{
  "_id": "6acb5ee0fe5cc25786e8ee37",
  "Package": "SEEPS",
  "Title": "Sequence evolution and epidemiological process simulator",
  "Version": "0.2.0",
  "Authors@R": "c(person(given = \"Michael\",\nfamily = \"Kupperman\",\nrole = c(\"aut\", \"cre\"),\nemail = \"mkupperman@lanl.gov\",\ncomment = c(ORCID = \"0000-0003-0340-488X\")),\nperson(given = \"Ruian\",\nfamily = \"Ke\",\nrole = \"aut\",\nemail = \"rke@lanl.gov\",\ncomment = c(ORCID=\"0000-0001-5307-8934\")),\nperson(given = \"Erik\",\nfamily = \"Lundgren\",\nemail = \"elundgren@lanl.gov\",\nrole = \"aut\")\n)",
  "Description": "A modular, modern simulation suite and toolkit for\nsimulating transmission networks, phylogenies, and evolutionary\npairwise distance matrices under different models and\nassumptions for viral/sequence evolution. While intially\ndeveloped for HIV, SEEPS offers modular utilities for custom\nworkflows for extension beyond HIV.",
  "License": "file LICENSE",
  "maintainer": "Michael D. Kupperman <mkupperman@lanl.gov>",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://molevolepid.r-universe.dev",
  "Date/Publication": "2026-02-12 21:28:09 UTC",
  "RemoteUrl": "https://github.com/MolEvolEpid/SEEPS",
  "RemoteRef": "HEAD",
  "RemoteSha": "d987ce02234beecd0a1de51f709a672c3ed04c45",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-11 09:47:06 UTC",
    "User": "root"
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  "Author": "Michael Kupperman [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0340-488X>),\nRuian Ke [aut] (ORCID: <https://orcid.org/0000-0001-5307-8934>),\nErik Lundgren [aut]",
  "Maintainer": "Michael Kupperman <mkupperman@lanl.gov>",
  "_user": "molevolepid",
  "_type": "src",
  "_file": "SEEPS_0.2.0.tar.gz",
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  "_expires": "2027-01-19T10:03:10.000Z",
  "_created": "2026-10-11T09:47:06.000Z",
  "_published": "2026-10-11T10:03:12.649Z",
  "_buildurl": "https://github.com/r-universe/molevolepid/actions/runs/38129401927",
  "_status": "success",
  "_host": "GitHub-Actions",
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  "_upstream": "https://github.com/MolEvolEpid/SEEPS",
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    "author": "Thomas Leitner <61990531+tkleitner@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update README.md\n\nSigned-off-by: Thomas Leitner <61990531+tkleitner@users.noreply.github.com>",
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    "email": "mkupperman@lanl.gov",
    "login": "mkupperman",
    "description": "Data scientst and mathematical biologist. \n\nProgrammer, computational biologist, and applied mathematician with @MolEvolEpid",
    "uuid": 53378682,
    "orcid": "0000-0003-0340-488X"
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  "_dependencies": [
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    {
      "package": "ape",
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      "package": "phyclust",
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  "_owner": "molevolepid",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-07",
      "n": 2
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  ],
  "_tags": [],
  "_topics": [
    "biological-sequences",
    "epidemiology",
    "evolution",
    "hiv",
    "simulation-framework"
  ],
  "_stars": 4,
  "_contributors": [
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  "_userbio": {
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    "type": "organization",
    "name": "LANL Molecular Evolution & Epidemiology Team",
    "followers": 11,
    "description": "Public health-related work done in the Theoretical Biology & Biophysics Group at Los Alamos National Laboratory"
  },
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SEEPS"
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  "_exports": [
    "add_root_to_newick",
    "assign_parental_factory",
    "assign_random_factory",
    "assign_random_with_inheritance_factory",
    "biphasic_HIV_rate",
    "build_distance_matrix_from_df",
    "clean_sample_structure",
    "clean_up",
    "constant_dispersion_sampler",
    "contact_traced_uniform_ids",
    "contact_traced_uniform_restarts_ids",
    "contact_tracing_core",
    "contact_tracing_engine",
    "dispersion_calculator",
    "exponential_dispersion_sampler",
    "fasta_string_to_dataframe",
    "gen_const_phase",
    "gen_exp_phase",
    "gen_transmission_history_balanced_tree",
    "gen_transmission_history_exponential_constant",
