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  • Description of mtspecgrampb
    finite size corrections or 1 use finite size corrections optional available only for spikes Defaults 0 Output S spectrum in form time x frequency x channels trials for trialave 0 or as a function of frequency if trialave 1 t times f frequencies R rate Serr error bars only for err 1 1 CROSS REFERENCE INFORMATION This function calls mtspectrumpb Multi taper spectrum binned point process This function is called by mtspecgramtrigpb Multi taper event triggered time frequency spectrum binned point process SOURCE CODE 0001 function S t f R Serr mtspecgrampb data movingwin params fscorr 0002 Multi taper time frequency spectrum binned point process 0003 0004 Usage 0005 0006 S t f R Serr mtspecgrampb data movingwin params fscorr 0007 Input 0008 data in form samples x channels trials or single vector required 0009 movingwin in the form window winstep i e length of moving 0010 window and step size 0011 0012 params structure with fields tapers pad Fs fpass err trialave 0013 optional 0014 tapers precalculated tapers from dpss or in the one of the following 0015 forms 0016 1 A numeric vector TW K where TW is the 0017 time bandwidth product and K is the number of 0018 tapers to be used less than or equal to 0019 2TW 1 0020 2 A numeric vector W T p where W is the 0021 bandwidth T is the duration of the data and p 0022 is an integer such that 2TW p tapers are used In 0023 this form there is no default i e to specify 0024 the bandwidth you have to specify T and p as 0025 well Note that the units of W and T have to be 0026 consistent if W is in Hz T must be in seconds 0027 and vice versa Note that these units must also 0028 be consistent with the units of params Fs W can 0029 be in Hz if and only if params Fs is in Hz 0030 The default is to use form 1 with TW 3 and K 5 0031 Note that T has to be equal to movingwin 1 0032 0033 pad padding factor for the FFT optional can take values 1 0 1 2 0034 1 corresponds to no padding 0 corresponds to padding 0035 to the next highest power of 2 etc 0036 e g For N 500 if PAD 1 we do not pad if PAD 0 we pad the FFT 0037 to 512 points if pad 1 we pad to 1024 points etc 0038 Defaults to 0 0039 Fs sampling frequency optional Default 1 0040 fpass frequency band to be used in the calculation in the form 0041 fmin fmax optional 0042 Default all frequencies between 0 and Fs 2 0043 err error calculation 1 p Theoretical error bars 2 p Jackknife error bars 0044 0 p or 0 no error bars optional Default 0 0045 trialave average over trials channnels when 1 don t average when 0 optional Default

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/pointbinned/mtspecgrampb.html (2015-03-27)
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  • Description of spsvd
    optional Default is the maximum possible modes determined by taper parameters Outputs sv sp fm singular values space modes frequency modes CROSS REFERENCE INFORMATION This function calls This function is called by SOURCE CODE 0001 function sv sp fm spsvd data params mdkp 0002 Space frequency SVD of input data continuous processes 0003 Usage sv sp fm spsvd data params mdkp 0004 Inputs 0005 data data matrix in timexchannels form required 0006 params structure containing parameters params has the 0007 following fields tapers Fs fpass pad 0008 tapers precalculated tapers from dpss or in the one of the following 0009 forms 0010 1 A numeric vector TW K where TW is the 0011 time bandwidth product and K is the number of 0012 tapers to be used less than or equal to 0013 2TW 1 0014 2 A numeric vector W T p where W is the 0015 bandwidth T is the duration of the data and p 0016 is an integer such that 2TW p tapers are used In 0017 this form there is no default i e to specify 0018 the bandwidth you have to specify T and p as 0019 well Note that the units of W and T have to be 0020 consistent if W is in Hz T must be in seconds 0021 and vice versa Note that these units must also 0022 be consistent with the units of params Fs W can 0023 be in Hz if and only if params Fs is in Hz 0024 The default is to use form 1 with TW 3 and K 5 0025 0026 Fs sampling frequency optional Defaults to 1 0027 fpass frequency band to be used in the calculation in the form 0028 fmin fmax optional 0029 Default all frequencies between 0 and Fs 2

