{
  "access": {
    "embargo": {
      "active": false,
      "reason": null
    },
    "files": "public",
    "record": "public",
    "status": "open"
  },
  "created": "2019-10-29T21:12:49.171591+00:00",
  "custom_fields": {},
  "deletion_status": {
    "is_deleted": false,
    "status": "P"
  },
  "files": {
    "count": 1,
    "enabled": true,
    "entries": {
      "matthewwolak/nadiv-552b35115f.zip": {
        "access": {
          "hidden": false
        },
        "checksum": "md5:2c88cecff1d776eb5abcf7c8dda829ed",
        "ext": "zip",
        "id": "94565805-02df-467b-b181-5e4ce2afa683",
        "key": "matthewwolak/nadiv-552b35115f.zip",
        "links": {
          "content": "https://zenodo.org/api/records/3522399/files/matthewwolak/nadiv-552b35115f.zip/content",
          "self": "https://zenodo.org/api/records/3522399/files/matthewwolak/nadiv-552b35115f.zip"
        },
        "metadata": null,
        "mimetype": "application/zip",
        "size": 775843,
        "storage_class": "L"
      }
    },
    "order": [],
    "total_bytes": 775843
  },
  "id": "3522399",
  "is_draft": false,
  "is_published": true,
  "links": {
    "access": "https://zenodo.org/api/records/3522399/access",
    "access_grants": "https://zenodo.org/api/records/3522399/access/grants",
    "access_links": "https://zenodo.org/api/records/3522399/access/links",
    "access_request": "https://zenodo.org/api/records/3522399/access/request",
    "access_users": "https://zenodo.org/api/records/3522399/access/users",
    "archive": "https://zenodo.org/api/records/3522399/files-archive",
    "archive_media": "https://zenodo.org/api/records/3522399/media-files-archive",
    "communities": "https://zenodo.org/api/records/3522399/communities",
    "communities-suggestions": "https://zenodo.org/api/records/3522399/communities-suggestions",
    "doi": "https://doi.org/10.5281/zenodo.3522399",
    "draft": "https://zenodo.org/api/records/3522399/draft",
    "file_modification": "https://zenodo.org/api/records/3522399/file-modification",
    "files": "https://zenodo.org/api/records/3522399/files",
    "latest": "https://zenodo.org/api/records/3522399/versions/latest",
    "latest_html": "https://zenodo.org/records/3522399/latest",
    "media_files": "https://zenodo.org/api/records/3522399/media-files",
    "parent": "https://zenodo.org/api/records/1471659",
    "parent_doi": "https://doi.org/10.5281/zenodo.1471659",
    "parent_doi_html": "https://zenodo.org/doi/10.5281/zenodo.1471659",
    "parent_html": "https://zenodo.org/records/1471659",
    "preview_html": "https://zenodo.org/records/3522399?preview=1",
    "quota_increase": "https://zenodo.org/api/records/3522399/quota-increase",
    "request_deletion": "https://zenodo.org/api/records/3522399/request-deletion",
    "requests": "https://zenodo.org/api/records/3522399/requests",
    "reserve_doi": "https://zenodo.org/api/records/3522399/draft/pids/doi",
    "self": "https://zenodo.org/api/records/3522399",
    "self_doi": "https://doi.org/10.5281/zenodo.3522399",
    "self_doi_html": "https://zenodo.org/doi/10.5281/zenodo.3522399",
    "self_html": "https://zenodo.org/records/3522399",
    "self_iiif_manifest": "https://zenodo.org/api/iiif/record:3522399/manifest",
    "self_iiif_sequence": "https://zenodo.org/api/iiif/record:3522399/sequence/default",
    "versions": "https://zenodo.org/api/records/3522399/versions"
  },
  "media_files": {
    "count": 0,
    "enabled": false,
    "entries": {},
    "order": [],
    "total_bytes": 0
  },
  "metadata": {
    "creators": [
      {
        "affiliations": [
          {
            "name": "Auburn University"
          }
        ],
        "person_or_org": {
          "family_name": "Matthew",
          "name": "Matthew",
          "type": "personal"
        }
      }
    ],
