{
  "_id": "6a16b957acfb0bcc41d869a0",
  "Package": "soilfoodwebs",
  "Type": "Package",
  "Title": "Soil Food Web Analysis",
  "Version": "1.0.2",
  "Authors@R": "c(person(\"Robert\",\"Buchkowski\", email = \"robert.buchkowski@gmail.com\",role = c(\"aut\", \"cre\", \"cph\")),person(\"Zoë\", \"Lindo\",role = c(\"aut\")),person(\"Carlos\", \"Barreto\",role = c(\"aut\")))",
  "Maintainer": "Robert Buchkowski <robert.buchkowski@gmail.com>",
  "Description": "Analyzing soil food webs or any food web measured at\nequilibrium. The package calculates carbon and nitrogen fluxes\nand stability properties using methods described by Hunt et al.\n(1987) <doi:10.1007/BF00260580>, de Ruiter et al. (1995)\n<doi:10.1126/science.269.5228.1257>, Holtkamp et al. (2011)\n<doi:10.1016/j.soilbio.2010.10.004>, and Buchkowski and Lindo\n(2021) <doi:10.1111/1365-2435.13706>. The package can also\nmanipulate the structure of the food web as well as simulate\nfood webs away from equilibrium and run decomposition\nexperiments.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.1",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://robertwbuchkowski.r-universe.dev",
  "Date/Publication": "2024-04-29 15:37:12 UTC",
  "RemoteUrl": "https://github.com/robertwbuchkowski/soilfoodwebs",
  "RemoteRef": "HEAD",
  "RemoteSha": "90414e71f429a0477e2d78d0fb6037a8d17caa8e",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-27 09:25:44 UTC",
    "User": "root"
  },
  "Author": "Robert Buchkowski [aut, cre, cph],\nZoë Lindo [aut],\nCarlos Barreto [aut]",
  "MD5sum": "3b83a68a2db0b99a452d3e0027183d96",
  "_user": "robertwbuchkowski",
  "_type": "src",
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  "_created": "2026-05-27T09:25:44.000Z",
  "_published": "2026-05-27T09:28:55.282Z",
  "_distro": "noble",
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    "author": "Robert Buchkowski <robert.buchkowski@gmail.com>",
    "committer": "Robert Buchkowski <robert.buchkowski@gmail.com>",
    "message": "Updated roxygen version.\n",
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    "email": "robert.buchkowski@gmail.com",
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    "description": "I am an Assistant Professor and Canada Research Chair at Western University studying carbon and nitrogen cycling.",
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  "_contributors": [
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    "name": "Robert Buchkowski",
    "description": "I am an Assistant Professor and Canada Research Chair at Western University studying carbon and nitrogen cycling."
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  "_assets": [
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  "_realowner": "robertwbuchkowski",
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  "_exports": [
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    "build_foodweb",
    "calc_smin",
    "calculate_inputs",
    "can_mutfeed",
    "checkcomm",
    "checkeqm",
    "Cijfcn",
    "CNsim",
    "comana",
    "comtrosp",
    "corrstoich",
    "decompexpt",
    "getPARAMS",
    "Jacobsindex",
    "newnode",
    "parameter_uncertainty",
    "removenodes",
    "renamenode",
    "stability",
    "stability2",
    "TLcheddar",
    "TLsort",
    "whomineralizes"
  ],
  "_datasets": [
    {
      "name": "Andres2016",
      "title": "The soil food webs published for grazed and ungrazed plots in the Shortgrass Steppe long-term research station.",
      "object": "Andres2016",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "deRuiter1994",
      "title": "The soil food webs published for conventional (CON) and integrated (INT) management at Lovinkhoeve experimental farm.",
      "object": "deRuiter1994",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "Holtkamp2011",
      "title": "The soil food webs published along a chronosequence in the Netherlands.",
      "object": "Holtkamp2011",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "Hunt1987",
      "title": "The soil food web published for CPER",
      "object": "Hunt1987",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "intro_comm",
      "title": "A baseline community for examples",
      "object": "intro_comm",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "Koltz2018",
      "title": "The soil food web published for an Arctic Tundra site",
      "object": "Koltz2018",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "Aijfcn",
      "title": "A function to calculate the nitrogen surplus or deficit each species gets from consuming another species",
      "topics": [
        "Aijfcn"
      ]
    },
    {
      "page": "Andres2016",
      "title": "The soil food webs published for grazed and ungrazed plots in the Shortgrass Steppe long-term research station.",
      "topics": [
        "Andres2016"
      ]
    },
    {
      "page": "build_foodweb",
      "title": "A function to compile the food web from simple data inputs",
      "topics": [
        "build_foodweb"
      ]
    },
    {
      "page": "calc_smin",
      "title": "Calculate the strength of stability as smin.",
      "topics": [
        "calc_smin"
      ]
    },
    {
      "page": "calculate_inputs",
      "title": "A function to calculate the inputs and outputs at equilibrium and print them for the user.",
      "topics": [
        "calculate_inputs"
      ]
    },
    {
      "page": "calculate_smin",
      "title": "Function used inside the calc_smin function",
      "topics": [
        "calculate_smin"
      ]
    },
    {
      "page": "can_mutfeed",
      "title": "A function that identifies cannibalism and mutual feeding",
      "topics": [
        "can_mutfeed"
      ]
    },
    {
      "page": "checkcomm",
      "title": "A function check the community for errors before it is used in calculations.",
      "topics": [
        "checkcomm"
      ]
    },
    {
      "page": "checkeqm",
      "title": "Check the carbon flux equilibrium output by comana.",
      "topics": [