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/continuous/spsvd.html (2015-03-27)
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  • Description of coherencypb
    confidence level for C at 1 p only for err 1 1 phistd jackknife theoretical standard deviation for phi Note that phi 2 phistd and phi 2 phistd will give 95 confidence bands for phi only for err 1 1 Cerr Jackknife error bars for C use only for Jackknife err 1 2 CROSS REFERENCE INFORMATION This function calls mtfftpb Multi taper fourier transform binned point process data This function is called by coherencysegpb Multi taper coherency cross spectrum and individual spectra computed by segmenting cohgrampb Multi taper time frequency coherence cross spectrum and individual spectra two binned point processes SOURCE CODE 0001 function C phi S12 S1 S2 f zerosp confC phistd Cerr coherencypb data1 data2 params fscorr 0002 Multi taper coherency cross spectrum and individual spectra binned point process 0003 0004 Usage 0005 0006 C phi S12 S1 S2 f zerosp confC phistd Cerr coherencypb data1 data2 params fscorr 0007 Input 0008 data1 in form samples x trials required 0009 data2 in form samples x trials required 0010 params structure with fields tapers pad Fs fpass err trialave 0011 optional 0012 tapers precalculated tapers from dpss or in the one of the following 0013 forms 0014 1 A numeric vector TW K where TW is the 0015 time bandwidth product and K is the number of 0016 tapers to be used less than or equal to 0017 2TW 1 0018 2 A numeric vector W T p where W is the 0019 bandwidth T is the duration of the data and p 0020 is an integer such that 2TW p tapers are used In 0021 this form there is no default i e to specify 0022 the bandwidth you have to specify T and p as 0023 well Note that the units of W and T have to be 0024 consistent if W is in Hz T must be in seconds 0025 and vice versa Note that these units must also 0026 be consistent with the units of params Fs W can 0027 be in Hz if and only if params Fs is in Hz 0028 The default is to use form 1 with TW 3 and K 5 0029 0030 pad padding factor for the FFT optional can take values 1 0 1 2 0031 1 corresponds to no padding 0 corresponds to padding 0032 to the next highest power of 2 etc 0033 e g For N 500 if PAD 1 we do not pad if PAD 0 we pad the FFT 0034 to 512 points if pad 1 we pad to 1024 points etc 0035 Defaults to 0 0036 Fs sampling frequency optional Default 1 0037 fpass frequency band to be used in the calculation in the form 0038 fmin fmax optional 0039 Default all frequencies between 0 and Fs 2 0040 err error calculation 1 p Theoretical error bars 2 p Jackknife error bars 0041 0 p or 0 no error bars optional Default 0 0042 trialave average over trials when 1 don t

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/pointbinned/coherencypb.html (2015-03-27)
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  • Description of fig7_3
    data CROSS REFERENCE INFORMATION This function calls This function is called by runbook SOURCE CODE 0001 Local Regression and Likelihood Figure 7 3 0002 0003 Censored local regression 0004 0005 Author Catherine Loader 0006 0007 NEEDS Kaplan Meier based estimate Identify curves and cens uncens data 0008 0009 load heart 0010 fit locfit age log 0 5 surv 0011 figure Name fig7 3 censored local regression Kaplan Meier based 0012

