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  "Package": "genscore",
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  "Title": "Generalized Score Matching Estimators",
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  "Author": "Shiqing Yu, Lina Lin, Wally Gilks",
  "Maintainer": "Shiqing Yu <syu.phd@gmail.com>",
  "Description": "Implementation of the Generalized Score Matching estimator\nin Yu et al. (2019) <http://jmlr.org/papers/v20/18-278.html>\nfor non-negative graphical models (truncated Gaussian,\nexponential square-root, gamma, a-b models) and univariate\ntruncated Gaussian distributions. Also includes the original\nestimator for untruncated Gaussian graphical models from Lin et\nal. (2016) <doi:10.1214/16-EJS1126>, with the addition of a\ndiagonal multiplier.",
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    "search_bin",
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    "test_lambda_bounds2",
    "tp_fp",
    "update_finite_infinity_for_uniform",
    "varhat"
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      "page": "calc_crit",
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      ]
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      "topics": [
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      ]
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      "page": "compare_two_sub_results",
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      "topics": [
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      "topics": [
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      ]
    },
    {
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    },
    {
      "page": "crbound_sigma",
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      "topics": [
        "crbound_sigma"
      ]
    },
    {
      "page": "diff_lists",
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      ]
    },
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      "page": "diff_vecs",
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      "topics": [
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      ]
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    {
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      "title": "Returns a list to be passed to C that represents the domain.",
      "topics": [
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      ]
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      "page": "eBIC",
      "title": "eBIC score with or without refitting.",
      "topics": [
        "eBIC"
      ]
    },
    {
      "page": "estimate",
      "title": "The main function for the generalized score-matching estimator for graphical models.",
      "topics": [
        "estimate"
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    },
    {
      "page": "find_max_ind",
      "title": "Finds the max index in a vector that does not exceed a target number.",
      "topics": [
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    },
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      "page": "frac_pow",
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      "topics": [
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    },
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      "topics": [
        "gcd"
      ]
    },
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      "page": "gen",
      "title": "Random data generator from general 'a'-'b' distributions with general domain types, assuming a and b are rational numbers.",
      "topics": [
        "gen"
      ]
    },
    {
      "page": "get_crit_nopenalty",
      "title": "Minimized loss for unpenalized restricted asymmetric models.",
      "topics": [
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      "page": "get_dist",
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    },
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    },
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        "get_elts_exp"
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    },
    {
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      "topics": [
        "get_elts_gamma"
      ]
    },
    {
      "page": "get_elts_gauss",
      "title": "The R implementation to get the elements necessary for calculations for the gaussian setting on R^p.",
      "topics": [
        "get_elts_gauss"
      ]
    },
    {
      "page": "get_elts_loglog",
      "title": "The R implementation to get the elements necessary for calculations for the log-log setting (a=0, b=0).",
      "topics": [
        "get_elts_loglog"
      ]
    },
    {
      "page": "get_elts_loglog_simplex",
      "title": "The R implementation to get the elements necessary for calculations for the log-log setting (a=0, b=0) on the p-simplex.",
      "topics": [
        "get_elts_loglog_simplex"
      ]
    },
    {
      "page": "get_elts_trun_gauss",
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      "topics": [
        "get_elts_trun_gauss"
      ]
    },
    {
      "page": "get_g0",
      "title": "Calculates the l2 distance to the boundary of the domain and its gradient for some domains.",
      "topics": [
        "get_g0"
      ]
    },
    {
      "page": "get_g0_ada",
      "title": "Adaptively truncates the l2 distance to the boundary of the domain and its gradient for some domains.",
      "topics": [
        "get_g0_ada"
      ]
    },
    {
      "page": "get_h_hp",
      "title": "Generator of h and hp (derivative of h) functions.",
      "topics": [
        "get_h_hp"
      ]
    },
    {
      "page": "get_h_hp_adaptive",
      "title": "Generator of adaptive h and hp (derivative of h) functions.",
      "topics": [
        "get_h_hp_adaptive"
      ]
    },
    {
      "page": "get_h_hp_vector",
      "title": "Generator of h and hp (derivative of h) functions.",
      "topics": [
        "get_h_hp_vector"
      ]
    },
    {
      "page": "get_postfix_rule",
      "title": "Changes a logical expression in infix notation to postfix notation using the shunting-yard algorithm.",
      "topics": [
        "get_postfix_rule"
      ]
    },
    {
      "page": "get_results",
      "title": "Estimate K and eta using elts from 'get_elts()' given one lambda_K (and lambda_eta if non-profiled non-centered) and applying warm-start with strong screening rules.",
      "topics": [
        "get_results"
      ]
    },
    {
      "page": "get_safe_log_h_hp",
      "title": "Asymptotic log of 'h' and 'hp' functions for large 'x' for modes with an unbounded 'h'.",
      "topics": [
        "get_safe_log_h_hp"
      ]
    },
    {
      "page": "get_trun",
      "title": "The truncation point for 'h' for 'h' that is truncated (bounded but not naturally bounded).",
      "topics": [
        "get_trun"
      ]
    },
    {
      "page": "h_of_dist",
