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        "lefko3"
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      "page": "actualstage3",
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    {
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      "title": "Matrix Set of _Anthyllis vulneraria_ Populations in Belgium",
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    },
    {
      "page": "append_lP",
      "title": "Append Projections To Create New lefkoProj Object",
      "topics": [
        "append_lP"
      ]
    },
    {
      "page": "arlefko2",
      "title": "Create Raw Ahistorical Age x Stage Matrix Projection Model",
      "topics": [
        "arlefko2"
      ]
    },
    {
      "page": "beverton3",
      "title": "Two-Parameter Beverton-Holt Function",
      "topics": [
        "beverton3"
      ]
    },
    {
      "page": "bootstrap3",
      "title": "Bootstrap Standardized hfv_data Datasets",
      "topics": [
        "bootstrap3"
      ]
    },
    {
      "page": "cond_diff",
      "title": "Extract Conditional Ahistorical Difference Matrices",
      "topics": [
        "cond_diff"
      ]
    },
    {
      "page": "cond_hmpm",
      "title": "Extract Conditional Ahistorical Matrices from Historical MPM",
      "topics": [
        "cond_hmpm"
      ]
    },
    {
      "page": "create_lM",
      "title": "Create lefkoMat Object from Given Input Matrices or an MPM Database",
      "topics": [
        "create_lM"
      ]
    },
    {
      "page": "create_pm",
      "title": "Creates a Skeleton Paramnames Object for Use in Function-based Modeling",
      "topics": [
        "create_pm"
      ]
    },
    {
      "page": "cycle_check",
      "title": "Check Continuity of Life Cycle through Matrices in lefkoMat Objects",
      "topics": [
        "cycle_check"
      ]
    },
    {
      "page": "cypdata",
      "title": "Demographic Dataset of _Cypripedium candidum_ Population, in Horizontal Format",
      "topics": [
        "cypdata"
      ]
    },
    {
      "page": "cypvert",
      "title": "Demographic Dataset of _Cypripedium candidum_ Population, in Vertical Format",
      "topics": [
        "cypvert"
      ]
    },
    {
      "page": "delete_lM",
      "title": "Delete Matrices from lefkoMat or lefkoMatList Object",
      "topics": [
        "delete_lM"
      ]
    },
    {
      "page": "density_input",
      "title": "Set Density Dependence Relationships in Matrix Elements",
      "topics": [
        "density_input"
      ]
    },
    {
      "page": "density_vr",
      "title": "Set Density Dependence Relationships in Vital Rates",
      "topics": [
        "density_vr"
      ]
    },
    {
      "page": "diff_lM",
      "title": "Calculate Difference Matrices Between lefkoMat Objects of Equal Dimensions",
      "topics": [
        "diff_lM"
      ]
    },
    {
      "page": "edit_lM",
      "title": "Edit lefkoMat or lefkoMatList Object based on Supplemental Data",
      "topics": [
        "edit_lM"
      ]
    },
    {
      "page": "elasticity3",
      "title": "Estimate Elasticity of Population Growth Rate to Matrix Elements",
      "topics": [
        "elasticity3"
      ]
    },
    {
      "page": "elasticity3.dgCMatrix",
      "title": "Estimate Elasticity of Population Growth Rate of a Single Sparse Matrix",
      "topics": [
        "elasticity3.dgCMatrix"
      ]
    },
    {
      "page": "elasticity3.lefkoMat",
      "title": "Estimate Elasticity of Population Growth Rate of a lefkoMat Object",
      "topics": [
        "elasticity3.lefkoMat"
      ]
    },
    {
      "page": "elasticity3.lefkoMatList",
      "title": "Estimate Elasticity of Population Growth Rate of a lefkoMatList Object",
      "topics": [
        "elasticity3.lefkoMatList"
      ]
    },
    {
      "page": "elasticity3.list",
