{
  "_id": "6a1037fdacfb0bcc41c9a92b",
  "Package": "pttstability",
  "Title": "Particle-Takens Stability",
  "Version": "1.4",
  "Authors@R": "person(\"Adam\", \"Clark\", email = \"adam.tclark@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-8843-3278\"))",
  "Description": "Includes a collection of functions presented in \"Measuring\nstability in ecological systems without static equilibria\" by\nClark et al. (2022) <doi:10.1002/ecs2.4328> in Ecosphere. These\ncan be used to estimate the parameters of a stochastic state\nspace model (i.e. a model where a time series is observed with\nerror). The goal of this package is to estimate the variability\naround a deterministic process, both in terms of observation\nerror - i.e. variability due to imperfect observations that\ndoes not influence system state - and in terms of process noise\n- i.e. stochastic variation in the actual state of the process.\nUnlike classical methods for estimating variability, this\npackage does not necessarily assume that the deterministic\nstate is fixed (i.e. a fixed-point equilibrium), meaning that\nvariability around a dynamic trajectory can be estimated (e.g.\nstochastic fluctuations during predator-prey dynamics).",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.2.3",
  "Collate": "'bayesfun.R' 'data.R' 'fake_data.R' 'logit_funs.R'\n'particlefilter.R' 'pttstability_man.R' 'smapping_functions.R'",
  "NeedsCompilation": "no",
  "Author": "Adam Clark [aut, cre] (<https://orcid.org/0000-0002-8843-3278>)",
  "Maintainer": "Adam Clark <adam.tclark@gmail.com>",
  "Packaged": {
    "Date": "2026-05-12 06:09:00 UTC",
    "User": "root"
  },
  "Repository": "https://adamtclark.r-universe.dev",
  "Date/Publication": "2024-01-10 02:44:55 UTC",
  "RemoteUrl": "https://github.com/cran/pttstability",
  "RemoteRef": "HEAD",
  "RemoteSha": "01a8e46af84e0c2c3ce4b58b9237cc8439347019",
  "MD5sum": "f8688c607de5c5026c17a59a01122384",
  "_user": "adamtclark",
  "_type": "src",
  "_file": "pttstability_1.4.tar.gz",
  "_fileid": "f0bc2ef93876e32eed5dc5c94e3fa385563f3f0291050ade402bb64be6de5d3d",
  "_filesize": 193823,
  "_sha256": "f0bc2ef93876e32eed5dc5c94e3fa385563f3f0291050ade402bb64be6de5d3d",
  "_created": "2026-05-12T06:09:00.000Z",
  "_published": "2026-05-22T11:03:25.529Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77366810596,
      "time": 143,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6936938728"
    },
    {
      "job": 77366810651,
      "time": 134,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6936938314"
    },
    {
      "job": 77366810701,
      "time": 96,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6936953797"
    },
    {
      "job": 77366810359,
      "time": 87,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6936949793"
    },
    {
      "job": 77366809774,
      "time": 190,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6936903730"
    },
    {
      "job": 77366809729,
      "time": 110,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7158945220"
    },
    {
      "job": 77366810248,
      "time": 103,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6936929246"
    },
    {
      "job": 77366810521,
      "time": 90,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6936926761"
    },
    {
      "job": 77366810568,
      "time": 102,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6936928849"
    }
  ],
  "_buildurl": "https://github.com/r-universe/adamtclark/actions/runs/25716689461",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/pttstability",
  "_commit": {
    "id": "01a8e46af84e0c2c3ce4b58b9237cc8439347019",
    "author": "Adam Clark <adam.tclark@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.4\n",
    "time": 1704854695
  },
  "_maintainer": {
    "name": "Adam Clark",
    "email": "adam.tclark@gmail.com",
    "login": "adamtclark",
    "mastodon": "@adam_t_clark@ecoevo.social",
    "twitter": "@adam_t_clark",
    "uuid": 5502690,
    "orcid": "0000-0002-8843-3278"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4",
      "role": "Depends"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BayesianTools",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "adamtclark",
      "count": 4,
      "uuid": 5502690
    }
  ],
  "_userbio": {
    "uuid": 5502690,
    "type": "user",
    "name": "Adam Clark",
    "description": "Associate Professor in the Department of Biology at the University of Graz."
