{
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  "Title": "Dynamic Structural Equation Models",
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  "Date": "2026-06-10",
  "Authors@R": "c(person(given = \"James\",\nfamily = \"Thorson\",\nrole = c(\"aut\", \"cre\"),\nemail = \"James.Thorson@noaa.gov\",\ncomment = c(ORCID = \"0000-0001-7415-1010\")),\nperson(given = \"Maurice\",\nfamily = \"Goodman\",\nrole = c(\"ctb\"),\nemail = \"goodman.maurice@gmail.com\",\ncomment = c(ORCID = \"0000-0002-6874-2313\")),\nperson(given = \"Wouter\",\nfamily = \"van der Bijl\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-7366-1868\", \"template for d-separation test\")),\nperson(given = \"Giovanni M.\",\nfamily = \"Marchetti\",\nemail = \"giovanni.marchetti@unifi.it\",\nrole = c(\"ctr\"),\ncomment = c(\"creator of ggm, from which functions are copied to avoid dependency on package graph not on CRAN\"))\n)",
  "Description": "Applies dynamic structural equation models to time-series\ndata with generic and simplified specification for simultaneous\nand lagged effects. Methods are described in Thorson et al.\n(2024) \"Dynamic structural equation models synthesize ecosystem\ndynamics constrained by ecological mechanisms.\"",
  "License": "GPL-3",
  "Encoding": "UTF-8",
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  "URL": "https://james-thorson-noaa.github.io/dsem/",
  "BugReports": "https://github.com/James-Thorson-NOAA/dsem/issues/",
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  "Author": "James Thorson [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-7415-1010>), Maurice Goodman [ctb]\n(ORCID: <https://orcid.org/0000-0002-6874-2313>), Wouter van\nder Bijl [ctb] (ORCID: <https://orcid.org/0000-0002-7366-1868>,\ntemplate for d-separation test), Giovanni M. Marchetti [ctr]\n(creator of ggm, from which functions are copied to avoid\ndependency on package graph not on CRAN)",
  "Maintainer": "James Thorson <James.Thorson@noaa.gov>",
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    "dsem_control",
    "fixed",
    "gaussian_fixed_sd",
    "list_parameters",
    "lognormal",
    "loo_residuals",
    "make_dfa",
    "make_dsem_ram",
    "make_matrices",
    "make_msv",
    "parse_path",
    "partition_variance",
    "rk4sys",
    "stepwise_selection",
    "test_dsep",
    "TMBAIC",
    "total_effect",
    "tweedie"
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      "title": "Bering Sea marine ecosystem",
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        "log_seaice",
        "log_Cfall",
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        "lynx"
      ],
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      "title": "Isle Royale wolf and moose",
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      "class": [
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        "wolves",
        "moose"
      ],
      "rows": 61,
      "table": true,
      "tojson": true
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      "title": "Lake washington plankton",
      "object": "lake_washington",
      "class": [
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      ],
      "fields": [
        "Year",
        "Month",
        "Temp",
        "Daphnia",
        "Leptodora",
        "Cryptomonas"
      ],
      "rows": 396,
      "table": true,
      "tojson": true
    },
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      "name": "paramesium_didinium",
      "title": "Paramesium-Didinium dynamics",
      "object": "paramesium_didinium",
      "class": [
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      ],
      "fields": [
        "time",
        "paramecium",
        "didinium"
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      "table": true,
      "tojson": true
    },
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      "object": "pdo_departure_bay",
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        "PDO"
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      "table": true,
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        "log_Kelp_CANNERY_UC",
        "Pycno_CANNERY_UC",
        "log_Urchins_CANNERY_UC",
        "log_Otter_Count_CANNERY_UC",
        "log_Kelp_HOPKINS_DC",
        "Pycno_HOPKINS_DC",
        "log_Urchins_HOPKINS_DC",
        "log_Otter_Count_HOPKINS_DC",
        "log_Kelp_HOPKINS_UC",
        "Pycno_HOPKINS_UC",
        "log_Urchins_HOPKINS_UC",
        "log_Otter_Count_HOPKINS_UC",
        "log_Kelp_LOVERS_DC",
        "Pycno_LOVERS_DC",
        "log_Urchins_LOVERS_DC",
        "log_Otter_Count_LOVERS_DC",
        "log_Kelp_LOVERS_UC",
        "Pycno_LOVERS_UC",
        "log_Urchins_LOVERS_UC",
        "log_Otter_Count_LOVERS_UC",
        "log_Kelp_MACABEE_DC",
        "Pycno_MACABEE_DC",
        "log_Urchins_MACABEE_DC",
        "log_Otter_Count_MACABEE_DC",
        "log_Kelp_MACABEE_UC",
        "Pycno_MACABEE_UC",
        "log_Urchins_MACABEE_UC",
        "log_Otter_Count_MACABEE_UC",
        "log_Kelp_OTTER_PT_DC",
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        "log_Urchins_OTTER_PT_DC",
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        "log_Kelp_OTTER_PT_UC",
        "Pycno_OTTER_PT_UC",
        "log_Urchins_OTTER_PT_UC",
        "log_Otter_Count_OTTER_PT_UC",
        "log_Kelp_PINOS_CEN",
        "Pycno_PINOS_CEN",
        "log_Urchins_PINOS_CEN",
        "log_Otter_Count_PINOS_CEN",
        "log_Kelp_SIREN_CEN",
        "Pycno_SIREN_CEN",
        "log_Urchins_SIREN_CEN",
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      "table": true,
      "tojson": true