      "title": "Estimate Elasticity of Population Growth Rate of a List of Matrices",
      "topics": [
        "elasticity3.list"
      ]
    },
    {
      "page": "elasticity3.matrix",
      "title": "Estimate Elasticity of Population Growth Rate of a Single Matrix",
      "topics": [
        "elasticity3.matrix"
      ]
    },
    {
      "page": "f_projection3",
      "title": "Project Function-based Matrix Projection Model",
      "topics": [
        "f_projection3"
      ]
    },
    {
      "page": "flefko2",
      "title": "Create Function-based Ahistorical Matrix Projection Model",
      "topics": [
        "flefko2"
      ]
    },
    {
      "page": "flefko3",
      "title": "Create Function-based Historical Matrix Projection Model",
      "topics": [
        "flefko3"
      ]
    },
    {
      "page": "fleslie",
      "title": "Create Function-based Age-based (Leslie) Matrix Projection Model",
      "topics": [
        "fleslie"
      ]
    },
    {
      "page": "hfv_qc",
      "title": "Assess Quality of hfv Datasets",
      "topics": [
        "hfv_qc"
      ]
    },
    {
      "page": "hist_null",
      "title": "Create Historical MPMs Assuming No Influence of Individual History",
      "topics": [
        "hist_null"
      ]
    },
    {
      "page": "historicalize3",
      "title": "Create Historical Vertical Data Frame from Ahistorical Vertical Data Frame",
      "topics": [
        "historicalize3"
      ]
    },
    {
      "page": "image3",
      "title": "Create Matrix Image",
      "topics": [
        "image3"
      ]
    },
    {
      "page": "image3.dgCMatrix",
      "title": "Create a Matrix Image for a Single Sparse Matrix",
      "topics": [
        "image3.dgCMatrix"
      ]
    },
    {
      "page": "image3.lefkoElas",
      "title": "Create Matrix Image(s) for lefkoElas Object",
      "topics": [
        "image3.lefkoElas"
      ]
    },
    {
      "page": "image3.lefkoMat",
      "title": "Create Matrix Image(s) for lefkoMat Object",
      "topics": [
        "image3.lefkoMat"
      ]
    },
    {
      "page": "image3.lefkoSens",
      "title": "Create Matrix Image(s) for lefkoSens Object",
      "topics": [
        "image3.lefkoSens"
      ]
    },
    {
      "page": "image3.list",
      "title": "Create Matrix Images for Matrices in a List",
      "topics": [
        "image3.list"
      ]
    },
    {
      "page": "image3.matrix",
      "title": "Create a Matrix Image for a Single Matrix",
      "topics": [
        "image3.matrix"
      ]
    },
    {
      "page": "lambda3",
      "title": "Estimate Actual or Deterministic Population Growth Rate",
      "topics": [
        "lambda3"
      ]
    },
    {
      "page": "lathyrus",
      "title": "Demographic Dataset of _Lathyrus vernus_ Population",
      "topics": [
        "lathyrus"
      ]
    },
    {
      "page": "lmean",
      "title": "Estimate Mean Projection Matrices",
      "topics": [
        "lmean"
      ]
    },
    {
      "page": "logistic3",
      "title": "Two-Parameter logistic Function",
      "topics": [
        "logistic3"
      ]
    },
    {
      "page": "ltre3",
      "title": "Conduct a Life Table Response Experiment",
      "topics": [
        "ltre3"
      ]
    },
    {
      "page": "markov_run",
      "title": "Creates Vector of Times Based on First-Order Markov Transition Matrix",
      "topics": [
        "markov_run"
      ]
    },
    {
      "page": "matrix_interp",
      "title": "Arranges Matrix Elements in Order of Magnitude for Interpretation",
      "topics": [
        "matrix_interp"
      ]
    },
    {
      "page": "miniMod",
      "title": "Minimize lefkoMod Object by Conversion to vrm_input Object",
      "topics": [
        "miniMod"
      ]
    },
    {
      "page": "modelsearch",
      "title": "Develop Best-fit Vital Rate Estimation Models for MPM Development",
      "topics": [
