{
  "_id": "6a253b174b233be198398a5a",
  "Package": "doremi",
  "Type": "Package",
  "Title": "Dynamics of Return to Equilibrium During Multiple Inputs",
  "Version": "1.0.0",
  "Authors@R": "c(person(\"Mongin\", \"Denis\", email = \"Denis.Mongin@unige.ch\", role = c(\"aut\",\"cre\"), comment = c(ORCID = \"0000-0002-4801-8395\")),\nperson(\"Uribe\", \"Adriana\", email = \"adriana.uribe@unige.ch\", role = \"aut\"),\nperson(\"Courvoisier\", \"Delphine\", email = \"Delphine.Courvoisier@hcuge.ch\", role = \"aut\", comment = c(ORCID = \"0000-0002-1956-2607\")))",
  "Description": "Provides models to fit the dynamics of a regulated system\nexperiencing exogenous inputs. The underlying models use\ndifferential equations and linear mixed-effects regressions to\nestimate the coefficients of the equation. With them, the\nfunctions can provide an estimated signal. The package provides\nsimulation and analysis functions and also print, summary, plot\nand predict methods, adapted to the function outputs, for easy\nimplementation and presentation of results.",
  "License": "GPL-3",
  "URL": "https://github.com/dcourvoisier/doremi",
  "BugReports": "https://github.com/dcourvoisier/doremi/issues",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.1.1",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake make",
  "Repository": "https://dcourvoisier.r-universe.dev",
  "Date/Publication": "2022-01-13 09:42:00 UTC",
  "RemoteUrl": "https://github.com/dcourvoisier/doremi",
  "RemoteRef": "HEAD",
  "RemoteSha": "f2adc5037fef7e621eec4c32990896f3279e67ab",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-07 09:30:20 UTC",
    "User": "root"
  },
  "Author": "Mongin Denis [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-4801-8395>),\nUribe Adriana [aut],\nCourvoisier Delphine [aut] (ORCID:\n<https://orcid.org/0000-0002-1956-2607>)",
  "Maintainer": "Mongin Denis <Denis.Mongin@unige.ch>",
  "MD5sum": "9fdce400031db6af0a60ae9b6a30cc02",
  "_user": "dcourvoisier",
  "_type": "src",
  "_file": "doremi_1.0.0.tar.gz",
  "_fileid": "890e420cd2793fd0f801f1fd91a73e2731597051cd3a75489782c2633c5d5435",
  "_filesize": 7535068,
  "_sha256": "890e420cd2793fd0f801f1fd91a73e2731597051cd3a75489782c2633c5d5435",
  "_created": "2026-06-07T09:30:20.000Z",
  "_published": "2026-06-07T09:34:15.799Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79948076064,
      "time": 182,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7462856932"
    },
    {
      "job": 79948076069,
      "time": 198,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7462858996"
    },
    {
      "job": 79948076094,
      "time": 175,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7462852260"
    },
    {
      "job": 79948076082,
      "time": 187,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7462854087"
    },
    {
      "job": 79947807792,
      "time": 270,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7462833517"
    },
    {
      "job": 79948076068,
      "time": 137,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7462851249"
    },
    {
      "job": 79948076062,
      "time": 137,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7462851362"
    },
    {
      "job": 79948076053,
      "time": 124,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7462849535"
    },
    {
      "job": 79948076070,
      "time": 142,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7462851902"
    }
  ],
  "_buildurl": "https://github.com/r-universe/dcourvoisier/actions/runs/27088590781",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/dcourvoisier/doremi",
  "_commit": {
    "id": "f2adc5037fef7e621eec4c32990896f3279e67ab",
    "author": "dmongin <denis.mongin@gmail.com>",
    "committer": "dmongin <denis.mongin@gmail.com>",
    "message": "debug log\n",
    "time": 1642066920
  },
  "_maintainer": {
    "name": "Mongin Denis",
    "email": "denis.mongin@unige.ch",
    "login": "dmongin",
    "description": "",
    "uuid": 19406581,
    "orcid": "0000-0002-4801-8395"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "zoo",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "lme4",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "lmerTest",
      "role": "Imports"
    },
    {
      "package": "deSolve",
      "role": "Imports"
    },
    {
