{
  "_id": "6a10780dacfb0bcc41cad179",
  "Package": "templateICAr",
  "Type": "Package",
  "Title": "Estimate Brain Networks and Connectivity with ICA and Empirical\nPriors",
  "Version": "0.10.0",
  "Authors@R": "c(\nperson(given = \"Amanda\",\nfamily = \"Mejia\",\nemail = \"mandy.mejia@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(given = \"Damon\",\nfamily = \"Pham\",\nemail = \"damondpham@gmail.com\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-7563-4727\")),\nperson(given = \"Daniel\",\nfamily = \"Spencer\",\nemail = \"danieladamspencer@gmail.com\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-9705-3605\")),\nperson(given = \"Mary Beth\",\nfamily = \"Nebel\",\nemail = \"Nebel@kennedykrieger.org\",\nrole = c(\"ctb\"))\n)",
  "Maintainer": "Amanda Mejia <mandy.mejia@gmail.com>",
  "Description": "Implements the template ICA (independent components\nanalysis) model proposed in Mejia et al. (2020)\n<doi:10.1080/01621459.2019.1679638> and the spatial template\nICA model proposed in proposed in Mejia et al. (2022)\n<doi:10.1080/10618600.2022.2104289>. Both models estimate\nsubject-level brain as deviations from known population-level\nnetworks, which are estimated using standard ICA algorithms.\nBoth models employ an expectation-maximization algorithm for\nestimation of the latent brain networks and unknown model\nparameters. Includes direct support for 'CIFTI', 'GIFTI', and\n'NIFTI' neuroimaging file formats.",
  "License": "GPL-3",
  "Additional_repositories": "https://inla.r-inla-download.org/R/testing",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "URL": "https://github.com/mandymejia/templateICAr",
  "BugReports": "https://github.com/mandymejia/templateICAr/issues",
  "Repository": "https://mandymejia.r-universe.dev",
  "Date/Publication": "2025-05-20 19:12:51 UTC",
  "RemoteUrl": "https://github.com/mandymejia/templateicar",
  "RemoteRef": "HEAD",
  "RemoteSha": "d3b501c02b536e2ebe5538e0be1332945affcb96",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-06 09:22:43 UTC",
    "User": "root"
  },
  "Author": "Amanda Mejia [aut, cre],\nDamon Pham [aut] (ORCID: <https://orcid.org/0000-0001-7563-4727>),\nDaniel Spencer [ctb] (ORCID: <https://orcid.org/0000-0002-9705-3605>),\nMary Beth Nebel [ctb]",
  "MD5sum": "ed93890c7150fb3cc30e7fd9e49c5654",
  "_user": "mandymejia",
  "_type": "src",
  "_file": "templateICAr_0.10.0.tar.gz",
  "_fileid": "e06185716636f24fd8325a6a4c8b1902f6999ca877ec852ce9077f017b8f6df6",
  "_filesize": 375416,
  "_sha256": "e06185716636f24fd8325a6a4c8b1902f6999ca877ec852ce9077f017b8f6df6",
  "_created": "2026-05-06T09:22:43.000Z",
  "_published": "2026-05-22T15:36:45.857Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77412120510,
      "time": 169,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6826753218"
    },
    {
      "job": 77412120317,
      "time": 175,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6826752712"
    },
    {
      "job": 77412120178,
      "time": 106,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6826729048"
    },
    {
      "job": 77412120530,
      "time": 151,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6826744907"
    },
    {
      "job": 77412120277,
      "time": 179,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6826693598"
    },
    {
      "job": 77412119827,
      "time": 128,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7164427289"
    },
    {
      "job": 77412120515,
      "time": 119,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6826733861"
    },
    {
      "job": 77412120322,
      "time": 111,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6826731000"
    },
    {
      "job": 77412120324,
      "time": 130,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6826738587"
    }
  ],
  "_buildurl": "https://github.com/r-universe/mandymejia/actions/runs/25426864530",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/mandymejia/templateicar",
  "_commit": {
    "id": "d3b501c02b536e2ebe5538e0be1332945affcb96",
    "author": "Damon Pham <damondpham@gmail.com>",
    "committer": "Damon Pham <damondpham@gmail.com>",
    "message": "acceptance on CRAN\n",
    "time": 1747768371
  },
  "_maintainer": {
    "name": "Amanda Mejia",
    "email": "mandy.mejia@gmail.com",
    "login": "mandymejia",
    "twitter": "@mandyfmejia",
    "uuid": 5199186
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "abind",
      "role": "Imports"
    },
    {
      "package": "fMRItools",
      "version": ">= 0.5.3",
      "role": "Imports"
    },
    {
      "package": "fMRIscrub",
      "version": ">= 0.14.5",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "ica",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "pesel",
      "role": "Imports"
    },
    {
      "package": "SQUAREM",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "ciftiTools",
      "version": ">= 0.13.2",
      "role": "Suggests"
    },
    {
      "package": "excursions",
      "role": "Suggests"
    },
    {
      "package": "RNifti",
      "role": "Suggests"
    },
    {
      "package": "oro.nifti",
      "role": "Suggests"
    },
    {
      "package": "gifti",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "parallel",
      "role": "Suggests"
    },
    {
      "package": "doParallel",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "INLA",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "mandymejia",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-21",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 11,
  "_contributors": [
    {
      "user": "damondpham",
      "count": 526,
      "uuid": 14958204
    },
    {
      "user": "mandymejia",
      "count": 190,
      "uuid": 5199186
    },
    {
      "user": "danieladamspencer",
      "count": 11,
      "uuid": 13244331
    }
  ],
  "_userbio": {
    "uuid": 5199186,
    "type": "user",
    "name": "Mandy Mejia",
    "description": "Associate Professor in the Department of Statistics at Indiana University.  PI of the StatMIND (Statistical Methods for Individualized Neuro-Discovery) lab."
