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  "Title": "Life History Metrics from Matrix Population Models",
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  "Description": "Functions for calculating life history metrics using\nmatrix population models ('MPMs'). Described in Jones et al.\n(2021) <doi:10.1101/2021.04.26.441330>.",
  "License": "GPL-3",
  "URL": "https://github.com/jonesor/Rage, https://jonesor.github.io/Rage/",
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  "Repository": "https://jonesor.r-universe.dev",
  "Date/Publication": "2026-05-04 06:49:02 UTC",
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  "Author": "Patrick Barks [aut] (ORCID: <https://orcid.org/0000-0002-5947-8151>),\nDanny Buss [ctb],\nPol Capdevila [aut] (ORCID: <https://orcid.org/0000-0002-2842-4302>),\nHal Caswell [aut] (ORCID: <https://orcid.org/0000-0003-4394-6894>),\nJudy P. Che-Castaldo [aut] (ORCID:\n<https://orcid.org/0000-0002-9118-9202>),\nRichard A. Hinrichsen [aut] (ORCID:\n<https://orcid.org/0000-0003-0761-3005>),\nJohn Jackson [aut] (ORCID: <https://orcid.org/0000-0002-4563-2840>),\nTamora James [aut] (ORCID: <https://orcid.org/0000-0003-1363-4742>),\nOwen Jones [aut, cre] (ORCID: <https://orcid.org/0000-0001-5720-4686>),\nSam Levin [aut] (ORCID: <https://orcid.org/0000-0002-3289-9925>),\nWilliam K. Petry [aut] (ORCID: <https://orcid.org/0000-0002-5230-5987>),\nRoberto Salguero-Gomez [aut] (ORCID:\n<https://orcid.org/0000-0002-6085-4433>),\nCaroline Schuette [ctb] (ORCID:\n<https://orcid.org/0000-0002-2063-8736>),\nIain Stott [aut] (ORCID: <https://orcid.org/0000-0003-2724-7436>),\nChelsea C. Thomas [aut] (ORCID:\n<https://orcid.org/0000-0002-8155-9353>),\nChristina M. Hernández [aut] (ORCID:\n<https://orcid.org/0000-0002-7188-8217>),\nLotte de Vries [aut] (ORCID: <https://orcid.org/0000-0001-8955-0479>),\nStefano Giaimo [aut] (ORCID: <https://orcid.org/0000-0003-0421-3065>)",
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    "entropy_d",
    "entropy_k",
    "entropy_k_age",
    "entropy_k_stage",
    "evenness_shannon",
    "gen_time",
    "hx_to_lx",
    "hx_to_px",
    "is_leslie_matrix",
    "leslie_collapse",
    "life_elas",
    "life_expect_mean",
    "life_expect_var",
    "longevity",
    "lx_to_hx",
    "lx_to_px",
    "mature_age",
    "mature_distrib",
    "mature_prob",
    "mpm_collapse",
    "mpm_rearrange",
    "mpm_split",
    "mpm_standardise",
    "mpm_standardize",
    "mpm_to_hx",
    "mpm_to_lx",
    "mpm_to_mx",
    "mpm_to_px",
    "mpm_to_table",
    "name_stages",
    "net_repro_rate",
    "perturb_matrix",
    "perturb_stochastic",
    "perturb_trans",
    "perturb_vr",
    "plot_life_cycle",
    "pop_vectors",
    "px_to_hx",
    "px_to_lx",
    "qsd_converge",
    "repro_stages",
    "scale_mpm_to_lambda1",
    "shape_rep",
    "shape_surv",
    "stage_at_death_dist",
    "standard_stages",
    "vital_rates",
    "vr_dorm_enter",
    "vr_dorm_exit",
    "vr_fecundity",
    "vr_growth",
    "vr_mat_R",
    "vr_mat_U",
    "vr_shrinkage",
    "vr_stasis",
    "vr_survival",
    "vr_vec_dorm_enter",
    "vr_vec_dorm_exit",
    "vr_vec_growth",
    "vr_vec_reproduction",
    "vr_vec_shrinkage",
    "vr_vec_stasis",
    "vr_vec_survival"
  ],
  "_datasets": [
    {
      "name": "leslie_mpm1",
      "title": "Example Leslie matrix population model (MPM)",
      "object": "leslie_mpm1",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "mpm1",
      "title": "Example matrix population model (MPM)",
      "object": "mpm1",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "age_from_stage",
      "title": "Calculate age-specific traits from a matrix population model",
      "concept": [
        "life tables"
      ],
      "topics": [
        "age_from_stage",
        "mpm_to_hx",
        "mpm_to_lx",
        "mpm_to_mx",
        "mpm_to_px"
      ]
    },
    {
      "page": "entropy_d",
      "title": "Calculate Demetrius' entropy from trajectories of age-specific survivorship and fecundity",
      "concept": [
        "life history traits"
      ],
      "topics": [
        "entropy_d"
      ]
    },
    {
      "page": "entropy_k",
      "title": "Calculate Keyfitz's entropy from a trajectory of age-specific survivorship",
      "concept": [
        "life history traits"
      ],
      "topics": [
        "entropy_k"
      ]
    },
    {
      "page": "entropy_k_age",
      "title": "Calculate Keyfitz entropy for an age-based matrix population model",
      "concept": [
        "life history traits"
      ],
      "topics": [
        "entropy_k_age"
      ]
    },
    {
      "page": "entropy_k_stage",
      "title": "Calculate Keyfitz entropy for a stage-based matrix population model",
      "concept": [
        "life history traits"
      ],
      "topics": [
        "entropy_k_stage"