        "modelsearch"
      ]
    },
    {
      "page": "mpm_create",
      "title": "General Matrix Projection Model and Bootstrapped MPM Creation",
      "topics": [
        "mpm_create"
      ]
    },
    {
      "page": "overwrite",
      "title": "Create Overwrite Table for MPM Development",
      "topics": [
        "overwrite"
      ]
    },
    {
      "page": "plot.lefkoProj",
      "title": "Plot Projection Simulations",
      "topics": [
        "plot.lefkoProj"
      ]
    },
    {
      "page": "projection3",
      "title": "Conduct Population Projection Simulations",
      "topics": [
        "projection3"
      ]
    },
    {
      "page": "pyrola",
      "title": "Demographic Dataset of _Pyrola japonica_ and _Pyrola subaphylla_ Populations, in Horizontal Format",
      "topics": [
        "pyrola"
      ]
    },
    {
      "page": "repvalue3",
      "title": "Estimate Reproductive Value",
      "topics": [
        "repvalue3"
      ]
    },
    {
      "page": "repvalue3.dgCMatrix",
      "title": "Estimate Reproductive Value Vector for a Single Population Projection Matrix",
      "topics": [
        "repvalue3.dgCMatrix"
      ]
    },
    {
      "page": "repvalue3.lefkoMat",
      "title": "Estimate Reproductive Value Vectors of Matrices in a lefkoMat Object",
      "topics": [
        "repvalue3.lefkoMat"
      ]
    },
    {
      "page": "repvalue3.lefkoMatList",
      "title": "Estimate Reproductive Value Vectors of Matrices in a lefkoMatList Object",
      "topics": [
        "repvalue3.lefkoMatList"
      ]
    },
    {
      "page": "repvalue3.list",
      "title": "Estimate Reproductive Value Vector for a List of Projection Matrices",
      "topics": [
        "repvalue3.list"
      ]
    },
    {
      "page": "repvalue3.matrix",
      "title": "Estimate Reproductive Value Vector for a Single Population Projection Matrix",
      "topics": [
        "repvalue3.matrix"
      ]
    },
    {
      "page": "ricker3",
      "title": "Two-Parameter Ricker Function",
      "topics": [
        "ricker3"
      ]
    },
    {
      "page": "rlefko2",
      "title": "Create Raw Ahistorical Matrix Projection Model",
      "topics": [
        "rlefko2"
      ]
    },
    {
      "page": "rlefko3",
      "title": "Create Raw Historical Matrix Projection Model",
      "topics": [
        "rlefko3"
      ]
    },
    {
      "page": "rleslie",
      "title": "Create Raw Leslie (Age-based) Matrix Projection Model",
      "topics": [
        "rleslie"
      ]
    },
    {
      "page": "sensitivity3",
      "title": "Estimate Sensitivity of Population Growth Rate to Matrix Elements",
      "topics": [
        "sensitivity3"
      ]
    },
    {
      "page": "sensitivity3.dgCMatrix",
      "title": "Estimate Sensitivity of Population Growth Rate of a Single Matrix",
      "topics": [
        "sensitivity3.dgCMatrix"
      ]
    },
    {
      "page": "sensitivity3.lefkoMat",
      "title": "Estimate Sensitivity of Population Growth Rate of a lefkoMat Object",
      "topics": [
        "sensitivity3.lefkoMat"
      ]
    },
    {
      "page": "sensitivity3.lefkoMatList",
      "title": "Estimate Sensitivity of Population Growth Rate of a lefkoMatList Object",
      "topics": [
        "sensitivity3.lefkoMatList"
      ]
    },
    {
      "page": "sensitivity3.list",
      "title": "Estimate Sensitivity of Population Growth Rate of a List of Matrices",
      "topics": [
        "sensitivity3.list"
      ]
    },
    {
      "page": "sensitivity3.matrix",
      "title": "Estimate Sensitivity of Population Growth Rate of a Single Matrix",
      "topics": [
        "sensitivity3.matrix"
      ]
    },
    {
      "page": "sf_create",
      "title": "Create Stageframe for Population Matrix Projection Analysis",
      "topics": [
        "sf_create"
      ]
    },
    {
      "page": "sf_distrib",
