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  "Title": "Simulation-Based Landscape Construction for Dynamical Systems",
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  "Description": "A toolbox for constructing potential landscapes for\ndynamical systems using Monte Carlo simulation.  The method is\nbased on the potential landscape definition by Wang et al.\n(2008) <doi:10.1073/pnas.0800579105> (also see Zhou & Li, 2016\n<doi:10.1063/1.4943096> for further mathematical discussions)\nand can be used for a large variety of models.",
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  "Repository": "https://sciurus365.r-universe.dev",
  "Date/Publication": "2025-02-12 15:46:59 UTC",
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    "make_2d_single",
    "make_2d_static",
    "make_2d_tidy_dist",
    "make_3d_animation",
    "make_3d_matrix",
    "make_3d_single",
    "make_3d_static",
    "make_4d_single",
    "make_4d_static",
    "make_arg_grid",
    "make_barrier_grid_2d",
    "make_barrier_grid_3d",
    "modified_simulation",
    "multi_init_simulation",
    "narg",
    "nele",
    "new_arg_set",
    "save_landscape",
    "sim_fun_grad",
    "sim_fun_nongrad",
    "sim_fun_test",
    "sim_fun_test2",
    "sim_SDE"
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      "page": "arg_set-class",
      "title": "Create and modify argument sets, then make an argument grid for batch simulation",
      "topics": [
        "add_arg_ele",
        "arg_set-class",
        "make_arg_grid",
        "narg",
        "nele",
        "new_arg_set",
        "print.arg_grid",
        "print.arg_set"
      ]
    },
    {
      "page": "as.mcmc.list.list",
      "title": "Convert a list of simulation output to a mcmc.list object",
      "topics": [
        "as.mcmc.list.list"
      ]
    },
    {
      "page": "attach_all_matrices",
      "title": "Attach all matrices in a batch simulation",
      "topics": [
        "attach_all_matrices"
      ]
    },
    {
      "page": "autolayer.barrier",
      "title": "Get a ggplot2 layer from a barrier object",
      "topics": [
        "autolayer.barrier"
      ]
    },
    {
      "page": "batch_simulation",
      "title": "Perform a batch simulation.",
      "topics": [
        "batch_simulation",
        "print.batch_simulation"
      ]
    },
    {
      "page": "calculate_barrier",
      "title": "Functions for calculating energy barrier from landscapes",
      "topics": [
        "calculate_barrier",
        "calculate_barrier.2d_landscape",
        "calculate_barrier.2d_landscape_batch",
        "calculate_barrier.3d_landscape",
        "calculate_barrier.3d_landscape_batch"
      ]
    },
    {
      "page": "check_conv",
      "title": "Graphical diagnoses to check if the simulation converges",
      "topics": [
        "check_conv",
        "print.check_conv"
      ]
    },
    {
      "page": "get_dist",
      "title": "Get the probability distribution from a landscape object",
      "topics": [
        "get_dist"
      ]
    },
    {
      "page": "hash_big_matrix-class",
      "title": "Class \"hash_big_matrix\": big matrix with a md5 hash reference",
      "topics": [
        "as_hash_big_matrix",
        "attach_hash_big_matrix",
        "hash_big_matrix",
        "hash_big_matrix-class"
      ]
    },
    {
      "page": "make_2d_matrix",
      "title": "Make a matrix of 2D static landscape plots for one or two parameters",
      "topics": [
        "make_2d_matrix"
      ]
    },
    {
      "page": "make_2d_static",
      "title": "Make 2D static landscape plot for a single simulation output",
      "topics": [
        "make_2d_single",
        "make_2d_static"
      ]
    },
    {
      "page": "make_3d_animation",
      "title": "Make 3d animations from multiple simulations",
      "topics": [
        "make_3d_animation"
      ]
    },
    {
      "page": "make_3d_matrix",
      "title": "Make a matrix of 3D static landscape plots for one or two parameters",
      "topics": [
        "make_3d_matrix"
      ]
    },
    {
      "page": "make_3d_static",
      "title": "Make 3D static landscape plots from simulation output",
      "topics": [
        "make_3d_single",
        "make_3d_static"
      ]
    },
    {
      "page": "make_4d_static",
      "title": "Make 4D static space-color plots from simulation output",
      "topics": [
        "make_4d_single",
        "make_4d_static"
      ]
    },
    {
      "page": "make_barrier_grid_2d",
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      ]
    },
    {
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