obtain_u_set_mix3: Obtain set of thresholds with high posterior density for the...

In crandep: Network Analysis of Dependencies of CRAN Packages

Obtain set of thresholds with high posterior density for the 3-component mixture model

Description

obtain_u_set_mix3 computes the profile posterior density of the thresholds v & u, and subsets the thresholds (and other parameter values) with high profile values i.e. within a certain value from the maximum posterior density. The sets of v & u can then be used for mcmc_mix3.

Usage

obtain_u_set_mix3(
  df,
  powerlaw1 = FALSE,
  powerlaw2 = FALSE,
  positive1 = FALSE,
  positive2 = TRUE,
  name = TRUE,
  log_diff_max = 11,
  v_max = 100L,
  u_max = 2000L,
  alpha_init = 0.01,
  theta_init = exp(-1),
  shape_init = 1,
  sigma_init = 1,
  a_psi1 = 1,
  a_psi2 = 1,
  a_psiu = 0.001,
  b_psiu = 0.9,
  m_alpha = 0,
  s_alpha = 10,
  a_theta = 1,
  b_theta = 1,
  m_shape = 0,
  s_shape = 10,
  a_sigma = 1,
  b_sigma = 0.01
)

Arguments

df	A data frame with at least two columns, degree & count
powerlaw1	Boolean, is the power law (TRUE) or polylogarithm (FALSE, default) assumed for the left tail?
powerlaw2	Boolean, is the power law (TRUE) or polylogarithm (FALSE, default) assumed for the middle bulk?
positive1	Boolean, is alpha positive (TRUE) or unbounded (FALSE, default) for the left tail?
positive2	Boolean, is alpha positive (TRUE) or unbounded (FALSE, default) for the middle bulk?
name	Boolean; if the column name exists, are its unique values printed?
log_diff_max	Positive real number, the value such that thresholds with profile posterior density not less than the maximum posterior density - log_diff_max will be kept
v_max	Positive integer for the maximum lower threshold
u_max	Positive integer for the maximum upper threshold
alpha_init	Scalar, initial value of alpha
theta_init	Scalar, initial value of theta
shape_init	Scalar, initial value of shape parameter
sigma_init	Scalar, initial value of sigma
a_psi1, a_psi2, a_psiu, b_psiu, m_alpha, s_alpha, a_theta, b_theta, m_shape, s_shape, a_sigma, b_sigma	Scalars, hyperparameters of the priors for the parameters

Value

A list: v_set is the vector of lower thresholds with high posterior density, u_set is the vector of upper thresholds with high posterior density, init is the data frame with the maximum profile posterior density and associated parameter values, profile is the data frame with all thresholds with high posterior density and associated parameter values, scalars is the data frame with all arguments (except df)

See Also

mcmc_mix3_wrapper that wraps obtain_u_set_mix3 and mcmc_mix3

crandep documentation built on Nov. 22, 2023, 1:08 a.m.