      "package": "futile.logger",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "roxygen2",
      "role": "Suggests"
    }
  ],
  "_owner": "dcourvoisier",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "auricap",
      "count": 60,
      "uuid": 38041958
    },
    {
      "user": "dmongin",
      "count": 46,
      "uuid": 19406581
    }
  ],
  "_userbio": {
    "uuid": 38043567,
    "type": "user",
    "name": "Delphine Courvoisier",
    "description": "Statistician working at a tertiary academic hospital"
  },
  "_downloads": {
    "count": 42,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/doremi"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/dcourvoisier/doremi",
  "_searchresults": 32,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/doremi.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/dcourvoisier/doremi",
  "_realowner": "dcourvoisier",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2018-08-30"
    },
    {
      "version": "0.1.1",
      "date": "2019-03-25"
    },
    {
      "version": "1.0.0",
      "date": "2021-01-29"
    }
  ],
  "_exports": [
    "analyze.1order",
    "analyze.2order",
    "calculate.fda",
    "calculate.glla",
    "calculate.gold",
    "generate.1order",
    "generate.2order",
    "generate.excitation",
    "generate.panel.1order",
    "generate.panel.2order",
    "optimum_param"
  ],
  "_datasets": [
    {
      "name": "cardio",
      "title": "Measurements of cardiac frequency in 21 patients during effort tests",
      "object": "cardio",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "id",
        "time",
        "load",
        "hr"
      ],
      "rows": 1686,
      "table": true,
      "tojson": true
    },
    {
      "name": "rotation",
      "title": "Measurements of response time of 17 individuals when carrying out mental rotation tasks",
      "object": "rotation",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "id",
        "sex",
        "days",
        "meanRT",
        "logmeanRT"
      ],
      "rows": 619,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "analyze.1order",
      "title": "DOREMI first order analysis function",
      "topics": [
        "analyze.1order"
      ]
    },
    {
      "page": "analyze.2order",
      "title": "DOREMI second order analysis function",
      "topics": [
        "analyze.2order"
      ]
    },
    {
      "page": "calculate.fda",
      "title": "Calculation of derivatives using the Functional Data Analysis (FDA) method.",
      "topics": [
        "calculate.fda"
      ]
    },
    {
      "page": "calculate.glla",
      "title": "Calculation of derivatives using the GLLA method",
      "topics": [
        "calculate.glla"
      ]
    },
    {
      "page": "calculate.gold",
      "title": "Calculation of derivatives using the GOLD method",
      "topics": [
        "calculate.gold"
      ]
    },
    {
      "page": "cardio",
      "title": "Measurements of cardiac frequency in 21 patients during effort tests",
      "topics": [
        "cardio"
      ]
    },
    {
      "page": "errorcheck",
      "title": "Displays error messages for the analysis function according to the nature of the error 'errorcheck' displays error messages and/or warnings concerning the validity of input arguments provided to the analysis function",
      "topics": [
        "errorcheck"
      ]
    },
    {
      "page": "generate.1order",
      "title": "Generation of the first order differential equation solution with deSolve, for given fixed coefficients and initial condition",
      "topics": [
        "generate.1order"
      ]
    },
    {
      "page": "generate.2order",
      "title": "Generation of the second order differential equation solution with deSolve",
      "topics": [
        "generate.2order"
      ]
    },
    {
      "page": "generate.excitation",
      "title": "Excitation signal generation",
      "topics": [
        "generate.excitation"
      ]
    },
    {
      "page": "generate.panel.1order",
      "title": "Generation of first order differential equation solutions for several individuals with intra-individual and inter-individual noise",
      "topics": [
        "generate.panel.1order"
      ]
    },
    {
      "page": "generate.panel.2order",
      "title": "Generation of second order differential equation solutions for several individuals with intra-individual and inter-individual noise",