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    {
      "page": "as_fitted_DAG",
      "title": "Convert output from package dsem to phylopath",
      "topics": [
        "as_fitted_DAG"
      ]
    },
    {
      "page": "bering_sea",
      "title": "Bering Sea marine ecosystem",
      "topics": [
        "bering_sea"
      ]
    },
    {
      "page": "cAIC",
      "title": "Calculate conditional AIC",
      "topics": [
        "cAIC"
      ]
    },
    {
      "page": "classify_variables",
      "title": "Classify variables path",
      "topics": [
        "classify_variables"
      ]
    },
    {
      "page": "convert_equations",
      "title": "Convert equations notation",
      "topics": [
        "convert_equations"
      ]
    },
    {
      "page": "dsem",
      "title": "Fit dynamic structural equation model",
      "topics": [
        "dsem"
      ]
    },
    {
      "page": "dsem_control",
      "title": "Detailed control for dsem structure",
      "topics": [
        "dsem_control"
      ]
    },
    {
      "page": "dsemRTMB",
      "title": "Fit dynamic structural equation model",
      "topics": [
        "dsemRTMB"
      ]
    },
    {
      "page": "fixed",
      "title": "Family for data that are known without error",
      "topics": [
        "fixed"
      ]
    },
    {
      "page": "gaussian_fixed_sd",
      "title": "Gaussian with known standard deviation for measurement errors",
      "topics": [
        "gaussian_fixed_sd"
      ]
    },
    {
      "page": "hare_lynx",
      "title": "Lynx-Hare dynamics",
      "topics": [
        "hare_lynx"
      ]
    },
    {
      "page": "isle_royale",
      "title": "Isle Royale wolf and moose",
      "topics": [
        "isle_royale"
      ]
    },
    {
      "page": "lake_washington",
      "title": "Lake washington plankton",
      "topics": [
        "lake_washington"
      ]
    },
    {
      "page": "list_parameters",
      "title": "List fixed and random effects",
      "topics": [
        "list_parameters"
      ]
    },
    {
      "page": "logLik.dsem",
      "title": "Marginal log-likelihood",
      "topics": [
        "logLik.dsem"
      ]
    },
    {
      "page": "lognormal",
      "title": "Lognormal distribution",
      "topics": [
        "lognormal"
      ]
    },
    {
      "page": "loo_residuals",
      "title": "Calculate leave-one-out residuals",
      "topics": [
        "loo_residuals"
      ]
    },
    {
      "page": "make_dfa",
      "title": "Make text for dynamic factor analysis",
      "topics": [
        "make_dfa"
      ]
    },
    {
      "page": "make_dsem_ram",
      "title": "Make a RAM (Reticular Action Model)",
      "topics": [
        "make_dsem_ram"
      ]
    },
    {
      "page": "make_matrices",
      "title": "Make path matrices",
      "topics": [
        "make_matrices"
      ]
    },
    {
      "page": "make_msv",
      "title": "Make text for multivariate stochastic volatility model",
      "topics": [
        "make_msv"
      ]
    },
    {
      "page": "paramesium_didinium",
      "title": "Paramesium-Didinium dynamics",
      "topics": [
        "paramesium_didinium"
      ]
    },
    {
      "page": "parse_path",
      "title": "Parse path",
      "topics": [
        "parse_path"
      ]
    },
    {
      "page": "partition_variance",
      "title": "Partition variance in one variable due to another (EXPERIMENTAL)",
      "topics": [
        "partition_variance"
      ]
    },
    {
      "page": "pdo_departure_bay",
      "title": "Pacific Decadal Oscillation and Departure Bay temperatures",
      "topics": [
        "pdo_departure_bay"
      ]
    },
    {
      "page": "plot.dsem",
      "title": "Simulate dsem",
      "topics": [
        "plot.dsem"
      ]
    },
    {
      "page": "predict.dsem",
      "title": "predictions using dsem",
      "topics": [
        "predict.dsem"
      ]
    },
    {
      "page": "print.dsem",
      "title": "Print fitted dsem object",
      "topics": [
        "print.dsem"
      ]
    },
    {
      "page": "read_model",
      "title": "Make a RAM (Reticular Action Model)",
      "topics": [
        "read_model"
      ]
    },
    {
      "page": "residuals.dsem",
      "title": "Calculate residuals",
      "topics": [
        "residuals.dsem"
      ]
    },
    {
      "page": "rk4sys",
      "title": "Classical Runge-Kutta for system of equations",
      "topics": [
        "rk4sys"
      ]
    },
    {
      "page": "sea_otter",
      "title": "Sea otter trophic cascade",
      "topics": [
        "sea_otter"
      ]
    },
    {
      "page": "simulate.dsem",
      "title": "Simulate dsem",
      "topics": [
        "simulate.dsem"
      ]
    },
    {
      "page": "stepwise_selection",
      "title": "Simulate dsem",
      "topics": [
        "stepwise_selection"
      ]
    },
    {
      "page": "summary.dsem",
      "title": "summarize dsem",
      "topics": [
        "summary.dsem"
      ]
    },
    {
      "page": "test_dsep",
      "title": "Test d-separation",
      "topics": [
        "test_dsep"
      ]
    },
    {
      "page": "TMBAIC",
      "title": "Calculate marginal AIC for a fitted model",
      "topics": [
        "TMBAIC"
      ]
    },
    {
      "page": "total_effect",
      "title": "Calculate total effects",
      "topics": [
        "total_effect"
      ]
    },
    {
      "page": "tweedie",
      "title": "Tweedie distribution",
      "topics": [
        "tweedie"
      ]
    },
    {
      "page": "vcov.dsem",
      "title": "Extract Variance-Covariance Matrix",
      "topics": [
        "vcov.dsem"
      ]
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