      ]
    },
    {
      "page": "evenness_shannon",
      "title": "Shannon Evenness (Pielou's J)",
      "topics": [
        "evenness_shannon"
      ]
    },
    {
      "page": "gen_time",
      "title": "Calculate generation time from a matrix population model",
      "concept": [
        "life history traits"
      ],
      "topics": [
        "gen_time"
      ]
    },
    {
      "page": "is_leslie_matrix",
      "title": "Determine if a matrix is a Leslie matrix population model",
      "concept": [
        "transformation"
      ],
      "topics": [
        "is_leslie_matrix"
      ]
    },
    {
      "page": "leslie_collapse",
      "title": "Aggregate a Leslie matrix",
      "concept": [
        "transformation"
      ],
      "topics": [
        "leslie_collapse"
      ]
    },
    {
      "page": "leslie_mpm1",
      "title": "Example Leslie matrix population model (MPM)",
      "topics": [
        "leslie_mpm1"
      ]
    },
    {
      "page": "life_elas",
      "title": "Calculate Keyfitz's entropy from a trajectory of age-specific survivorship",
      "concept": [
        "life history traits"
      ],
      "topics": [
        "life_elas"
      ]
    },
    {
      "page": "life_expect",
      "title": "Calculate mean and variance of life expectancy from a matrix population model",
      "concept": [
        "life history traits"
      ],
      "topics": [
        "life_expect_mean",
        "life_expect_var"
      ]
    },
    {
      "page": "lifetable_convert",
      "title": "Convert between age-specific survivorship, survival, or mortality hazard",
      "concept": [
        "life tables"
      ],
      "topics": [
        "hx_to_lx",
        "hx_to_px",
        "lifetable_convert",
        "lx_to_hx",
        "lx_to_px",
        "px_to_hx",
        "px_to_lx"
      ]
    },
    {
      "page": "longevity",
      "title": "Calculate longevity from a matrix population model",
      "concept": [
        "life history traits"
      ],
      "topics": [
        "longevity"
      ]
    },
    {
      "page": "mpm_collapse",
      "title": "Collapse a matrix population model to a smaller number of stages",
      "concept": [
        "transformation"
      ],
      "topics": [
        "mpm_collapse"
      ]
    },
    {
      "page": "mpm_rearrange",
      "title": "Rearrange stages of a matrix population model to segregate reproductive and non-reproductive stages",
      "concept": [
        "transformation"
      ],
      "topics": [
        "mpm_rearrange"
      ]
    },
    {
      "page": "mpm_split",
      "title": "Convert matrix population model into U, F and C matrices",
      "concept": [
        "transformation"
      ],
      "topics": [
        "mpm_split"
      ]
    },
    {
      "page": "mpm_standardize",
      "title": "Transform a matrix population model to a standardized form",
      "concept": [
        "transformation"
      ],
      "topics": [
        "mpm_standardise",
        "mpm_standardize"
      ]
    },
    {
      "page": "mpm_to_table",
      "title": "Generate a life table from a matrix population model",
      "concept": [
        "life tables"
      ],
      "topics": [
        "mpm_to_table"
      ]
    },
    {
      "page": "mpm1",
      "title": "Example matrix population model (MPM)",
      "topics": [
        "mpm1"
      ]
    },
    {
      "page": "name_stages",
      "title": "Add stage names to matrices",
      "concept": [
        "transformation"
      ],
      "topics": [
        "name_stages"
      ]
    },
    {
      "page": "net_repro_rate",
      "title": "Calculate net reproductive rate (R0) from a matrix population model",
      "concept": [
        "life history traits"
      ],
      "topics": [
        "net_repro_rate"
      ]
    },
    {
      "page": "perturb_matrix",
      "title": "Perturbation analysis of a matrix population model",
      "concept": [
        "perturbation analysis"
      ],
      "topics": [
        "perturb_matrix"
      ]
    },
    {
      "page": "perturb_stochastic",
      "title": "Calculate stochastic elasticities from a time-series of matrix population models and corresponding population vectors",
      "concept": [
        "perturbation analysis"
      ],
      "topics": [
        "perturb_stochastic"
      ]
    },
    {
      "page": "perturb_trans",
      "title": "Perturbation analysis of transition types within a matrix population model",
      "concept": [
        "perturbation analysis"
      ],
      "topics": [
        "perturb_trans"
      ]
    },
    {
      "page": "perturb_vr",
      "title": "Perturbation analysis of vital rates in a matrix population model",
      "concept": [
        "perturbation analysis"
      ],
      "topics": [
        "perturb_vr"
      ]
    },
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