  },
  "_downloads": {
    "count": 660,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/templateICAr"
  },
  "_devurl": "https://github.com/mandymejia/templateicar",
  "_searchresults": 28,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/templateICAr.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/mandymejia/templateicar",
  "_realowner": "mandymejia",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.3.1",
      "date": "2022-03-09"
    },
    {
      "version": "0.6.2",
      "date": "2023-01-27"
    },
    {
      "version": "0.6.4",
      "date": "2024-01-17"
    },
    {
      "version": "0.8.8",
      "date": "2024-10-14"
    },
    {
      "version": "0.9.1",
      "date": "2024-11-21"
    },
    {
      "version": "0.10.0",
      "date": "2025-05-19"
    }
  ],
  "_exports": [
    "activations",
    "dim_reduce",
    "estimate_template",
    "estimate_template_FC",
    "estimate_template_from_DR",
    "export_template",
    "getInvCovAR",
    "groupICA.cifti",
    "make_mesh",
    "make_mesh_2D",
    "norm_BOLD",
    "orthonorm",
    "resample_template",
    "sqrt_XtX",
    "templateICA"
  ],
  "_help": [
    {
      "page": "activations",
      "title": "Activations of (spatial) template ICA",
      "topics": [
        "activations"
      ]
    },
    {
      "page": "bdiag_m2",
      "title": "Bdiag m2",
      "topics": [
        "bdiag_m2"
      ]
    },
    {
      "page": "Chol_samp_fun",
      "title": "Cholesky-based FC sampling",
      "topics": [
        "Chol_samp_fun"
      ]
    },
    {
      "page": "dim_reduce",
      "title": "PCA-based Dimension Reduction and Prewhitening",
      "topics": [
        "dim_reduce"
      ]
    },
    {
      "page": "EM_templateICA",
      "title": "EM Algorithms for Template ICA Models",
      "topics": [
        "EM_templateICA",
        "EM_templateICA.independent",
        "EM_templateICA.spatial"
      ]
    },
    {
      "page": "estimate_nu",
      "title": "Universally estimate IW dof parameter nu based on method of moments, so that no empirical variance is under-estimated",
      "topics": [
        "estimate_nu"
      ]
    },
    {
      "page": "estimate_nu_matrix",
      "title": "Estimate IW dof parameter nu based on method of moments",
      "topics": [
        "estimate_nu_matrix"
      ]
    },
    {
      "page": "estimate_template",
      "title": "Estimate template",
      "topics": [
        "estimate_template",
        "estimate_template.cifti",
        "estimate_template.gifti",
        "estimate_template.nifti"
      ]
    },
    {
      "page": "estimate_template_FC",
      "title": "Estimate FC template",
      "topics": [
        "estimate_template_FC"
      ]
    },
    {
      "page": "estimate_template_from_DR",
      "title": "Estimate template from DR",
      "topics": [
        "estimate_template_from_DR"
      ]
    },
    {
      "page": "estimate.ESS",
      "title": "Estimation of effective sample size",
      "topics": [
        "estimate.ESS"
      ]
    },
    {
      "page": "export_template",
      "title": "Export template",
      "topics": [
        "export_template"
      ]
    },
    {
      "page": "getInvCovAR",
      "title": "Compute inverse covariance matrix for AR process (up to a constant scaling factor)",
      "topics": [
        "getInvCovAR"
      ]
    },
    {
      "page": "groupICA.cifti",
      "title": "Perform group ICA based on CIFTI data",
      "topics": [
        "groupICA.cifti"
      ]
    },
    {
      "page": "IW_var",
      "title": "Compute theoretical Inverse-Wishart variance of covariance matrix elements",
      "topics": [
        "IW_var"
      ]
    },
    {
      "page": "IW_var_cor",
      "title": "Compute theoretical Inverse-Wishart variance of correlation matrix elements",
      "topics": [
        "IW_var_cor"
      ]
    },
    {
      "page": "lik",
      "title": "Compute likelihood in SPDE model for ESS estimation",
      "topics": [
        "lik"
      ]
    },
    {
      "page": "make_mesh",
      "title": "Make INLA mesh from '\"surf\"' object",
      "topics": [
        "make_mesh"
      ]
    },
    {
      "page": "make_mesh_2D",
      "title": "Make 2D INLA mesh",