    "gen_transmission_history_exponential_constant_classic",
    "geneology_to_distance_matrix",
    "geneology_to_distance_matrix_classic",
    "geneology_to_phylogeny_bpb",
    "generate_rate_model",
    "generate_sequences",
    "get_biphasic_HIV_rate",
    "get_biphasic_HIV_rate_function",
    "get_Kphasic_hiv_rate_function",
    "get_p17_rate_model",
    "get_V3_rate_model",
    "initialize",
    "keep_samples",
    "lookup_sequence_by_name",
    "multi_sampler",
    "negative_binomial_dispersion_sampler",
    "never_terminate_early_factory",
    "phylogeny_to_newick",
    "poisson_dispersion_sampler",
    "random_fixed_size_ids",
    "random_prop_ids",
    "rate_calculator",
    "reduce_large_matrix",
    "reduce_transmission_history",
    "reduce_transmission_history_bpb",
    "reduce_transmission_history_bpb2",
    "reduce_transmission_history_mt",
    "remove_samples",
    "show_available_regions",
    "show_available_sequences",
    "simulate_all_paradigms_HIV_V3",
    "simulate_classic_HIV",
    "simulate_modern_HIV",
    "simulate_sequences_HIV_V3",
    "step",
    "stochastify_transmission_history",
    "sufficient_data_data_factory",
    "uniform_discovery_factory",
    "validate_state",
    "wrap_parameters"
  ],
  "_help": [
    {
      "page": "add_root_to_newick",
      "title": "Add a root node to a newick tree string with distance 0 from the root",
      "topics": [
        "add_root_to_newick"
      ]
    },
    {
      "page": "biphasic_HIV_rate",
      "title": "Simple biphasic rate function used in [Kupperman et al.]",
      "topics": [
        "biphasic_HIV_rate"
      ]
    },
    {
      "page": "build_distance_matrix_from_df",
      "title": "Build a distance matrix from a dataframe of sequences using ape",
      "topics": [
        "build_distance_matrix_from_df"
      ]
    },
    {
      "page": "check_rate_model",
      "title": "Check that a rate model is mathematically valid",
      "topics": [
        "check_rate_model"
      ]
    },
    {
      "page": "clean_up",
      "title": "Clean up the simulation state and return the relevant data.",
      "topics": [
        "clean_up"
      ]
    },
    {
      "page": "contact_traced_uniform_ids",
      "title": "Obtain a sample using a iterative contact tracing with a uniform discovery rate",
      "topics": [
        "contact_traced_uniform_ids"
      ]
    },
    {
      "page": "contact_traced_uniform_restarts_ids",
      "title": "Obtain a sample using a iterative contact tracing with a uniform discovery rate If a minimum number is not found, the algorithm is restarted with a new initial detection",
      "topics": [
        "contact_traced_uniform_restarts_ids"
      ]
    },
    {
      "page": "contact_tracing_core",
      "title": "Core contact tracing algorithm",
      "topics": [
        "contact_tracing_core"
      ]
    },
    {
      "page": "contact_tracing_engine",
      "title": "Perform contact tracing on a simulated contact network",
      "topics": [
        "contact_tracing_engine"
      ]
    },
    {
      "page": "fasta_string_to_dataframe",
      "title": "Convert a fasta string output by seq-gen to a dataframe",
      "topics": [
        "fasta_string_to_dataframe"
      ]
    },
    {
      "page": "gen_const_phase",
      "title": "Simulate a fixed number of steps",
      "topics": [
        "gen_const_phase"
      ]
    },
    {
      "page": "gen_exp_phase",
      "title": "Simulate an exponential growth.",
      "topics": [
        "gen_exp_phase"
      ]
    },
    {
      "page": "gen_transmission_history_balanced_tree",
      "title": "Generate a transmission history for a given number of individuals under a optimally balanced tree",
      "topics": [
        "gen_transmission_history_balanced_tree"
      ]
    },
    {
      "page": "gen_transmission_history_exponential_constant",
      "title": "Generate transmission history for full population",
      "topics": [
        "gen_transmission_history_exponential_constant"
      ]
    },
    {
      "page": "geneology_to_distance_matrix",
      "title": "Reduce a geneology to a pairwise distance matrix.",
      "topics": [
        "geneology_to_distance_matrix"
      ]
    },
    {
      "page": "geneology_to_distance_matrix_classic",
      "title": "Reduce a geneology to a pairwise distance matrix.",
      "topics": [
        "geneology_to_distance_matrix_classic"
      ]
    },
    {
      "page": "geneology_to_phylogeny_bpb",
      "title": "Generate a phylogeny from a transmission history using BioPhyBreak's coalescent simulator",
