boot.ergoInfo: Bootstrap Test for the Ergodicity Information Index

Description Usage Arguments Value Author(s) Examples

View source: R/boot.ergoInfo.R

Description

Computes a parametric Bootstrap Test for the Ergodicity Information Index, comparing the empirical Ergodicity Information index to values obtained in data generated using N parametric bootstraps of the correlation matrix estimated using the dynEGA function, for the population structure. The p-values in the bootstrap test can be calculated as (sum(EII>=boot.EII)+1)/(iter+1) and as (sum(EII<=boot.EII)+1)/(iter+1), where EII is the empirical Ergodicity Information Index, boot.EII is the values of the Ergodicity Information Index obtained in the bootstraped samples, and iter is the number of random samples generated in the simulation. The two-sided p-value is computed as two times the lowest p-value. In the bootstrap Test for the Ergodicity Information Index, the null hypothesis is that the empirical value of EII is equal to the values of EII obtained in multiple individuals with the same structure as the population structure estimated via dynEGA. Small values of p indicate that is very unlikely to obtain an EII as large as the one obtained in the empirical sample if the null hypothesis is true (i.e. all individuals have the same structure as the population structure), thus there is convincing evidence that the empirical Ergodicity Information Index is different than it could be expected if all individuals had a similar latent structure.

Usage

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boot.ergoInfo(
  dynEGA.pop,
  iter,
  EII,
  use,
  embed,
  tau,
  delta,
  derivatives,
  model,
  model.args = list(),
  algorithm = c("walktrap", "louvain"),
  algorithm.args = list(),
  corr,
  ncores,
  ...
)

Arguments

dynEGA.pop

A dynEGA or a dynEGA.pop.ind object.

iter

Numeric integer. Number of random samples to generate in the Monte-Carlo simulation. At least 500 is recommended

EII

Numeric. Empirical Ergodicity Information Index obtained via the ergoInfo function.

use

Character. A string indicating what network element will be used to compute the algorithm complexity in the ergoInfo function, the list of edges or the weights of the network. Defaults to use = "edge.list". Current options are:

  • edge.list Calculates the algorithm complexity using the list of edges.

  • weights Calculates the algorithm complexity using the weights of the network.

embed

Integer. Number of embedded dimensions (the number of observations to be used in the Embed function). For example, an "embed = 5" will use five consecutive observations to estimate a single derivative. Default is "embed = 5".

tau

Integer. Number of observations to offset successive embeddings in the Embed function. A tau of one uses adjacent observations. Default is "tau = 1".

delta

Integer. The time between successive observations in the time series. Default is "delta = 1".

derivatives

Integer. The order of the derivative to be used in the EGA procedure. Default to 1.

model

Character. A string indicating the method to use. Defaults to glasso. Current options are:

  • glasso Estimates the Gaussian graphical model using graphical LASSO with extended Bayesian information criterion to select optimal regularization parameter. This is the default method

  • TMFG Estimates a Triangulated Maximally Filtered Graph

model.args

List. A list of additional arguments for EBICglasso.qgraph or TMFG

algorithm

A string indicating the algorithm to use or a function from igraph

Current options are:

  • walktrap Computes the Walktrap algorithm using cluster_walktrap

  • louvain Computes the Walktrap algorithm using cluster_louvain

algorithm.args

List. A list of additional arguments for cluster_walktrap, cluster_louvain, or some other community detection algorithm function (see examples)

corr

Type of correlation matrix to compute. The default uses cor_auto. Current options are:

  • cor_auto Computes the correlation matrix using the cor_auto function from qgraph.

  • pearson Computes Pearson's correlation coefficient using the pairwise complete observations via the cor function.

  • spearman Computes Spearman's correlation coefficient using the pairwise complete observations via the cor function.

ncores

Numeric. Number of cores to use in computing results. Defaults to parallel::detectCores() / 2 or half of your computer's processing power. Set to 1 to not use parallel computing. Recommended to use maximum number of cores minus one

If you're unsure how many cores your computer has, then use the following code: parallel::detectCores()

...

Additional arguments. Used for deprecated arguments from previous versions of EGA

Value

Returns a list containing:

boot.ergoInfo

The values of the Ergodicity Information Index obtained in the Monte-Carlo Simulation

p.value.twosided

The p-value of the Monte-Carlo test for the Ergodicity Information Index. The null hypothesis is that the empirical Ergodicity Information index is equal to the expected value of the EII if the all individuals had similar latent structures.

effect

Indicates wheter the empirical EII is greater or less then the Monte-Carlo obtained EII.

plot.dist

Histogram of the bootstrapped ergodicity information index

Author(s)

Hudson Golino <hfg9s at virginia.edu>

Examples

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## Not run: 
\donttest{
dyn1 <- dynEGA.ind.pop(data = sim.dynEGA[,-c(22)], n.embed = 5, tau = 1,
                      delta = 1, id = 21, use.derivatives = 1,
                    model = "glasso", ncores = 2, corr = "pearson")

eii1 <- ergoInfo(data = dyn1)$EII

testing.ergoinfo <- boot.ergoInfo(dynEGA.pop = dyn1, iter = 10,EII = eii1,
embed = 5, tau = 1, delta = 1, derivatives = 1,
model = "glasso", ncores = 2, corr = "pearson")
}
## End(Not run)

EGAnet documentation built on Feb. 17, 2021, 1:06 a.m.