      "topics": [
        "make_mesh_2D"
      ]
    },
    {
      "page": "norm_BOLD",
      "title": "Normalize BOLD data",
      "topics": [
        "norm_BOLD"
      ]
    },
    {
      "page": "orthonorm",
      "title": "Orthonormalizes a square, invertible matrix",
      "topics": [
        "orthonorm"
      ]
    },
    {
      "page": "plot.template.cifti",
      "title": "Plot template",
      "topics": [
        "plot.template.cifti"
      ]
    },
    {
      "page": "plot.template.gifti",
      "title": "Plot template",
      "topics": [
        "plot.template.gifti"
      ]
    },
    {
      "page": "plot.template.matrix",
      "title": "Plot template",
      "topics": [
        "plot.template.matrix"
      ]
    },
    {
      "page": "plot.template.nifti",
      "title": "Plot template",
      "topics": [
        "plot.template.nifti"
      ]
    },
    {
      "page": "plot.tICA_act.cifti",
      "title": "Plot activations",
      "topics": [
        "plot.tICA_act.cifti"
      ]
    },
    {
      "page": "plot.tICA.cifti",
      "title": "Plot template",
      "topics": [
        "plot.tICA.cifti"
      ]
    },
    {
      "page": "plot.tICA.matrix",
      "title": "Plot template",
      "topics": [
        "plot.tICA.matrix"
      ]
    },
    {
      "page": "plot.tICA.nifti",
      "title": "Plot template",
      "topics": [
        "plot.tICA.nifti"
      ]
    },
    {
      "page": "pw_estimate",
      "title": "Estimate residual autocorrelation for prewhitening",
      "topics": [
        "pw_estimate"
      ]
    },
    {
      "page": "resample_template",
      "title": "Resample CIFTI template",
      "topics": [
        "resample_template"
      ]
    },
    {
      "page": "sqrt_XtX",
      "title": "Compute matrix square root of X'X",
      "topics": [
        "sqrt_XtX"
      ]
    },
    {
      "page": "summary.template.cifti",
      "title": "Summarize a '\"template.cifti\"' object",
      "topics": [
        "print.summary.template.cifti",
        "print.template.cifti",
        "summary.template.cifti"
      ]
    },
    {
      "page": "summary.template.gifti",
      "title": "Summarize a '\"template.gifti\"' object",
      "topics": [
        "print.summary.template.gifti",
        "print.template.gifti",
        "summary.template.gifti"
      ]
    },
    {
      "page": "summary.template.matrix",
      "title": "Summarize a '\"template.matrix\"' object",
      "topics": [
        "print.summary.template.matrix",
        "print.template.matrix",
        "summary.template.matrix"
      ]
    },
    {
      "page": "summary.template.nifti",
      "title": "Summarize a '\"template.nifti\"' object",
      "topics": [
        "print.summary.template.nifti",
        "print.template.nifti",
        "summary.template.nifti"
      ]
    },
    {
      "page": "summary.tICA_act.cifti",
      "title": "Summarize a '\"tICA_act.cifti\"' object",
      "topics": [
        "print.summary.tICA_act.cifti",
        "print.tICA_act.cifti",
        "summary.tICA_act.cifti"
      ]
    },
    {
      "page": "summary.tICA_act.matrix",
      "title": "Summarize a '\"tICA_act.matrix\"' object",
      "topics": [
        "print.summary.tICA_act.matrix",
        "print.tICA_act.matrix",
        "summary.tICA_act.matrix"
      ]
    },
    {
      "page": "summary.tICA_act.nifti",
      "title": "Summarize a '\"tICA_act.nifti\"' object",
      "topics": [
        "print.summary.tICA_act.nifti",
        "print.tICA_act.nifti",
        "summary.tICA_act.nifti"
      ]
    },
    {
      "page": "summary.tICA.cifti",
      "title": "Summarize a '\"tICA.cifti\"' object",
      "topics": [
        "print.summary.tICA.cifti",
        "print.tICA.cifti",
        "summary.tICA.cifti"
      ]
    },
    {
      "page": "summary.tICA.matrix",
      "title": "Summarize a '\"tICA.matrix\"' object",
      "topics": [
        "print.summary.tICA.matrix",
        "print.tICA.matrix",
        "summary.tICA.matrix"
      ]
    },
    {
      "page": "summary.tICA.nifti",
      "title": "Summarize a '\"tICA.nifti\"' object",
      "topics": [
        "print.summary.tICA.nifti",
        "print.tICA.nifti",
        "summary.tICA.nifti"