    Original URL path: http://www.chronux.org/Documentation/chronux/locfit/Book/fig7_3.html (2015-03-27)
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  • Description of mtspecgrampt
    use finite size corrections optional available only for spikes Defaults 0 Output S spectrogram with dimensions time x frequency x channels trials if trialave 0 dimensions time x frequency if trialave 1 t times f frequencies Serr error bars only if err 1 1 CROSS REFERENCE INFORMATION This function calls extractdatapt Extract segements of spike times between t 1 and t 2 minmaxsptimes Find the minimum and maximum of the spike times in each channel mtspectrumpt Multi taper spectrum point process times This function is called by mtspecgramtrigpt Multi taper event triggered time frequency spectrum point process times SOURCE CODE 0001 function S t f R Serr mtspecgrampt data movingwin params fscorr 0002 Multi taper time frequency spectrum point process times 0003 0004 Usage 0005 0006 S t f R Serr mtspecgrampt data movingwin params fscorr 0007 Input 0008 data structure array of spike times with dimension channels trials 0009 also accepts 1d array of spike times required 0010 movingwin in the form window winstep i e length of moving 0011 window and step size 0012 0013 params structure with fields tapers pad Fs fpass err trialave 0014 optional 0015 tapers precalculated tapers from dpss or in the one of the following 0016 forms 0017 1 A numeric vector TW K where TW is the 0018 time bandwidth product and K is the number of 0019 tapers to be used less than or equal to 0020 2TW 1 0021 2 A numeric vector W T p where W is the 0022 bandwidth T is the duration of the data and p 0023 is an integer such that 2TW p tapers are used In 0024 this form there is no default i e to specify 0025 the bandwidth you have to specify T and p as 0026 well Note that the units of W and T have to be 0027 consistent if W is in Hz T must be in seconds 0028 and vice versa Note that these units must also 0029 be consistent with the units of params Fs W can 0030 be in Hz if and only if params Fs is in Hz 0031 The default is to use form 1 with TW 3 and K 5 0032 Note that T has to be equal to movingwin 1 0033 0034 pad padding factor for the FFT optional can take values 1 0 1 2 0035 1 corresponds to no padding 0 corresponds to padding 0036 to the next highest power of 2 etc 0037 e g For N 500 if PAD 1 we do not pad if PAD 0 we pad the FFT 0038 to 512 points if pad 1 we pad to 1024 points etc 0039 Defaults to 0 0040 Fs sampling frequency optional Default 1 0041 fpass frequency band to be used in the calculation in the form 0042 fmin fmax optional 0043 Default all frequencies between 0 and Fs 2 0044 err error calculation 1 p Theoretical error bars 2 p Jackknife error bars 0045 0

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/pointtimes/mtspecgrampt.html (2015-03-27)
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  • Description of sta
    0030 data spk padNaN data spk create a zero padded data matrix from input structural array 0031 sz size data spk 0032 if sz 1 sz 2 data spk data spk end transpose data to get in form compatible with Murray s routine 0033 else 0034 sz size data spk 0035 if sz 1 sz 2 data spk data spk end transpose data to get in form compatible with Murray s routine 0036 end 0037 sz size data lfp 0038 if sz 1 sz 2 data lfp data lfp end transpose data to get in form compatible with Murray s routine 0039 verbose 1 0040 t smp 0041 if nargin 4 plt r end 0042 if nargin 5 w 0 end 0043 if nargin 6 T min t max t end 0044 if nargin 7 D 0 25 1 1 end 0045 if nargin 8 err 1 end 0046 0047 if isempty plt plt r end 0048 if isempty w w 0 end 0049 if isempty T T min t max t end 0050 if isempty D D 0 25 1 1 end 0051 if isempty err err 1 end 0052 0053 if w T 2 T 1 2 0054 disp Smoothing data segment should be in seconds turn off smoothing 0055 w 0 0056 end 0057 0058 sz size data spk 0059 NT sz 1 0060 mlfp 0 0061 slfp 0 0062 Nspk 0 0063 smp t 2 t 1 0064 if D 1 0 D 2 0 0065 t1 D 1 smp smp eps 0 smp D 2 eps 0066 else 0067 t1 round D 1 smp smp smp D 2 0068 end 0069 0070 count up the spikes 0071 0072 if err 0073 for n 1 NT 0074 indx find t T 1 t T 2 0075 lfp data lfp n indx 0076 spk data spk n data spk n T 1 data spk n T 2 data spk n 0 0077 tt t indx 0078 if isempty spk 0 0079 ND length spk 0080 for s 1 ND 0081 spktime spk s 0082 t0 tt spktime eps 0083 if min t0 D 1 smp max t0 D 2 smp break end 0084 Nspk Nspk 1 0085 end 0086 end 0087 end 0088 Err zeros Nspk length t1 0089 Nspk 0 0090 end 0091 0092 for n 1 NT 0093 indx find t T 1 t T 2 0094 lfp data lfp n indx 0095 spk data spk n data spk n T 1 data spk n T 2 data spk n 0 0096 tt t indx 0097 if isempty spk 0 0098 ND length spk 0099 for s 1 ND 0100 spktime spk s 0101 t0 tt spktime eps 0102 if min t0 D 1 smp max t0 D 2 smp 0103 indx find t0 D 1 0104 indx indx length indx 0105 offset t0 indx D 1 smp 0106 indx indx indx length t1 1 0107 lfp t1 lfp indx lfp indx 1 lfp indx