      "title": "Test Overdispersion and Zero Inflation in Size and Fecundity Distributions",
      "topics": [
        "sf_distrib"
      ]
    },
    {
      "page": "sf_skeleton",
      "title": "Create Skeleton Stageframe",
      "topics": [
        "sf_skeleton"
      ]
    },
    {
      "page": "slambda3",
      "title": "Estimate Stochastic Population Growth Rate",
      "topics": [
        "slambda3"
      ]
    },
    {
      "page": "stablestage3",
      "title": "Estimate Stable Stage Distribution",
      "topics": [
        "stablestage3"
      ]
    },
    {
      "page": "stablestage3.dgCMatrix",
      "title": "Estimate Stable Stage Distribution of a Single Population Projection Matrix",
      "topics": [
        "stablestage3.dgCMatrix"
      ]
    },
    {
      "page": "stablestage3.lefkoMat",
      "title": "Estimate Stable Stage Distribution of Matrices in lefkoMat Object",
      "topics": [
        "stablestage3.lefkoMat"
      ]
    },
    {
      "page": "stablestage3.lefkoMatList",
      "title": "Estimate Stable Stage Distribution of Matrices in lefkoMatList Object",
      "topics": [
        "stablestage3.lefkoMatList"
      ]
    },
    {
      "page": "stablestage3.list",
      "title": "Estimate Stable Stage Distribution of a List of Projection Matrices",
      "topics": [
        "stablestage3.list"
      ]
    },
    {
      "page": "stablestage3.matrix",
      "title": "Estimate Stable Stage Distribution of a Single Population Projection Matrix",
      "topics": [
        "stablestage3.matrix"
      ]
    },
    {
      "page": "stage_weight",
      "title": "Create a Vector of Stage Weights for Density Dependence Calculations",
      "topics": [
        "stage_weight"
      ]
    },
    {
      "page": "start_input",
      "title": "Create a Starting Vector for Population Projection",
      "topics": [
        "start_input"
      ]
    },
    {
      "page": "subset_lM",
      "title": "Create New lefkoMat or lefkoMatList Object as Subset of Another",
      "topics": [
        "subset_lM"
      ]
    },
    {
      "page": "summary_hfv",
      "title": "Summary of Classes \"hfvdata\" and \"hfvlist",
      "topics": [
        "summary_hfv"
      ]
    },
    {
      "page": "summary.lefkoCondMat",
      "title": "Summary of Class \"lefkoCondMat\"",
      "topics": [
        "summary.lefkoCondMat"
      ]
    },
    {
      "page": "summary.lefkoElas",
      "title": "Summarize lefkoElas Objects",
      "topics": [
        "summary.lefkoElas"
      ]
    },
    {
      "page": "summary.lefkoLTRE",
      "title": "Summarize lefkoLTRE Objects",
      "topics": [
        "summary.lefkoLTRE"
      ]
    },
    {
      "page": "summary.lefkoMat",
      "title": "Summary of Class \"lefkoMat\"",
      "topics": [
        "summary.lefkoMat"
      ]
    },
    {
      "page": "summary.lefkoMatList",
      "title": "Summary of Class \"lefkoMatList\"",
      "topics": [
        "summary.lefkoMatList"
      ]
    },
    {
      "page": "summary.lefkoMod",
      "title": "Summary of Class \"lefkoMod\"",
      "topics": [
        "summary.lefkoMod"
      ]
    },
    {
      "page": "summary.lefkoProj",
      "title": "Summarize lefkoProj Objects",
      "topics": [
        "summary.lefkoProj"
      ]
    },
    {
      "page": "sup_skeleton",
      "title": "Create A Supplement Skeleton Data Frame",
      "topics": [
        "sup_skeleton"
      ]
    },
    {
      "page": "supplemental",
      "title": "Create a Data Frame of Supplemental Data for MPM Development",
      "topics": [
        "supplemental"
      ]
    },
    {
      "page": "usher3",
      "title": "Two-Parameter Usher Function",
      "topics": [
        "usher3"
      ]
    },
    {
      "page": "verticalize3",
      "title": "Create Historical Vertical Data Frame from Horizontal Data Frame",
