% This library performs time-frequency analysis (mostly using the
% multi-taper spectral estimation method) of univariate and multivariate
% data, both for continuous processes such as LFP/EEG and for point
% processes such as spike times. Point process can either be stored as
% times or as a binned process of counts. The routines in this library
% are named differently for the three cases. For calculations
% that can be performed for each of the three data types, we use suffixes
% c, pb, or pt to refer to continuous, point process binned counts, or
% point process times. For example, the spectrum calculation is performed
% mtspectrumc for continuous processes, mtspectrumpb for a binned point
% process, and mtspectrumpt for a point process consisting of times. There
% are also routines for calculating hybrid quantities involving one continuous
% and one point process. These are suffixed in a similar manner. For
% example, coherencycpb calculates the coherency between a binned point process
% and a continuous process.
% Certain variables are used repeatedly in this library.
% data in most cases can be univariate or multivariate, and either point process,
% or continuous.
% Continuous data: Continuous data is assumed to be a matrix with
% dimensions samples x channels/trials.
% Point Process: A single time series of spike times can be in the form of
% a column vector.
% Multichannel/trial spike time data is not amenable to this
% storage format, since there are generally different
% number of spikes in each channel/trial. Instead,
% multichannel/trial spike data is stored in a structure
% array. A structure is a matlab data object with various
% fields. These fields contain the elements
% e.g. The command data=struct('times',); creates an empty
% structure with field 'times'. Similarly, the command
% data=struct('times',[1 2 3]); creates the structure with
% the field 'times' containing integers 1, 2, and 3.
% We can also have a structure array (or an array of structures)
% defined for example, by
% data(1)=struct('times',rand(1,100)); and
% This is a 2 dimensional structure array where the
% first field is a 100 dimensional random vector, and
% the second field is a 200 dimensional random vector.
% This format allows storage of multichannel point
% process times in a single variable data.
% The above holds for point processes stored as times.
% If instead, the point processes are binned, then one
% can use a matrix to represent them
% Summary: data - array of continuous data with dimensions time x channels
% structural array of spike times with dimensions
% equal to the number of channels
% 1d array of spike times as a column vector
% array of binned spike counts with dimensions time x channels
% These are various parameters used in the spectral calculations. Since
% these parameters are used by most routines in Chronux, they are stored in
% a single structure params. The fields of params are
% tapers : precalculated tapers from dpss or in the one of the following
% (1) A numeric vector [TW K] where TW is the
% time-bandwidth product and K is the number of
% tapers to be used (less than or equal to
% (2) A numeric vector [W T p] where W is the
% bandwidth, T is the duration of the data and p
% is an integer such that 2TW-p tapers are used. In
% this form there is no default i.e. to specify
% the bandwidth, you have to specify T and p as
% well. Note that the units of W and T have to be
% consistent: if W is in Hz, T must be in seconds
% and vice versa. Note that these units must also
% be consistent with the units of params.Fs: W can
% be in Hz if and only if params.Fs is in Hz.
% The default is to use form 1 with TW=3 and K=5
% pad: (padding factor for the FFT) - optional (can take values -1,0,1,2...).
% -1 corresponds to no padding, 0 corresponds to padding
% to the next highest power of 2 etc.
% e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
% to 512 points, if pad=1, we pad to 1024 points etc.
% Defaults to 0.
% Fs:sampling frequency.optional (default 1)
% fpass: frequencies in an fft calculation can range from 0 to Fs/2 where
% Fs is the sampling frequency. Sometimes it may be useful to
% compute fourier transforms (and resulting quantities like the
% spectrum over a smaller range of frequencies). This is specified
% by fpass, which can be in the form [fmin fmax] where fmin >=0 and
% fmax<=Fs/2. optional (default [0 Fs/2])
% err=[errtype p] calculates theoretical error bars (confidence levels)
% when errtype=1 and jackknife error bars when errchk=2. In each case, the
% error is calculated at a p value specified by p. -
% optional (default 0)
% trialave: trialave controls whether or not to average over channels/trials for
% multichannel/trial analyses. trialave=0 (default) implies no trial
% averaging, trialave=1 implies that the quantity of interest is averaged
% over channels/trials. optional (default 0)
% Other parameters are discussed in individual routines as and when they
% are used.