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/hybrid/sta.html (2015-03-27)
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  • Description of coherencypt
    for err 1 1 Cerr Jackknife error bars for C use only for Jackknife err 1 2 CROSS REFERENCE INFORMATION This function calls minmaxsptimes Find the minimum and maximum of the spike times in each channel mtfftpt Multi taper fourier transform for point process given as times This function is called by coherencysegpt Multi taper coherency computed by segmenting two univariate point processes into chunks cohgrampt Multi taper time frequency coherence two point processes given as times SOURCE CODE 0001 function C phi S12 S1 S2 f zerosp confC phistd Cerr coherencypt data1 data2 params fscorr t 0002 Multi taper coherency point process times 0003 0004 Usage 0005 0006 C phi S12 S1 S2 f zerosp confC phistd Cerr coherencypt data1 data2 params fscorr t 0007 Input 0008 data1 structure array of spike times with dimension trials also accepts 1d array of spike times required 0009 data2 structure array of spike times with dimension trials also accepts 1d array of spike times required 0010 params structure with fields tapers pad Fs fpass err trialave 0011 optional 0012 tapers precalculated tapers from dpss or in the one of the following 0013 forms 0014 1 A numeric vector TW K where TW is the 0015 time bandwidth product and K is the number of 0016 tapers to be used less than or equal to 0017 2TW 1 0018 2 A numeric vector W T p where W is the 0019 bandwidth T is the duration of the data and p 0020 is an integer such that 2TW p tapers are used In 0021 this form there is no default i e to specify 0022 the bandwidth you have to specify T and p as 0023 well Note that the units of W and T have to be 0024 consistent if W is in Hz T must be in seconds 0025 and vice versa Note that these units must also 0026 be consistent with the units of params Fs W can 0027 be in Hz if and only if params Fs is in Hz 0028 The default is to use form 1 with TW 3 and K 5 0029 0030 pad padding factor for the FFT optional can take values 1 0 1 2 0031 1 corresponds to no padding 0 corresponds to padding 0032 to the next highest power of 2 etc 0033 e g For N 500 if PAD 1 we do not pad if PAD 0 we pad the FFT 0034 to 512 points if pad 1 we pad to 1024 points etc 0035 Defaults to 0 0036 Fs sampling frequency optional Default 1 0037 fpass frequency band to be used in the calculation in the form 0038 fmin fmax optional 0039 Default all frequencies between 0 and Fs 2 0040 err error calculation 1 p Theoretical error bars 2 p Jackknife error bars 0041 0 p or 0 no error bars optional Default 0 0042 trialave average over trials when 1 don t average when 0 optional Default 0

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/pointtimes/coherencypt.html (2015-03-27)
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  • Description of fig7_4
    fine Memory leak somewhere also works if i ignore censoring CROSS REFERENCE INFORMATION This function calls This function is called by runbook SOURCE CODE 0001 Local Regression and Likelihood Figure 7 4 0002 0003 Censored Local Likelihood 0004 0005 Author Catherine Loader 0006 0007 NEED this is given problems for unknown reasons something 0008 to do with censored observations and the ibeta routine 0009 if i replace this by 0010

    Original URL path: http://www.chronux.org/Documentation/chronux/locfit/Book/fig7_4.html (2015-03-27)
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