QtAC_CTE: QtAC_CTE

In hannahschrenk/QtAC: Quantifying the Adaptive Cycle

QtAC_CTE

Description

This function calculates the collective transfer entropy of each species for shifting time windows of fixed length or local values. The output is a list of adjacency matrices and the corresponding significance matrices.

Usage

QtAC_CTE(
  data,
  num_timepoints = 5,
  javapath,
  noise_level = "1e-20",
  num_permcheck = 1000L,
  k = 1L,
  k_tau = 1L,
  l = 1L,
  l_tau = 1L,
  delay = 1L,
  condEmbedDims = 1L,
  cond_taus = 1L,
  cond_delays = 1L,
  mode = c("average", "local"),
  save = FALSE,
  filename = "result_QtAC"
)

Arguments

data	data array containing time series of the system's components' abundance data
num_timepoints	length of the time windows of abundance data serving as basis of the collective transfer entropy estimations
javapath	path of the file "MTinfodynamics.jar"
noise_level	amount of random Gaussian noise added in the estimation
num_permcheck	number of surrogate samples to bootstrap to generate the distribution in the significance test
k	embedding length of destination past history to consider
k_tau	embedding delay for the destination variable
l	embedding length of source past history to consider
l_tau	embedding delay for the source variable
delay	time lag between last element of source and destination next value
condEmbedDims	array of embedding lengths for each conditional variable
cond_taus	array of embedding delays for the conditional variables
cond_delays	array of time lags between last element of each conditional variable and destination next value
mode	Transfer entropy is either averaged over time windows ("average") or local values are estimated ("local"). In the latter case, the value of num_timepoints is ignored.
save	If save=TRUE, the output is saved in a file called filename.

Value

list of two lists (adjacency and corresponding significance matrices)

hannahschrenk/QtAC documentation built on July 27, 2023, 5:35 a.m.