      "topics": [
        "generate.panel.2order"
      ]
    },
    {
      "page": "optimum_param",
      "title": "Function to find the optimum parameter for derivative estimation (embedding or spar according to derivative estimation method chosen)",
      "topics": [
        "optimum_param"
      ]
    },
    {
      "page": "plot.doremi",
      "title": "S3 method to plot DOREMI objects",
      "topics": [
        "plot.doremi"
      ]
    },
    {
      "page": "plot.doremidata",
      "title": "S3 method to plot DOREMIDATA objects",
      "topics": [
        "plot.doremidata"
      ]
    },
    {
      "page": "plot.doremiparam",
      "title": "S3 method to plot DOREMIPARAM objects",
      "topics": [
        "plot.doremiparam"
      ]
    },
    {
      "page": "predict.doremi",
      "title": "S3 method to predict signal values in a DOREMI object when entering a new excitation",
      "topics": [
        "predict.doremi"
      ]
    },
    {
      "page": "print.doremi",
      "title": "S3 method to print DOREMI objects",
      "topics": [
        "print.doremi"
      ]
    },
    {
      "page": "print.doremidata",
      "title": "S3 method to print DOREMIDATA objects",
      "topics": [
        "print.doremidata"
      ]
    },
    {
      "page": "rotation",
      "title": "Measurements of response time of 17 individuals when carrying out mental rotation tasks",
      "topics": [
        "rotation"
      ]
    },
    {
      "page": "summary.doremi",
      "title": "S3 method for DOREMI object summary",
      "topics": [
        "summary.doremi"
      ]
    }
  ],
  "_rundeps": [
    "boot",
    "cli",
    "cpp11",
    "data.table",
    "deSolve",
    "farver",
    "formatR",
    "futile.logger",
    "futile.options",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "isoband",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "lme4",
    "lmerTest",
    "MASS",
    "Matrix",
    "minqa",
    "nlme",
    "nloptr",
    "numDeriv",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "derivatives.Rmd",
      "filename": "derivatives.html",
      "title": "derivatives",
      "engine": "knitr::rmarkdown",
      "headings": [
        "ESTIMATION OF THE DERIVATIVES"
      ],
      "created": "2021-01-05 19:04:38",
      "modified": "2021-01-07 19:59:45",
      "commits": 4
    },
    {
      "source": "first-order.Rmd",
      "filename": "first-order.html",
      "title": "first-order",
      "engine": "knitr::rmarkdown",
      "headings": [
        "FIRST ORDER DIFFERENTIAL EQUATIONS",
        "Two steps analysis procedure",
        "First order differential equation with no excitation term",
        "Simulating data",
        "Example 1a - Generating signals with no noise",
        "Example 1b - Changing initial condition, gain and equilibrium value",
        "Example 2a - Generating signals with noise",
        "Analyzing data",
        "Example 3 - Analyzing data when the excitation is unknown, with some inter- and intraindividual noise",
        "First order differential equation with an excitation term",
        "Example 2 - Generating signals with noise",
        "Example 3 - Analyzing data from a single individual",
        "Example 3a - Analyzing data with several individuals and some inter and intra-individual noise",
        "Example 3b - Enhancing the fit by changing the embedding number/ smoothing parameter.",
        "Example 4 - Analyzing data when the signal is subject to several excitations",
        "Example 5 - Analyzing data with missing values in the signal",
        "C - Applications",
        "Heart rate during effort tests",
        "Measuring heart frequency during effort tests by considering several excitations",
        "Measurements of response time of individuals when carrying out mental rotation tasks"
      ],
      "created": "2020-02-06 10:37:02",
      "modified": "2021-01-07 19:59:45",
      "commits": 13
    },
    {
      "source": "Introduction-to-doremi.Rmd",
      "filename": "Introduction-to-doremi.html",
      "title": "Introduction-to-doremi",
      "engine": "knitr::rmarkdown",
      "headings": [
        "EXAMPLES",
        "FIRST ORDER DIFFERENTIAL EQUATION MODEL",
        "SECOND ORDER DIFFERENTIAL EQUATION MODEL",