      "topics": [
        "geneology_to_phylogeny_bpb"
      ]
    },
    {
      "page": "generate_rate_model",
      "title": "Generate a rate model from provided paramters",
      "topics": [
        "generate_rate_model"
      ]
    },
    {
      "page": "generate_sequences",
      "title": "Generate sequences from a phylogeny using Seq-Gen through phyclust",
      "topics": [
        "generate_sequences"
      ]
    },
    {
      "page": "get_biphasic_HIV_rate",
      "title": "Biphasic rate function factory",
      "topics": [
        "get_biphasic_HIV_rate"
      ]
    },
    {
      "page": "get_biphasic_HIV_rate_function",
      "title": "Factory function to generate biphasic rate functions",
      "topics": [
        "get_biphasic_HIV_rate_function"
      ]
    },
    {
      "page": "get_Kphasic_hiv_rate_function",
      "title": "Kphasic HIV rate function factory Provide a list of relative importance (multiples over a \"base\" rate) for",
      "topics": [
        "get_Kphasic_hiv_rate_function"
      ]
    },
    {
      "page": "get_p17_rate_model",
      "title": "Rate model for gag p17 estimated from the Swedish transmission chain",
      "topics": [
        "get_p17_rate_model"
      ]
    },
    {
      "page": "get_pol_rate_model",
      "title": "Rate model for pol estimated from the Swedish transmission chain",
      "topics": [
        "get_pol_rate_model"
      ]
    },
    {
      "page": "get_V3_rate_model",
      "title": "Rate model for env V3 estimated from the Swedish transmission chain",
      "topics": [
        "get_V3_rate_model"
      ]
    },
    {
      "page": "initialize",
      "title": "Utility function for initializing the simulation",
      "topics": [
        "initialize"
      ]
    },
    {
      "page": "keep_samples",
      "title": "Keep a set of samples in the simulation",
      "topics": [
        "keep_samples"
      ]
    },
    {
      "page": "lookup_sequence_by_index",
      "title": "Obtain a sequence from the builtin reference sequences using coordinates",
      "topics": [
        "lookup_sequence_by_index"
      ]
    },
    {
      "page": "lookup_sequence_by_name",
      "title": "Obtain a sequence from the builtin reference sequences using an name and annotated region",
      "topics": [
        "lookup_sequence_by_name"
      ]
    },
    {
      "page": "never_terminate_early_factory",
      "title": "Factory function to never terminate contact tracing until all known nodes have been traced",
      "topics": [
        "never_terminate_early_factory"
      ]
    },
    {
      "page": "phylogeny_to_newick",
      "title": "Convert a phylogeny array to a newick tree",
      "topics": [
        "phylogeny_to_newick"
      ]
    },
    {
      "page": "random_fixed_size_ids",
      "title": "Sample a fixed number of of individuals randomly from the population.",
      "topics": [
        "random_fixed_size_ids"
      ]
    },
    {
      "page": "random_prop_ids",
      "title": "Sample a proportion of the active individuals",
      "topics": [
        "random_prop_ids"
      ]
    },
    {
      "page": "reduce_large_matrix",
      "title": "Reduce a large matrix by randomly sampling a cluster of closely related individuals",
      "topics": [
        "reduce_large_matrix"
      ]
    },
    {
      "page": "reduce_transmission_history",
      "title": "Reduce simulation output to transmission history for a subset.",
      "topics": [
        "reduce_transmission_history"
      ]
    },
    {
      "page": "reduce_transmission_history_bpb",
      "title": "Reduce simulation output to transmission history for a subset to include within host diversity.",
      "topics": [
        "reduce_transmission_history_bpb"
      ]
    },
    {
      "page": "reduce_transmission_history_mt",
      "title": "Reduce simulation output to transmission history for a subset.",
      "topics": [
        "reduce_transmission_history_mt"
      ]
    },
    {
      "page": "remove_samples",
      "title": "Remove samples from the simulation",
      "topics": [
        "remove_samples"
      ]
    },
    {
      "page": "show_available_regions",
      "title": "Show the list of available regions for a provided reference sequence",
      "topics": [
        "show_available_regions"
      ]
    },
    {
      "page": "show_available_sequences",
      "title": "Show the list of available reference sequences",
      "topics": [
        "show_available_sequences"