      "title": "Finds the distance of each element in a matrix x to the its boundary of the domain while fixing the others in the same row (dist(x, domain)), and calculates element-wise h(dist(x, domain)) and h\\'(dist(x, domain)) (w.r.t. each element in x).",
      "topics": [
        "h_of_dist"
      ]
    },
    {
      "page": "in_bound",
      "title": "Returns whether a vector or each row of a matrix falls inside a domain.",
      "topics": [
        "in_bound"
      ]
    },
    {
      "page": "interval_intersection",
      "title": "Finds the intersection between two unions of intervals.",
      "topics": [
        "interval_intersection"
      ]
    },
    {
      "page": "interval_union",
      "title": "Finds the union between two unions of intervals.",
      "topics": [
        "interval_union"
      ]
    },
    {
      "page": "lambda_max",
      "title": "Analytic solution for the minimum lambda_K that gives the empty graph.",
      "topics": [
        "lambda_max"
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    },
    {
      "page": "make_domain",
      "title": "Creates a list of elements that defines the domain for a multivariate distribution.",
      "topics": [
        "make_domain"
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    },
    {
      "page": "make_folds",
      "title": "Helper function for making fold IDs for cross validation.",
      "topics": [
        "make_folds"
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    },
    {
      "page": "makecoprime",
      "title": "Makes two integers coprime.",
      "topics": [
        "makecoprime"
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    },
    {
      "page": "mu_sigmasqhat",
      "title": "Estimates the mu and sigma squared parameters from a univariate truncated normal sample.",
      "topics": [
        "mu_sigmasqhat"
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    },
    {
      "page": "naiveSearch_bin",
      "title": "Finds the index of the bin a number belongs to using naive search.",
      "topics": [
        "naiveSearch_bin"
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    },
    {
      "page": "parse_ab",
      "title": "Parses an ab setting into rational numbers a and b.",
      "topics": [
        "parse_ab"
      ]
    },
    {
      "page": "parse_ineq",
      "title": "Parses an ineq expression into a list of elements that represents the ineq.",
      "topics": [
        "parse_ineq"
      ]
    },
    {
      "page": "ran_mat",
      "title": "Random generator of matrices with given eigenvalues.",
      "topics": [
        "ran_mat"
      ]
    },
    {
      "page": "random_init_polynomial",
      "title": "Randomly generate an initial point in the domain defined by a single polynomial with no negative coefficient.",
      "topics": [
        "random_init_polynomial"
      ]
    },
    {
      "page": "random_init_simplex",
      "title": "Generates a random point in the (p-1)-simplex.",
      "topics": [
        "random_init_simplex"
      ]
    },
    {
      "page": "random_init_uniform",
      "title": "Generates random numbers from a finite union of intervals.",
      "topics": [
        "random_init_uniform"
      ]
    },
    {
      "page": "read_exponent",
      "title": "Parses the exponent part into power_numer and power_denom.",
      "topics": [
        "read_exponent"
      ]
    },
    {
      "page": "read_exponential",
      "title": "Parses the integer coefficient in an exponential term.",
      "topics": [
        "read_exponential"
      ]
    },
    {
      "page": "read_one_term",
      "title": "Parses the first term of a non-uniform expression.",
      "topics": [
        "read_one_term"
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    },
    {
      "page": "read_uniform_term",
      "title": "Attempts to parse a single term in x into power_numer and power_denom.",
      "topics": [
        "read_uniform_term"
      ]
    },
    {
      "page": "refit",
      "title": "Loss for a refitted (restricted) unpenalized model",
      "topics": [
        "refit"
      ]
    },
    {
      "page": "rexp_truncated",
      "title": "Generates translated and truncated exponential variables.",
      "topics": [
        "rexp_truncated"
      ]
    },
    {
      "page": "rlaplace_truncated",
      "title": "Generates laplace variables truncated to a finite union of intervals.",
      "topics": [
        "rlaplace_truncated"
      ]
    },
    {
      "page": "rlaplace_truncated_centered",
      "title": "Generates centered laplace variables with scale 1.",
      "topics": [
        "rlaplace_truncated_centered"
      ]
    },
    {
      "page": "s_at",
      "title": "Returns the character at a position of a string.",
      "topics": [
        "s_at"
      ]
    },
    {
      "page": "s_output",
      "title": "Helper function for outputting if verbose.",
      "topics": [
        "s_output"
      ]
    },
    {
      "page": "search_bin",
      "title": "Finds the index of the bin a number belongs to.",
      "topics": [
        "search_bin"
      ]
    },
    {
      "page": "test_lambda_bounds",
      "title": "Searches for a tight bound for lambda_K that gives the empty or complete graph starting from a given lambda with a given step size",
      "topics": [
        "test_lambda_bounds"
      ]
    },
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      "source": "gen_vignette.Rmd",
      "filename": "gen_vignette.html",
      "title": "Generalized Score Matching on Generalized Domain Types",
      "author": "Shiqing Yu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Different domain types",
        "The entire real space",
        "The non-negative orthant of the real space",
        "The simplex domains",
        "Uniform-type domains",
        "Solution for infinite unions of intervals or non-uniform domains for each component",
        "Polynomial-type domains",
        "Inequalities",
        "Rule",
        "Examples of polynomial domains",
        "Distribution Models Supported",
        "Examples of Multivariate Graphical Models",
        "Truncated Gaussian Graphical Models on the Non-negative Orthant",
        "Data setup",
        "Estimation using estimate() with x directly",
        "Estimate using elts",
        "Results for one lambda",
        "Aggregating multiple ROC curves",
        "Exponential Square-Root Graphical Models on the Non-negative Orthant",
        "Estimation",
        "Gamma Graphical Models on the Non-negative Orthant",
        "General a-b Graphical Models on the Non-negative Orthant",
        "(Untruncated) Gaussian Graphical Models on the Entire Real Space",
        "Aitchison $A^d$ Models on the Simplex",
        "Univariate Truncated Normal Distributions on x > 0",
        "Introduction",
        "Variance Estimation and Confidence Intervals",
        "Plots from Yu et al (2019)"
      ],
      "created": "2019-08-05 04:27:56",
      "modified": "2020-04-24 19:19:49",
      "commits": 8
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