange",
    "diffFree",
    "diffRel",
    "diffRemove",
    "displayEst",
    "divergeZimage",
    "doClpConstr",
    "doConstrSuper",
    "doSVD",
    "efit2file",
    "examineFit",
    "fillK",
    "fillResult",
    "fit",
    "fitModel",
    "fullKF",
    "gaus",
    "getAutoClp0",
    "getC",
    "getCLP",
    "getClpConstr",
    "getClpindepX",
    "getCLPList",
    "getCoh",
    "getCohToPlot",
    "getConToPlot",
    "getDAS",
    "getData",
    "getDiffTheta",
    "getDiffThetaChange",
    "getDiffThetaCl",
    "getDiffThetaClChange",
    "getdim1",
    "getdim2",
    "getFixed",
    "getGroups",
    "getKinConcen",
    "getModel",
    "getOsc",
    "getPar",
    "getPrel",
    "getPrelTheta",
    "getResid",
    "getResidRet",
    "getResiduals",
    "getSelectedTracesMax",
    "getSpecList",
    "getSpecToPlot",
    "getSVDData",
    "getSVDResiduals",
    "getTheta",
    "getThetaCl",
    "getTraces",
    "getX",
    "getXList",
    "getXsuper",
    "initModel",
    "initModellist",
    "irfparF",
    "kin",
    "kinopt",
    "l2nu",
    "linloglines",
    "linlogplot",
    "linlogtics",
    "mass",
    "massopt",
    "matlinlogplot",
    "modifyModel",
    "multiLin",
    "multimodel",
    "multitheta",
    "normdat",
    "onls",
    "opt",
    "outlierCorr",
    "parEst",
    "plotClp",
    "plotFLIM",
    "plotHistAmp",
    "plotHistNormComp",
    "plotIntenImage",
    "plotKinBreakDown",
    "plotKinSpecEst",
    "plotNormComp",
    "plotSelIntenImage",
    "plotTau",
    "plotter",
    "plotTracesSuper",
    "preProcess",
    "processOrder",
    "readclp0",
    "readData",
    "res",
    "rescomp",
    "residPart",
    "sample_sel",
    "scaleConList",
    "simndecay_gen",
    "simpExp",
    "simpPol",
    "skew",
    "spec",
    "specModel",
    "specopt",
    "specparF",
    "sumKinSpecEst",
    "sumnls",
    "theta",
    "unitstep",
    "weightNL",
    "weightPsi",
    "writeAverage",
    "writeEst",
    "writeFit"
  ],
  "_datasets": [
    {
      "name": "c001",
      "title": "Fluorescent lifetime imaging microscopy (FLIM) data",
      "object": "donorTagged",
      "file": "donorTagged.rda",
      "class": [
        "dat"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "c003",
      "title": "Fluorescent lifetime imaging microscopy (FLIM) data",
      "object": "donorTagged",
      "file": "donorTagged.rda",
      "class": [
        "dat"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "C1",
      "title": "Ultrafast time-resolved fluorescence data",
      "object": "target",
      "file": "target.rda",
      "class": [
        "dat"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "C2",
      "title": "Ultrafast time-resolved fluorescence data",
      "object": "target",
      "file": "target.rda",
      "class": [
        "dat"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "C3",
      "title": "Ultrafast time-resolved fluorescence data",
      "object": "target",
      "file": "target.rda",
      "class": [
        "dat"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "cy005c",
      "title": "Fluorescent lifetime imaging microscopy (FLIM) data",
      "object": "donorAcceptorTagged",
      "file": "donorAcceptorTagged.rda",
      "class": [
        "dat"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "cy006",
      "title": "Fluorescent lifetime imaging microscopy (FLIM) data",
      "object": "donorAcceptorTagged",
      "file": "donorAcceptorTagged.rda",
      "class": [
        "dat"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "denS4",
      "title": "Time-resolved absorption data",
      "object": "denS4",
      "file": "denS4.rda",
      "class": [
        "dat"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "denS5",
      "title": "Time-resolved absorption data",
      "object": "denS5",
      "file": "denS5.rda",
      "class": [
        "dat"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mea_IRF",
      "title": "Instrument response for fluorescent lifetime imaging microscopy (FLIM) data",
      "object": "mea_IRF",
      "file": "mea_IRF.rda",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "TIMP-package",
      "title": "a problem solving environment for fitting separable nonlinear models in physics and chemistry applications",
      "topics": [
        "TIMP-package",
        "TIMP"
      ]
    },
    {
      "page": "amp-class",
      "title": "Class \"amp\" for diagonal matrix model specification.",
      "topics": [
        "amp",
        "amp-class"
      ]
    },
    {
      "page": "baseIRF",
      "title": "Baseline subtraction from a vector, usually representing an IRF.",
      "topics": [
        "baseIRF"
      ]
    },
    {
      "page": "dat-class",
      "title": "Class \"dat\" for model and data storage",
      "topics": [
        "dat",
        "dat-class"