      ]
    },
    {
      "page": "simulate_all_paradigms_HIV_V3",
      "title": "Sample distance matrices for all three major simulation paradigms: the transmission history, the phylogeny, and derived from simulated sequences (TN93)",
      "topics": [
        "simulate_all_paradigms_HIV_V3"
      ]
    },
    {
      "page": "simulate_classic_HIV",
      "title": "Classic HIV simulator for population level simulations.",
      "topics": [
        "simulate_classic_HIV"
      ]
    },
    {
      "page": "simulate_modern_HIV",
      "title": "Modern HIV simulator",
      "topics": [
        "simulate_modern_HIV"
      ]
    },
    {
      "page": "simulate_sequences_HIV_V3",
      "title": "Modern HIV epidemic sequences simulator",
      "topics": [
        "simulate_sequences_HIV_V3"
      ]
    },
    {
      "page": "step",
      "title": "Perform a single step of the simulation",
      "topics": [
        "step"
      ]
    },
    {
      "page": "stochastify_transmission_history",
      "title": "Sample evolutionary distances to an integer number of mutations per branch",
      "topics": [
        "stochastify_transmission_history"
      ]
    },
    {
      "page": "sufficient_data_data_factory",
      "title": "Factory function for a detection to check termination condition based on A sufficient amount of individuals Terminate when we have found a `minimum_size` number of active individuals",
      "topics": [
        "sufficient_data_data_factory"
      ]
    },
    {
      "page": "uniform_discovery_factory",
      "title": "A factory function to discover connections with uniform probability",
      "topics": [
        "uniform_discovery_factory"
      ]
    },
    {
      "page": "validate_state",
      "title": "Utility function to check that a state is (computationally) valid",
      "topics": [
        "validate_state"
      ]
    }
  ],
  "_readme": "https://github.com/MolEvolEpid/SEEPS/raw/HEAD/README.md",
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    "Rcpp",
    "rlang",
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    "stringi",
    "stringr",
    "vctrs"
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      "source": "Simulation_API.Rmd",
      "filename": "Simulation_API.html",
      "title": "Agent-based forward simulation API",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Initialization",
        "What's in a state",
        "Running the simulation",
        "Tricks for complex setups",
        "Cleaning up the simulation"
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      "created": "2025-01-22 22:32:12",
      "modified": "2025-01-22 22:32:12",
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      "filename": "Exporting_data.html",
      "title": "Exporting Data",
      "engine": "knitr::rmarkdown",
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        "Trees",
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      "headings": [
        "Simulator outputs.",
        "Internal representations of trees"
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      "modified": "2025-01-22 22:32:12",
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    {
      "source": "Longitudinal_sampling_with_SEEPS.Rmd",
      "filename": "Longitudinal_sampling_with_SEEPS.html",
      "title": "Longitudinal sampling with SEEPS",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Simulation",
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      "modified": "2025-01-22 22:32:12",
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      "engine": "knitr::rmarkdown",
      "headings": [
        "Independent random sampling",
        "Proportional sampling",
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      "created": "2025-01-22 22:32:12",
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      "title": "SEEPS",
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      "headings": [
        "Simulate a transmission network with gen_transmission_history_exponential_constant",
        "Exponential growth / offspring generation rate",
        "Maximum target population size",
        "Minimum population",
        "Length of the constant growth phase",
        "Sample a collection of tips",
        "Extract the subtree",
        "Exporting",
        "Newick string or ape tree",
        "Pairwise distance matrix"
      ],
      "created": "2025-01-22 22:32:12",
      "modified": "2025-01-22 22:32:12",
      "commits": 1
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