      "topics": [
        "verticalize3"
      ]
    },
    {
      "page": "vrm_import",
      "title": "Import Vital Rate Model Factor Values for Function-based MPM Development",
      "topics": [
        "vrm_import"
      ]
    }
  ],
  "_readme": "https://github.com/dormancy1/lefko3/raw/HEAD/README.md",
  "_rundeps": [
    "backports",
    "BH",
    "boot",
    "broom",
    "cli",
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    "cowplot",
    "cpp11",
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    "dplyr",
    "farver",
    "forecast",
    "fracdiff",
    "generics",
    "ggplot2",
    "glmmTMB",
    "glue",
    "gtable",
    "insight",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "mgcv",
    "microbenchmark",
    "minqa",
    "modelr",
    "MuMIn",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "pscl",
    "purrr",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "rlang",
    "S7",
    "sandwich",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "TMB",
    "urca",
    "utf8",
    "vctrs",
    "VGAM",
    "viridisLite",
    "withr",
    "zoo"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
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      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
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  ],
  "_vignettes": [
    {
      "source": "Chapter1.Rmd",
      "filename": "Chapter1.html",
      "title": "Basic theory and concepts",
      "author": "Richard P. Shefferson, Shun Kurokawa, and Johan Ehrlén",
      "engine": "knitr::rmarkdown",
      "headings": [
        "INTRODUCTION TO PACKAGE LEFKO3",
        "BASIC CONCEPTS",
        "Life history models and projection matrices",
        "Ahistorical vs. historical matrix models",
        "Raw vs. function-based matrix models, including integral projection models",
        "Different parameterizations of the historical MPM",
        "Leslie (age-classified) MPMs",
        "Age-by-stage MPMs",
        "WORKFLOW",
        "Step 1: Life history model development",
        "Step 2a: Dataset organization",
        "Step 2b: Provide supplemental information for matrix estimation",
        "Step 3: Assess whether historical MPM is justified, and develop models of demographic parameters",
        "Step 4: Estimate matrices",
        "Step 4a. Importing matrices and IPMs",
        "Step 4b. Edit matrices",
        "Step 5. MPM analyses",
        "Deterministic vs. stochastic analysis",
        "Density independent vs. density dependent analysis",
        "Population growth rate",
        "Stable stage distribution and reproductive value",
        "Sensitivity and elasticity",
        "Life table response experiments (LTREs)",
        "Custom projections",
        "Further analyses",
        "Acknowledgements",
        "Literature cited"
      ],
      "created": "2026-02-17 23:41:45",
      "modified": "2026-02-17 23:41:45",
      "commits": 1
    },
    {
      "source": "Chapter5.Rmd",
      "filename": "Chapter5.html",
      "title": "Cypripedium candidum function-based MPMs",
      "author": "Richard P. Shefferson, Shun Kurokawa, and Johan Ehrlén",
      "engine": "knitr::rmarkdown",
      "headings": [
        "ORGANISM AND POPULATION",
        "BASIC WORKFLOW",
        "Step 1. Life history model development",
        "Step 2a. Data standardization",
        "Step 2b. Vertical dataset standardization",
        "Step 2c. Provide supplemental information for matrix estimation",
        "Step 3. Tests of history, and vital rate modeling",
        "Step 3a. General modeling strategy",
        "Step 3b. Size and fecundity distributions",
        "Step 3c. Model building and selection",
        "Step 4. MPM estimation",
        "Step 5. MPM analysis",
        "Acknowledgements",
        "Literature cited"
      ],
      "created": "2026-02-17 23:41:45",