      ]
    },
    {
      "page": "templateICA",
      "title": "Template ICA",
      "topics": [
        "templateICA"
      ]
    },
    {
      "page": "UpdateTheta_templateICA",
      "title": "Parameter Estimates in EM Algorithm for Template ICA Model",
      "topics": [
        "UpdateTheta_templateICA",
        "UpdateTheta_templateICA.independent",
        "UpdateTheta_templateICA.spatial"
      ]
    },
    {
      "page": "UT2mat",
      "title": "Transform upper-triangular elements to matrix form",
      "topics": [
        "UT2mat"
      ]
    },
    {
      "page": "var_sq_err",
      "title": "Compute the error between empirical and theoretical variance of covariance matrix elements",
      "topics": [
        "var_sq_err"
      ]
    },
    {
      "page": "var_sq_err_constrained",
      "title": "Compute the overall error between empirical and theoretical variance of CORRELATION matrix elements",
      "topics": [
        "var_sq_err_constrained"
      ]
    }
  ],
  "_readme": "https://github.com/mandymejia/templateicar/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "class",
    "codetools",
    "DEoptimR",
    "e1071",
    "fMRIscrub",
    "fMRItools",
    "foreach",
    "ica",
    "iterators",
    "lattice",
    "MASS",
    "Matrix",
    "matrixStats",
    "pesel",
    "proxy",
    "robustbase",
    "SQUAREM"
  ],
  "_score": 4.488550716500444,
  "_indexed": true,
  "_nocasepkg": "templateicar",
  "_universes": [
    "mandymejia"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.10.0",
      "date": "2026-05-06T09:25:22.000Z",
      "distro": "noble",
      "commit": "d3b501c02b536e2ebe5538e0be1332945affcb96",
      "fileid": "c32b1dc0071b612bc125f635aa7ab5ffb174875fc7c4af5fcd74a8cb2fc8e27a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mandymejia/actions/runs/25426864530"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.10.0",
      "date": "2026-05-06T09:25:20.000Z",
      "distro": "noble",
      "commit": "d3b501c02b536e2ebe5538e0be1332945affcb96",
      "fileid": "31a3b7d60bca451fb2c5c5c8d14383bed9429e07eea86509d94b53e5d25494da",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mandymejia/actions/runs/25426864530"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.10.0",
      "date": "2026-05-06T09:24:26.000Z",
      "commit": "d3b501c02b536e2ebe5538e0be1332945affcb96",
      "fileid": "f4767437746ed1d83bd3fe1b2febaa249afde692dec12cdd622e6b1979cf212f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mandymejia/actions/runs/25426864530"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.10.0",
      "date": "2026-05-06T09:24:58.000Z",
      "commit": "d3b501c02b536e2ebe5538e0be1332945affcb96",
      "fileid": "4616e60f1ccb802457441b215e1a5ac69788816e9fbeff62a2bd4048cfae4867",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mandymejia/actions/runs/25426864530"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.10.0",
      "date": "2026-05-06T09:24:17.000Z",
      "commit": "d3b501c02b536e2ebe5538e0be1332945affcb96",
      "fileid": "4661fe424597693462d5ddb5985b6827e61952793bc14ac0f46a1e40945c2cd0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mandymejia/actions/runs/25426864530"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.10.0",
      "date": "2026-05-06T09:24:10.000Z",
      "commit": "d3b501c02b536e2ebe5538e0be1332945affcb96",
      "fileid": "bddf58393b83a63812d68a4910d09bdeed1daa0334e9593ef53a730a7ef9a2eb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mandymejia/actions/runs/25426864530"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.10.0",
      "date": "2026-05-06T09:24:30.000Z",
      "commit": "d3b501c02b536e2ebe5538e0be1332945affcb96",
      "fileid": "1a8ab3097c9361dcacaa1b22638f90318c986fbaa6f7768231ad3bfc11093295",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mandymejia/actions/runs/25426864530"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.10.0",
      "date": "2026-05-22T15:36:31.000Z",
      "commit": "d3b501c02b536e2ebe5538e0be1332945affcb96",
      "fileid": "60b1438efbb695899f11edab54130a37c3b14c4d5ec4254e5c162ae182c9656d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/mandymejia/actions/runs/25426864530"
    }
  ]
}