  },
  "_downloads": {
    "count": 177,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/pttstability"
  },
  "_searchresults": 0,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/pttstability.html",
    "manual.pdf"
  ],
  "_realowner": "adamtclark",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.1",
      "date": "2023-01-09"
    },
    {
      "version": "1.2",
      "date": "2023-10-22"
    },
    {
      "version": "1.3",
      "date": "2023-10-24"
    },
    {
      "version": "1.4",
      "date": "2024-01-09"
    }
  ],
  "_exports": [
    "colfun0",
    "density_fun0",
    "detfun0",
    "detfun0_sin",
    "EDMfun0",
    "getcm",
    "ilogit",
    "indexsort",
    "inv_fun0",
    "likelihood_EDM_piecewise",
    "likelihood0",
    "logit",
    "logitnormal_imode",
    "lognormal_imode",
    "makeblock",
    "makedynamics_general",
    "obsfun0",
    "parseparam0",
    "particleFilterLL",
    "particleFilterLL_piecewise",
    "process_scof",
    "procfun_ct",
    "procfun0",
    "S_map_Sugihara1994",
    "sampler_fun0",
    "sdproc_abstract"
  ],
  "_datasets": [
    {
      "name": "dat",
      "title": "Microcosm experimental data",
      "object": "dat",
      "class": [
        "data.frame"
      ],
      "fields": [
        "treatment",
        "number",
        "time",
        "Chlamydomonas.terricola"
      ],
      "rows": 1084,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "colfun0",
      "title": "default colonization function",
      "topics": [
        "colfun0"
      ]
    },
    {
      "page": "dat",
      "title": "Microcosm experimental data",
      "topics": [
        "dat"
      ]
    },
    {
      "page": "density_fun0",
      "title": "Default density function for prior",
      "topics": [
        "density_fun0"
      ]
    },
    {
      "page": "detfun0",
      "title": "default deterministic function",
      "topics": [
        "detfun0"
      ]
    },
    {
      "page": "detfun0_sin",
      "title": "deterministic function with time-varying carrying capacity",
      "topics": [
        "detfun0_sin"
      ]
    },
    {
      "page": "EDMfun0",
      "title": "EDM deterministic function",
      "topics": [
        "EDMfun0"
      ]
    },
    {
      "page": "getcm",
      "title": "Get rates",
      "topics": [
        "getcm"
      ]
    },
    {
      "page": "ilogit",
      "title": "Inverse logit",
      "topics": [
        "ilogit"
      ]
    },
    {
      "page": "indexsort",
      "title": "Sort output of particle filter",
      "topics": [
        "indexsort"
      ]
    },
    {
      "page": "inv_fun0",
      "title": "Default inverse transormation function",
      "topics": [
        "inv_fun0"
      ]
    },
    {
      "page": "likelihood_EDM_piecewise",
      "title": "calculate likelihood for piecewise data",
      "topics": [
        "likelihood_EDM_piecewise"
      ]
    },
    {
      "page": "likelihood0",
      "title": "Default likelihood function",
      "topics": [
        "likelihood0"
      ]
    },
    {
      "page": "logit",
      "title": "Logit",
      "topics": [
        "logit"
      ]
    },
    {
      "page": "logitnormal_imode",
      "title": "Get inverse logit-normal mode",
      "topics": [
        "logitnormal_imode"
      ]
    },
    {
      "page": "lognormal_imode",
      "title": "Get inverse log-normal mode",
      "topics": [
        "lognormal_imode"
      ]
    },
    {
      "page": "makeblock",
      "title": "Make an embedding block from timeseries data",
      "topics": [
        "makeblock"
      ]
    },
    {
      "page": "makedynamics_general",
      "title": "Simulate general time series",
      "topics": [
        "makedynamics_general"
      ]
    },
    {
      "page": "obsfun0",
      "title": "default observation noise function",
      "topics": [
        "obsfun0"
      ]
    },
    {
      "page": "parseparam0",
      "title": "Parse parameters",
      "topics": [
        "parseparam0"
      ]
    },
    {
      "page": "particleFilterLL",
