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```
#'motoRneuron: A package for computing motor unit analyses
#'
#'The motoRneuron package provides functions for time-domain analyses of motor
#'units.
#'
#'@section About: The motoRneuron package was developed at the United States
#' Army Research Laboratory.
#'
#'@section Details: The motoRneuron package provides functions to compute
#' time-domain synchronization between the two motor unit discharge trains.
#' MotoRneuron's primary functions configure and assess the cross correlation
#' histogram between motor unit discharge trains for a "peak". Peaks indicate
#' more synchronized firing at that latency than would be expected due to
#' chance. The magnitude of the peak is also thought to indicate the strength
#' of common input between the motor units and is characterized by
#' synchronization "indices", listed below. Three methods are available
#' for assessing the peak in the histogram. Details of specific methods are
#' documented in their respective help files. Motor unit characteristic data
#' and interspike intervals are automatically output.
#'
#' 'Recurrence_intervals', 'bin', and 'plot_bins' are support functions used
#' within the core functions, but can also be called separately for individual
#' use. Recurrence_intervals() calculates recurrence intervals between two
#' motor unit discharge trains. Bin() discretizes the recurrence intervals into
#' user-specified bins. Plot_bins() leverages ggplot2 to plot the resulting
#' histogram.
#'
#'@section Methods for Peak Determination: Visual method - subjective analysis
#' of normalized cumulative sum graph to determine peak location. (Nordstrom,
#' Fuglevand, and Enoka, 1992)
#'
#' Z-score method - a random uniform distribution is used to calculate a mean +
#' 1.96 standard deviation threshold for the experimental cross correlation
#' histogram. Any bins of the experimental histogram within +/- 10 ms of 0 that
#' crossed the threshold are considered to be significantly greater than
#' expected due to chance and subsequently used for analysis. (Defreitas, Beck,
#' Xin, and Stock, 2013)
#'
#' Cumulative Sum (cumsum) method - the cumulative sum of the bin count of the
#' histogram is calculated. The peak boundaries are calculated as 10% and 90% of
#' the range (maximum minus minimum) of the cumulative sum. The peak is
#' considered significant if its mean bin count exceeds the sum of the mean and
#' 1.96 * standard deviation of the baseline bins (<= -60 ms and >= 60 ms). If
#' no significant peak is detected, a default +/- 5 ms peak is used. (Keen,
#' D.A., Chou, L., Nordstrom, M.A., Fuglevand, A.J., 2012)
#'
#'@section Synchronization Indices: CIS = frequency of synchronized discharges.
#' (Nordstrom, Fuglevand, and Enoka, 1992)
#'
#' k' = ratio of synchronized discharges to expected discharges in peak. (Kamen
#' & Roy, 2000)
#'
#' k'-1 = ratio of extra synchronized discharges to expected discharges in
#' peak. (Kamen & Roy, 2000)
#'
#' S = ratio of synchronized discharges to total number of discharges of both
#' motor units. (Nordstrom, Fuglevand, and Enoka, 1992)
#'
#' E = ratio of synchronized discharges to non-synchronized discharges. (Datta
#' & Stephens 1990)
#'
#' SI = ratio of synchronized discharges to reference motor unit discharges.
#' (Defreitas, Beck, Xin, and Stock, 2013)
#'
#'@section Authors: Andrew Tweedell and Matthew Tenan, maintainer: Andrew Tweedell
#' (andrew.j.tweedell.civ@@mail.mil)
#'
#'@section References: Datta, A.K., & Stephens, J.A. (1990) Synchronization of
#' Motor Unit Activity During Voluntary Contraction in Man. Journal of
#' Physiology 422: 397-419
#'
#' DeFreitas, J.M., Beck, T.W., Xin, Y., Stock, M.S. (2013) Synchronization of
#' Low- and High-Threshold Motor Units. Muscle & Nerve DOI 10.1002/mus.23978
#'
#' Kamen, G. & Roy, A. (2000) Motor Unit Synchronization in Young and Elderly
#' Adults. European Journal of Applied Physiology. 81: 403-410
#'
#' Keen, D.A., Chou, L., Nordstrom, M.A., Fuglevand, A.J. (2012) Short-term
#' Synchrony in Diverse Motor Nuclei Presumed to Receive Different Extents of
#' Direct Cortical Input. Journal of Neurophysiology 108: 3264-3275
#'
#' Nordstrom, M.A., Fuglevand, A.J., Enoka, R.M. (1992) Estimating the Strength
#' of Common Input to Human Motoneurons from the Cross-Correlogram. Journal of
#' Physiology 453, pp. 547-574
#'
#'@docType package
#'@name motoRneuron
NULL
```

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