    "description": "2.16.2.0\nNEW\n<ul>\n<li><code>geneDrop()</code> conducts a gene dropping simulation down a user-supplied pedigree.</li>\n</ul>\n2.16.1.0\nNEW\n<ul>\n<li><code>simGG()</code> now simulates phenotypes with heterogeneous additive genetic variances among the genetic groups (i.e., immigrant and resident groups)<ul>\n<li>The change to this simulation function now ensures phenotypes and underlying breeding values are consistent with the mixed model genetic group analysis approach described by <a href=\"https://gsejournal.biomedcentral.com/articles/10.1186/s12711-019-0449-7\">Muff et al. 2019. Gen. Sel. Evol.</a></li>\n<li>Breeding values have now been \"split\" to track resident-specific and immigrant-specific breeding values</li>\n<li><strong>Users</strong> should interact with the function the same way as always, as no changes to the function arguments have been made.</li>\n</ul>\n</li>\n<li><code>makeGGAinv()</code> added as a <em>new</em> function to construct genetic group-specific inverse relatedness matrices (<strong>Ainv</strong>).<ul>\n<li>implements the approach in <a href=\"https://gsejournal.biomedcentral.com/articles/10.1186/s12711-019-0449-7\">Muff et al. 2019. Gen. Sel. Evol.</a></li>\n<li>An example is given in the help documentation (in R, run <code>?makeGGAinv</code>), but below is a basic example:<pre><code>ggPed &lt;- Q1988[-c(3:7), c(\"id\", \"damGG\", \"sireGG\")]\nAinvOut &lt;- makeGGAinv(ggPed, ggroups = 2)$Ainv  #&lt;-- list with 2 Ainv matrices\n</code></pre>\n</li>\n</ul>\n</li>\n<li>added <code>makeTinv()</code> and <code>makeDiiF()</code> functions<ul>\n<li>These create items used in the Cholesky factorization of a relatedness matrix (or its inverse) and/or the individual coefficients of inbreeding <code>f</code></li>\n<li>In particular, these are used to construct genetic group specific inverse relatedness matrices, and are used \"under the hood\" in <code>makeGGAinv()</code>.</li>\n<li><code>makeDiiF()</code> creates the <strong>D</strong> matrix of the Cholesky factorization of the relatedness matrix below (i.e., <strong>A</strong> and the coefficients of inbreeding (diagonals-1 of <strong>A</strong>)</li>\n<li><code>makeTinv()</code> creates <strong>Tinv</strong> of the Cholesky factorization of the inverse relatedness matrix below (i.e., <strong>Ainv</strong>)<ul>\n<li><strong>A</strong>= <strong>T' D T</strong></li>\n<li><strong>Ainv</strong>=<strong>Tinv' Dinv Tinv</strong></li>\n</ul>\n</li>\n<li>Note, because <strong>D</strong> and <strong>Dinv</strong> are <em>diagonal</em> matrices, <strong>Dinv</strong>= the element-wise operation of <code>1 / d_ii</code><ul>\n<li>Consequently, obtaining <strong>Dinv</strong> from <strong>D</strong> is trivial</li>\n<li>Simply do <code>Dinv &lt;- D</code> followed by <code>Dinv@x &lt;- 1 / D@x</code></li>\n</ul>\n</li>\n<li><strong>Users</strong> only need to supply a pedigree and the functions do the rest. For example:<pre><code>makeTinv(Mrode2)\nmakeDiiF(Mrode2)\n</code></pre>\n</li>\n</ul>\n</li>\n</ul>",
    "publication_date": "2019-10-29",
    "publisher": "Zenodo",
    "related_identifiers": [
      {
        "identifier": "https://github.com/matthewwolak/nadiv/tree/552b35115f",
        "relation_type": {
          "id": "issupplementto",
          "title": {
            "de": "Erg\u00e4nzt",
            "en": "Is supplement to"
          }
        },
        "scheme": "url"
      }
    ],
    "resource_type": {
      "id": "software",
      "title": {
        "de": "Software",
        "en": "Software"
      }
    },
    "rights": [
      {
        "description": {
          "en": ""
        },
        "id": "other-open",
        "title": {
          "en": "Other (Open)"
        }
      }
    ],
    "title": "matthewwolak/nadiv: CRAN v2.16.2",
    "version": "552b35115f"
  },
  "parent": {
    "access": {
      "owned_by": {
        "user": "54429"
      },
      "settings": {
        "accept_conditions_text": null,
        "allow_guest_requests": false,
        "allow_user_requests": false,
        "secret_link_expiration": 0
      }
    },
    "communities": {},
    "id": "1471659",
    "pids": {
      "doi": {
        "client": "datacite",
        "identifier": "10.5281/zenodo.1471659",
        "provider": "datacite"
      }
    }
  },
  "pids": {
    "doi": {
      "client": "datacite",
      "identifier": "10.5281/zenodo.3522399",
      "provider": "datacite"
    },
    "oai": {
      "identifier": "oai:zenodo.org:3522399",
      "provider": "oai"
    }
  },
  "revision_id": 8,
  "stats": {
    "all_versions": {
      "data_volume": 56498933.0,
      "downloads": 72,
      "unique_downloads": 69,
      "unique_views": 680,
      "views": 685
    },
    "this_version": {
      "data_volume": 5430901.0,
      "downloads": 7,
      "unique_downloads": 7,
      "unique_views": 106,
      "views": 107
    }
  },
  "status": "published",
  "swh": {},
  "updated": "2023-06-16T01:55:57.336350+00:00",
  "versions": {
    "index": 2,
    "is_latest": false
  }
}