      ]
    },
    {
      "page": "denS4",
      "title": "Time-resolved absorption data",
      "topics": [
        "denS4",
        "denS5"
      ]
    },
    {
      "page": "divergeZimage",
      "title": "Plots a matrix with a diverging palette, with the center value of the palette possible to set",
      "topics": [
        "divergeZimage"
      ]
    },
    {
      "page": "donorAcceptorTagged",
      "title": "Fluorescent lifetime imaging microscopy (FLIM) data",
      "topics": [
        "cy005c",
        "cy006",
        "donorAcceptorTagged"
      ]
    },
    {
      "page": "donorTagged",
      "title": "Fluorescent lifetime imaging microscopy (FLIM) data",
      "topics": [
        "c001",
        "c003",
        "donorTagged"
      ]
    },
    {
      "page": "efit2file",
      "title": "Convert 'tim' FORTRAN efit files to plain matrices in ASCII files",
      "topics": [
        "efit2file"
      ]
    },
    {
      "page": "examineFit",
      "title": "Examines the results of a call to fitModel",
      "topics": [
        "examineFit"
      ]
    },
    {
      "page": "fit-class",
      "title": "Class \"fit\" to store the results of model fitting associated with all datasets analyzed.",
      "topics": [
        "fit",
        "fit-class"
      ]
    },
    {
      "page": "fitModel",
      "title": "Performs optimization of (possibly multidataset) models.",
      "topics": [
        "fitModel"
      ]
    },
    {
      "page": "FLIMplots",
      "title": "Functions to plot FLIM results.",
      "topics": [
        "FLIMplots",
        "plotHistAmp",
        "plotHistNormComp",
        "plotIntenImage",
        "plotNormComp",
        "plotSelIntenImage",
        "plotTau"
      ]
    },
    {
      "page": "getClpindepX",
      "title": "Generic function getClpindepX in Package `TIMP'",
      "topics": [
        "getClpindepX",
        "getClpindepX,amp-method",
        "getClpindepX,kin-method",
        "getClpindepX,mass-method",
        "getClpindepX,spec-method",
        "getClpindepX-methods"
      ]
    },
    {
      "page": "getResid",
      "title": "For data correction, fits a model (but ignores plotting commands) in order to obtain the SVD of the residuals, which then can be used in data-correction.",
      "topics": [
        "getResid"
      ]
    },
    {
      "page": "getResults",
      "title": "Functions to print and return parts of the object returned by the fitting routines.",
      "topics": [
        "getC",
        "getCLP",
        "getCLPList",
        "getDAS",
        "getData",
        "getdim1",
        "getdim2",
        "getResiduals",
        "getResults",
        "getSVDData",
        "getSVDResiduals",
        "getTraces",
        "getX",
        "getXList",
        "onls",
        "parEst",
        "sumnls"
      ]
    },
    {
      "page": "initModel",
      "title": "Defines the model to be used in analysis.",
      "topics": [
        "initModel"
      ]
    },
    {
      "page": "kin-class",
      "title": "Class \"kin\" for kinetic model storage.",
      "topics": [
        "kin",
        "kin-class"
      ]
    },
    {
      "page": "kinopt-class",
      "title": "Class \"kinopt\" stores options for fitting and plotting kinetic models",
      "topics": [
        "kinopt",
        "kinopt-class"
      ]
    },
    {
      "page": "mass-class",
      "title": "Class \"mass\" for mass spectrometry model storage.",
      "topics": [
        "mass",
        "mass-class"
      ]
    },
    {
      "page": "massopt-class",
      "title": "Class \"massopt\" stores options for fitting and plotting models for mass spectrometry data",
      "topics": [
        "massopt",
        "massopt-class"
      ]
    },
    {
      "page": "mea_IRF",
      "title": "Instrument response for fluorescent lifetime imaging microscopy (FLIM) data",
      "topics": [
        "mea_IRF"
      ]
    },
    {
      "page": "modifyModel",
      "title": "Allows the starting values for parameters associated with a model to be updated with the values found in fitting the model.",
      "topics": [
        "modifyModel"
      ]
    },
    {
      "page": "multimodel-class",
      "title": "Class \"multimodel\" for storage of multidataset models, data and the results of fitting.",
      "topics": [
        "multimodel",
        "multimodel-class"
      ]
    },
    {
      "page": "multitheta-class",
      "title": "Class \"multitheta\" that stores a list with one element of class \"theta\" for each dataset modeled.",
      "topics": [
        "multitheta",
        "multitheta-class"
      ]
    },
    {
      "page": "opt-class",
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      "topics": [
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    },
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