        "FUNCTIONS INCLUDED ON THE PACKAGE",
        "Simulation functions",
        "Analysis functions",
        "derivative functions"
      ],
      "created": "2018-06-11 19:43:20",
      "modified": "2021-01-07 19:59:45",
      "commits": 34
    },
    {
      "source": "second-order.Rmd",
      "filename": "second-order.html",
      "title": "second-order",
      "engine": "knitr::rmarkdown",
      "headings": [
        "SECOND ORDER DIFFERENTIAL EQUATIONS",
        "Simulating data",
        "Example 1 - Generating Damped Linear Oscillator signals with inter-individual variability",
        "Example 2 - Using simulation functions to generate undamped, critically damped and overdamped signals",
        "Analyzing data",
        "Example 1 - Analyzing Damped Linear Oscillator signals",
        "SECOND ORDER DIFFERENTIAL EQUATION MODELS WITH AN EXCITATION TERM",
        "Example 1 - Generating signals with no noise",
        "Example 2 - Generating signals with noise",
        "Example 3 - Using an initial condition in a time different from t0=0",
        "Example 4 - studying the effect of periodical excitations",
        "Example 1 - Analyzing data from a single individual",
        "Example 2 - Analyzing data with several individuals and some inter and intra-individual noise",
        "Example 3 - Enhancing the fit by changing the embedding number/ smoothing parameter.",
        "Example 4 - Analyzing data when the signal is subject to several excitations and no noise"
      ],
      "created": "2020-02-06 10:37:02",
      "modified": "2021-01-07 19:59:45",
      "commits": 11
    }
  ],
  "_score": 4.584331224367531,
  "_indexed": true,
  "_nocasepkg": "doremi",
  "_universes": [
    "dcourvoisier",
    "dmongin"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-06-07T09:32:50.000Z",
      "distro": "noble",
      "commit": "f2adc5037fef7e621eec4c32990896f3279e67ab",
      "fileid": "3a3d0e42b24fda78249abdf3de1cff693e41461f13ff095656138b0342abc7da",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/dcourvoisier/actions/runs/27088590781"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-06-07T09:33:00.000Z",
      "distro": "noble",
      "commit": "f2adc5037fef7e621eec4c32990896f3279e67ab",
      "fileid": "d8ad3fe78759fdea642d5334ffaed62caac90620f6c8cb42c7e916f356b8bfc3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/dcourvoisier/actions/runs/27088590781"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-06-07T09:32:31.000Z",
      "commit": "f2adc5037fef7e621eec4c32990896f3279e67ab",
      "fileid": "92f6dc3f78b5acf89bd82dd85cb3da3d8e3a0d09d6a4d6d79e9d1c227012c601",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/dcourvoisier/actions/runs/27088590781"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-06-07T09:32:36.000Z",
      "commit": "f2adc5037fef7e621eec4c32990896f3279e67ab",
      "fileid": "4014d292a22897087f3ddcc5c79a29ab80b667ceede781355ae8adaffc3ef097",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/dcourvoisier/actions/runs/27088590781"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.0",
      "date": "2026-06-07T09:32:55.000Z",
      "commit": "f2adc5037fef7e621eec4c32990896f3279e67ab",
      "fileid": "fa4e51c4a089b7c864fcc2d653db20a02bfae326675d0cf47a47fdb10e5deb34",
      "status": "success",
      "buildurl": "https://github.com/r-universe/dcourvoisier/actions/runs/27088590781"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-06-07T09:31:54.000Z",
      "commit": "f2adc5037fef7e621eec4c32990896f3279e67ab",
      "fileid": "1a6d82417e2bc7937591df563b68ab16c56a2570d792fd380e568571cbaf0363",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/dcourvoisier/actions/runs/27088590781"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-06-07T09:31:40.000Z",
      "commit": "f2adc5037fef7e621eec4c32990896f3279e67ab",
      "fileid": "5165df7758072f11220984c0e7a0d3c519b63d7259754b9361174df510e2d4a9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/dcourvoisier/actions/runs/27088590781"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-06-07T09:31:56.000Z",
      "commit": "f2adc5037fef7e621eec4c32990896f3279e67ab",
      "fileid": "18ce4d474f98c5c986f86ebe6f83bd032ec1b450e24ba1815e96ef4c30df6a9d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/dcourvoisier/actions/runs/27088590781"
    }
  ]
}