      "modified": "2026-02-17 23:41:45",
      "commits": 1
    },
    {
      "source": "Chapter8.Rmd",
      "filename": "Chapter8.html",
      "title": "Lathyrus vernus function-based age-by-stage MPMs, LTRE and sLTRE analysis",
      "author": "Richard P. Shefferson, Shun Kurokawa, and Johan Ehrlén",
      "engine": "knitr::rmarkdown",
      "headings": [
        "ORGANISM AND POPULATION",
        "BASIC WORKFLOW",
        "Step 1. Life history model development",
        "Step 2a. Data standardization",
        "Step 2b. Provide supplemental information for matrix estimation",
        "Step 3. Tests of history, and vital rate modeling",
        "Step 4. MPM estimation",
        "Step 5. MPM analysis",
        "Acknowledgements",
        "Literature cited"
      ],
      "created": "2026-02-17 23:41:45",
      "modified": "2026-02-17 23:41:45",
      "commits": 1
    },
    {
      "source": "Chapter6.Rmd",
      "filename": "Chapter6.html",
      "title": "Lathyrus vernus IPMs",
      "author": "Richard P. Shefferson, Shun Kurokawa, and Johan Ehrlén",
      "engine": "knitr::rmarkdown",
      "headings": [
        "ORGANISM AND POPULATION",
        "BASIC WORKFLOW",
        "Step 1. Life history model development",
        "Step 2a. Dataset standardization",
        "Step 2b: Develop supplemental information for matrix estimation",
        "Step 3. Tests of history, and vital rate modeling",
        "Step 4. IPM estimation",
        "Step 5. MPM analysis",
        "Acknowledgements",
        "Literature cited"
      ],
      "created": "2026-02-17 23:41:45",
      "modified": "2026-02-17 23:41:45",
      "commits": 1
    },
    {
      "source": "Chapter2.Rmd",
      "filename": "Chapter2.html",
      "title": "Lathyrus vernus raw MPMs",
      "author": "Richard P. Shefferson, Shun Kurokawa, and Johan Ehrlén",
      "engine": "knitr::rmarkdown",
      "headings": [
        "ORGANISM AND POPULATION",
        "BASIC WORKFLOW",
        "Step 1. Life history model development",
        "Step 2a. Data standardization",
        "Step 2b. Provide supplemental information for matrix estimation",
        "Step 3. Tests of history",
        "Step 4. MPM estimation",
        "Step 5. MPM analysis",
        "Acknowledgements",
        "Literature cited"
      ],
      "created": "2026-02-17 23:41:45",
      "modified": "2026-02-17 23:41:45",
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    {
      "source": "Chapter9.Rmd",
      "filename": "Chapter9.html",
      "title": "LTREs, sLTREs, and MPM import with Anthyllis vulneraria",
      "author": "Richard P. Shefferson and Raziel Davison",
      "engine": "knitr::rmarkdown",
      "headings": [
        "ORGANISM AND POPULATIONS",
        "BASIC WORKFLOW",
        "Step 1. Life history model development",
        "Step 3. MPM analysis",
        "Highest stochastic mean LTRE contribution:",
        "Highest stochastic mean LTRE contribution is associated with element:",
        "Lowest stochastic mean LTRE contribution:",
        "Lowest stochastic mean LTRE contribution is associated with element:",
        "Highest stochastic SD LTRE contribution:",
        "Highest stochastic SD LTRE contribution is associated with element:",
        "Lowest stochastic SD LTRE contribution:",
        "Lowest stochastic SD LTRE contribution is associated with element:",
        "Total positive deterministic LTRE contributions:",
        "Total negative deterministic LTRE contributions:",
        "Total positive stochastic mean LTRE contributions:",
        "Total negative stochastic mean LTRE contributions:",
        "Total positive stochastic SD LTRE contributions:",
        "Total negative stochastic SD LTRE contributions:"
      ],
      "created": "2026-02-17 23:41:45",
      "modified": "2026-02-17 23:41:45",
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