compareTS: Community Time Series Comparison

In hallucigenia-sparsa/seqtime: Time Series Analysis of Sequencing Data

Community Time Series Comparison

Description

Compute properties of community time series generated with generateTS.

Usage

compareTS(input.folder = "", expIds = c(), modif.folder = "",
  modif = "", testNeutral = FALSE, sliceDef = c(1, NA),
  epsilon = 0.2, predef = FALSE, detrend = TRUE, norm = FALSE,
  hurstBins = c(0.5, 0.7, 0.9), maxautocorBins = c(0.3, 0.5, 0.8),
  timeDecaySliceDef = c(1, 50), varEvolSliceDef = c(),
  radSliceDef = c(), returnDistribs = FALSE, returnTS = FALSE)

Arguments

input.folder	the folder where results (settings and time series) of function generateTS are stored.
expIds	the experiment identifiers of time series to be considered
modif.folder	the folder with time series sub-sets as generated by sliceTS.R or with noisy time series as generated by addNoise.R (settings are read in from input.folder)
modif	modification (shared name of time series in modif.folder, sliced for time series sub-sets and pois/multi for time series with Poisson or multinomial noise, respectively)
testNeutral	test neutrality (requires libraries WrightFisher and logitnorm)
sliceDef	consider the time series sub-set defined by the given start and end time point for property computation, an end time point of NA means that the entire time series is considered, a single value T in the sliceDef vector means that the last T time points are considered; timeDecaySliceDef and varEvolSliceDef refer to the outcome of sliceDef
epsilon	allowed deviation from the expected slope for noise type identification
predef	recognize noise types with predefined slope boundaries (see identifyNoisetypes for details)
detrend	remove linear trends before computing the periodogram (recommended)
norm	normalize time series by dividing each entry in a sample by the sum of its sample; if norm is true, entropy computation is omitted
hurstBins	binning thresholds for Hurst exponent (three thresholds required for four bins)
maxautocorBins	binning thresholds for maximal autocorrelation (three thresholds required for four bins)
timeDecaySliceDef	the time series subset considered to compute the time decay, a vector with the start and the end time point (if the end time point is NA, the entire time series is used)
varEvolSliceDef	(optional, by default not computed) the time series subset considered to compute the evolution of variance, a vector with the start and the end time point (if the end time point is NA, the entire time series is used)
radSliceDef	(optional, by default not computed) the time series subset considered to analyse the (non-normalized also when norm is enabled) species abundance versus rank curve, a vector with the start and the end time point (if the end time point is NA, the entire time series is used); cannot be used together with sliceDef
returnDistribs	return distributions at the final time point (no time series properties are computed, cannot be used together with returnTS)
returnTS	return the time series (no time series properties are computed, cannot be used together with returnDistribs)

Details

If infotheo is installed, the entropy will be also computed. Noise types are computed with smooth set to true. The neutrality test is carried out with ntests set to 500 and method logitnorm.

Value

a table with experiment parameters (algorithm, connectance, sigma, theta and so on) and time series properties (noise types percentages, slope of Taylor's law etc.); if returnDistrib is true, a list with the abundances at the last time point, if returnTS is true, a list with the time series

hallucigenia-sparsa/seqtime documentation built on Jan. 9, 2023, 11:53 p.m.