        "checkeqm"
      ]
    },
    {
      "page": "Cijfcn",
      "title": "A utility function to calculate the consumption rate of each species on all prey assuming a type I functional response.",
      "topics": [
        "Cijfcn"
      ]
    },
    {
      "page": "CNsim",
      "title": "A function to simulate the dynamics over time wrapping getPARAMS and foodwebode",
      "topics": [
        "CNsim"
      ]
    },
    {
      "page": "comana",
      "title": "A function to calculate carbon and nitrogen fluxes in the food web.",
      "topics": [
        "comana"
      ]
    },
    {
      "page": "comtrosp",
      "title": "A function to combine trophic species.",
      "topics": [
        "comtrosp"
      ]
    },
    {
      "page": "correct_diet",
      "title": "A function to correct the diet of trophic species.",
      "topics": [
        "correct_diet"
      ]
    },
    {
      "page": "correction_function",
      "title": "A function to correct stoichiometry dynamically",
      "topics": [
        "correction_function"
      ]
    },
    {
      "page": "corrstoich",
      "title": "Correct stoichiometry",
      "topics": [
        "corrstoich"
      ]
    },
    {
      "page": "decompexpt",
      "title": "Decomposition rates and effect of individual organisms",
      "topics": [
        "decompexpt"
      ]
    },
    {
      "page": "deRuiter1994",
      "title": "The soil food webs published for conventional (CON) and integrated (INT) management at Lovinkhoeve experimental farm.",
      "topics": [
        "deRuiter1994"
      ]
    },
    {
      "page": "foodwebode",
      "title": "A function to simulation the food webs away from equilibrium.",
      "topics": [
        "foodwebode"
      ]
    },
    {
      "page": "getPARAMS",
      "title": "A function to get the parameters for a food web model.",
      "topics": [
        "getPARAMS"
      ]
    },
    {
      "page": "Holtkamp2011",
      "title": "The soil food webs published along a chronosequence in the Netherlands.",
      "topics": [
        "Holtkamp2011"
      ]
    },
    {
      "page": "Hunt1987",
      "title": "The soil food web published for CPER",
      "topics": [
        "Hunt1987"
      ]
    },
    {
      "page": "intro_comm",
      "title": "A baseline community for examples",
      "topics": [
        "intro_comm"
      ]
    },
    {
      "page": "Jacobsindex",
      "title": "Calculate Jacob's index.",
      "topics": [
        "Jacobsindex"
      ]
    },
    {
      "page": "Koltz2018",
      "title": "The soil food web published for an Arctic Tundra site",
      "topics": [
        "Koltz2018"
      ]
    },
    {
      "page": "newnode",
      "title": "Add node to the community",
      "topics": [
        "newnode"
      ]
    },
    {
      "page": "parameter_uncertainty",
      "title": "Parameter uncertainty returns community with new parameters drawn from a distribution of choice",
      "topics": [
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      ]
    },
    {
      "page": "productionadj",
      "title": "A function to fix production efficiency.",
      "topics": [
        "productionadj"
      ]
    },
    {
      "page": "removenodes",
      "title": "Remove nodes from community.",
      "topics": [
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      ]
    },
    {
      "page": "renamenode",
      "title": "Rename a node in a community.",
      "topics": [
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      ]
    },
    {
      "page": "RESCALE",
      "title": "A function to rescale a vector.",
      "topics": [
        "RESCALE"
      ]
    },
    {
      "page": "stability",
      "title": "Calculates the stability of the food web",
      "topics": [
        "stability"
      ]
    },
    {
      "page": "stability2",
      "title": "A function to run the stability analysis using the numerical simulation of the Jacobain matrix.",
      "topics": [
        "stability2"
      ]
    },
    {
      "page": "TLcheddar",
      "title": "Calculates the trophic level for each tropospecies",
      "topics": [
        "TLcheddar"
      ]
    },
    {
      "page": "TLsort",
      "title": "Sorts the trophic levels from lowest to highest",
      "topics": [
        "TLsort"
      ]
    },
    {
      "page": "whomineralizes",
      "title": "Direct and indirect contributions to mineralizations",
      "topics": [
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      ]
    }
  ],
  "_readme": "https://github.com/robertwbuchkowski/soilfoodwebs/raw/HEAD/README.md",
  "_rundeps": [
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    "glue",
    "lifecycle",
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  "_vignettes": [
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      "filename": "soilfoodweb_vignette.html",
      "title": "soilfoodweb_vignette",
      "author": "Robert W. Buchkowski",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "How to build a community",
        "Building the properties database:",
        "Building the interaction matrix:",
        "Building the community:",
        "Manual community building:",
        "Community analysis (comana)",
        "Parameter uncertainty",
        "Correcting stoichiometry",
        "Modifying the community structure",
        "Calibrating the fluxes to a specific ecosystem",
        "Using empirical measurements of mineralization",
        "Using defined relationships",
        "Contributions to carbon and nitrogen mineralization",
        "Calculate inputs",
        "Stability",
        "Simulate the food web away from equilibrium",
        "Decomposition constant",
        "Decomposition experiments in silico",
        "References"
      ],
      "created": "2021-08-09 23:14:35",
      "modified": "2023-05-09 00:12:58",
      "commits": 16
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  "_nocasepkg": "soilfoodwebs",
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