chronux

PURPOSE ^

This library performs time-frequency analysis (mostly using the

SYNOPSIS ^

function chronux

DESCRIPTION ^

 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
 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
                     data(2)=struct('times',rand(1,200));
                     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

 PARAMETERS:
 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
          forms: 
          (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
              2TW-1). 
          (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.

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function chronux
0002 % This library performs time-frequency analysis (mostly using the
0003 % multi-taper spectral estimation method) of univariate and multivariate
0004 % data, both for continuous processes such as LFP/EEG and for point
0005 % processes such as spike times. Point process can either be stored as
0006 % times or as a binned process of counts. The routines in this library
0007 % are named differently for the three cases. For calculations
0008 % that can be performed for each of the three data types, we use suffixes
0009 % c, pb, or pt to refer to continuous, point process binned counts, or
0010 % point process times. For example, the spectrum calculation is performed
0011 % mtspectrumc for continuous processes, mtspectrumpb for a binned point
0012 % process, and mtspectrumpt for a point process consisting of times. There
0013 % are also routines for calculating hybrid quantities involving one continuous
0014 % and one point process. These are suffixed in a similar manner. For
0015 % example, coherencycpb calculates the coherency between a binned point process
0016 % and a continuous process.
0017 %
0018 % Certain variables are used repeatedly in this library.
0019 %
0020 % DATA
0021 % data in most cases can be univariate or multivariate, and either point process,
0022 % or continuous.
0023 %
0024 %      Continuous data: Continuous data is assumed to be a matrix with
0025 %                       dimensions samples x channels/trials.
0026 %
0027 %      Point Process: A single time series of spike times can be in the form of
0028 %                     a column vector.
0029 %                     Multichannel/trial spike time data is not amenable to this
0030 %                     storage format, since there are generally different
0031 %                     number of spikes in each channel/trial. Instead,
0032 %                     multichannel/trial spike data is stored in a structure
0033 %                     array. A structure is a matlab data object with various
0034 %                     fields. These fields contain the elements
0035 %                       e.g. The command data=struct('times',[]); creates an empty
0036 %                            structure with field 'times'. Similarly, the command
0037 %                            data=struct('times',[1 2 3]); creates the structure with
0038 %                            the field 'times' containing integers 1, 2, and 3.
0039 %
0040 %                     We can also have a structure array (or an array of structures)
0041 %                     defined for example, by
0042 %                     data(1)=struct('times',rand(1,100)); and
0043 %                     data(2)=struct('times',rand(1,200));
0044 %                     This is a 2 dimensional structure array where the
0045 %                     first field is a 100 dimensional random vector, and
0046 %                     the second field is a 200 dimensional random vector.
0047 %                     This format allows storage of multichannel point
0048 %                     process times in a single variable data.
0049 %
0050 %                     The above holds for point processes stored as times.
0051 %                     If instead, the point processes are binned, then one
0052 %                     can use a matrix to represent them
0053 %
0054 %
0055 %      Summary: data - array of continuous data with dimensions time x channels
0056 %                      structural array of spike times with dimensions
0057 %                               equal to the number of channels
0058 %                      1d array of spike times as a column vector
0059 %                      array of binned spike counts with dimensions time x channels
0060 %
0061 % PARAMETERS:
0062 % These are various parameters used in the spectral calculations. Since
0063 % these parameters are used by most routines in Chronux, they are stored in
0064 % a single structure params. The fields of params are
0065 %
0066 % tapers : precalculated tapers from dpss or in the one of the following
0067 %          forms:
0068 %          (1) A numeric vector [TW K] where TW is the
0069 %              time-bandwidth product and K is the number of
0070 %              tapers to be used (less than or equal to
0071 %              2TW-1).
0072 %          (2) A numeric vector [W T p] where W is the
0073 %              bandwidth, T is the duration of the data and p
0074 %              is an integer such that 2TW-p tapers are used. In
0075 %              this form there is no default i.e. to specify
0076 %              the bandwidth, you have to specify T and p as
0077 %              well. Note that the units of W and T have to be
0078 %              consistent: if W is in Hz, T must be in seconds
0079 %              and vice versa. Note that these units must also
0080 %              be consistent with the units of params.Fs: W can
0081 %              be in Hz if and only if params.Fs is in Hz.
0082 %              The default is to use form 1 with TW=3 and K=5
0083 %
0084 %
0085 % pad:   (padding factor for the FFT) - optional (can take values -1,0,1,2...).
0086 %         -1 corresponds to no padding, 0 corresponds to padding
0087 %         to the next highest power of 2 etc.
0088 %              e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
0089 %                   to 512 points, if pad=1, we pad to 1024 points etc.
0090 %                   Defaults to 0.
0091 %
0092 % Fs:sampling frequency.optional (default 1)
0093 %
0094 %
0095 % fpass: frequencies in an fft calculation can range from 0 to Fs/2 where
0096 %        Fs is the sampling frequency. Sometimes it may be useful to
0097 %        compute fourier transforms (and resulting quantities like the
0098 %        spectrum over a smaller range of frequencies). This is specified
0099 %        by fpass, which can be in the form [fmin fmax] where fmin >=0 and
0100 %        fmax<=Fs/2. optional (default [0 Fs/2])
0101 %
0102 % err=[errtype p] calculates theoretical error bars (confidence levels)
0103 %                 when errtype=1 and jackknife error bars when errchk=2. In each case, the
0104 %                 error is calculated at a p value specified by p. -
0105 %                 optional (default 0)
0106 %
0107 % trialave: trialave controls whether or not to average over channels/trials for
0108 %           multichannel/trial analyses. trialave=0 (default) implies no trial
0109 %           averaging, trialave=1 implies that the quantity of interest is averaged
0110 %           over channels/trials. optional (default 0)
0111 %
0112 % Other parameters are discussed in individual routines as and when they
0113 % are used.

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