      "title": "particle filter",
      "topics": [
        "particleFilterLL"
      ]
    },
    {
      "page": "particleFilterLL_piecewise",
      "title": "run particle filter across piecewise data",
      "topics": [
        "particleFilterLL_piecewise"
      ]
    },
    {
      "page": "process_scof",
      "title": "Process S-mapping coefficients",
      "topics": [
        "process_scof"
      ]
    },
    {
      "page": "procfun_ct",
      "title": "continuous-time process noise function",
      "topics": [
        "procfun_ct"
      ]
    },
    {
      "page": "procfun0",
      "title": "default process noise function",
      "topics": [
        "procfun0"
      ]
    },
    {
      "page": "S_map_Sugihara1994",
      "title": "Apply S-mapping algorithm from Sugihara 1994",
      "topics": [
        "S_map_Sugihara1994"
      ]
    },
    {
      "page": "sampler_fun0",
      "title": "Default sampler function for prior",
      "topics": [
        "sampler_fun0"
      ]
    },
    {
      "page": "sdproc_abstract",
      "title": "calculate estimated total variance",
      "topics": [
        "sdproc_abstract"
      ]
    }
  ],
  "_rundeps": [],
  "_score": 1,
  "_indexed": true,
  "_nocasepkg": "pttstability",
  "_universes": [
    "adamtclark"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.4",
      "date": "2026-05-12T06:11:19.000Z",
      "distro": "noble",
      "commit": "01a8e46af84e0c2c3ce4b58b9237cc8439347019",
      "fileid": "b3a8047ffb4b9e17d4e285a5838c35b815e14ba6a547884b1ccc972ea1413b21",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/adamtclark/actions/runs/25716689461"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.4",
      "date": "2026-05-12T06:11:20.000Z",
      "distro": "noble",
      "commit": "01a8e46af84e0c2c3ce4b58b9237cc8439347019",
      "fileid": "ee3f3a0c9bad5a54681aa7b8f552a1d27da1f7ded055e2a982bfce3834d2087e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/adamtclark/actions/runs/25716689461"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.4",
      "date": "2026-05-12T06:12:24.000Z",
      "commit": "01a8e46af84e0c2c3ce4b58b9237cc8439347019",
      "fileid": "c1d30b2ec69f262fcf4e00c026dfa95c766b2e5a2be94beccbca289ab97080e7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/adamtclark/actions/runs/25716689461"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.4",
      "date": "2026-05-12T06:12:11.000Z",
      "commit": "01a8e46af84e0c2c3ce4b58b9237cc8439347019",
      "fileid": "b83b5e567f13d343b29877762040a5b3f96dec13a0a6a5ff52f3cf2bea2e609a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/adamtclark/actions/runs/25716689461"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.4",
      "date": "2026-05-12T06:10:32.000Z",
      "commit": "01a8e46af84e0c2c3ce4b58b9237cc8439347019",
      "fileid": "87637599385103388bfd8f9b7d8737eaa238b6b845b442386ab83a55ed4f1f2d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/adamtclark/actions/runs/25716689461"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.4",
      "date": "2026-05-12T06:10:25.000Z",
      "commit": "01a8e46af84e0c2c3ce4b58b9237cc8439347019",
      "fileid": "2d21fdab8fd6bae146a1201e45b4a90f8a9b4ec48f66c348092661734ebda5b8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/adamtclark/actions/runs/25716689461"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.4",
      "date": "2026-05-12T06:10:32.000Z",
      "commit": "01a8e46af84e0c2c3ce4b58b9237cc8439347019",
      "fileid": "0a81b19ccd25ed9cbccfe4bcf2ba4ef7ae36aee29d7b1fd87729c50df463193b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/adamtclark/actions/runs/25716689461"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.4",
      "date": "2026-05-22T11:03:03.000Z",
      "commit": "01a8e46af84e0c2c3ce4b58b9237cc8439347019",
      "fileid": "a8b65c68215bf2e846fa6394912173fa3e6bdb676b18af3fb1f5c3c1af18d744",
      "status": "success",
      "buildurl": "https://github.com/r-universe/adamtclark/actions/runs/25716689461"
    }
  ]
}