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- Description of mtspecgramc_fast

fmax optional Default all frequencies between 0 and Fs 2 err error calculation 1 p Theoretical error bars 2 p Jackknife error bars 0 p or 0 no error bars optional Default 0 trialave average over trials channels when 1 don t average when 0 optional Default 0 Output S spectrum in form time x frequency x channels trials if trialave 0 in the form time x frequency if trialave 1 t times f frequencies Serr error bars only for err 1 1 CROSS REFERENCE INFORMATION This function calls This function is called by SOURCE CODE 0001 function S t f Serr mtspecgramc data movingwin params 0002 Multi taper time frequency spectrum continuous process 0003 0004 Usage 0005 S t f Serr mtspecgramc data movingwin params 0006 Input 0007 Note units have to be consistent Thus if movingwin is in seconds Fs 0008 has to be in Hz see chronux m for more information 0009 data in form samples x channels trials required 0010 movingwin in the form window winstep i e length of moving 0011 window and step size 0012 Note that units here have 0013 to be consistent with 0014 units of Fs required 0015 params structure with fields tapers pad Fs fpass err trialave 0016 optional 0017 tapers precalculated tapers from dpss or in the one of the following 0018 forms 0019 1 A numeric vector TW K where TW is the 0020 time bandwidth product and K is the number of 0021 tapers to be used less than or equal to 0022 2TW 1 0023 2 A numeric vector W T p where W is the 0024 bandwidth T is the duration of the data and p 0025 is an integer such that 2TW p tapers are used In 0026 this form there is no default i e to specify 0027 the bandwidth you have to specify T and p as 0028 well Note that the units of W and T have to be 0029 consistent if W is in Hz T must be in seconds 0030 and vice versa Note that these units must also 0031 be consistent with the units of params Fs W can 0032 be in Hz if and only if params Fs is in Hz 0033 The default is to use form 1 with TW 3 and K 5 0034 Note that T has to be equal to movingwin 1 0035 0036 pad padding factor for the FFT optional Defaults to 0 0037 e g For N 500 if PAD 0 we pad the FFT 0038 to 512 points if PAD 2 we pad the FFT 0039 to 2048 points etc 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 p or 0 no error bars optional Default 0 0046 trialave

Original URL path: http://www.chronux.org/Documentation/chronux/test/mtspecgramc_fast.html (2015-03-27)

Open archived version from archive - Description of spence21

t the shortest computer program 0005 0006 oten ones 10 1 0007 n length y 0008 y oten y 1 y oten y n 0009 0010 n length y 0011 k 4 n 3 0012 y1 y k 3 y k 1 2 y k y k 1 y k 3 0013 0014 n length y1 0015 k 4 n 3 0016 y2 y1 k 3 y1 k 2 y1

Original URL path: http://www.chronux.org/Documentation/chronux/locfit/m/spence21.html (2015-03-27)

Open archived version from archive - Description of coherencycpb

for err 1 1 phistd theoretical jackknife depending on err 1 1 err 1 2 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 This function is called by coherencysegcpb Multi taper coherency cross spectrum and individual spectra with segmenting cohgramcpb Multi taper time frequency coherence cross spectrum and individual spectra SOURCE CODE 0001 function C phi S12 S1 S2 f zerosp confC phistd Cerr coherencycpb data1 data2 params fscorr 0002 Multi taper coherency cross spectrum and individual spectra continuous and binned point process data 0003 0004 Usage 0005 0006 C phi S12 S1 S2 f zerosp confC phistd Cerr coherencycpb data1 data2 params fscorr 0007 Inputs 0008 data1 continuous data in form samples x trials required 0009 data2 binned spike data 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 average when 0 optional Default 0

Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/hybrid/coherencycpb.html (2015-03-27)

Open archived version from archive - Description of fig7_1

censored observation 0 uncensored The xlim argument specifies bounds on the domain of the x variable survival times Usually survival times are non negative lower bound 0 but with theoretically no upper bound The specification 0 10000 gives the lower bound of 0 and the upper bound is effectively infinite Author Catherine Loader NEEDS m argument to lfplot Also lfplot symbols should distinguish between censored and uncensored data points CROSS REFERENCE INFORMATION This function calls This function is called by runbook SOURCE CODE 0001 Local Regression and Likelihood Figure 7 1 0002 0003 Estimating the hazard rate for censored survival or 0004 failure time data Hazard rate estimation is specified 0005 by family hazard 0006 0007 The censoring indicator variable is passed as the cens 0008 argument This should be a vector of 0 s and 1 s with 1 0009 indicating a censored observation 0 uncensored 0010 0011 The xlim argument specifies bounds on the domain of the 0012 x variable survival times Usually survival times are 0013 non negative lower bound 0 but with theoretically no 0014 upper bound The specification 0 10000 gives the lower 0015 bound of 0 and the upper bound is effectively infinite 0016

Original URL path: http://www.chronux.org/Documentation/chronux/locfit/Book/fig7_1.html (2015-03-27)

Open archived version from archive - Description of mtspecgramc_slow

optional Default all frequencies between 0 and Fs 2 err error calculation 1 p Theoretical error bars 2 p Jackknife error bars 0 p or 0 no error bars optional Default 0 trialave average over trials channels when 1 don t average when 0 optional Default 0 Output S spectrum in form time x frequency x channels trials if trialave 0 in the form time x frequency if trialave 1 t times f frequencies Serr error bars only for err 1 1 CROSS REFERENCE INFORMATION This function calls This function is called by testspecgram cd C Documents and Settings Admin Desktop SOURCE CODE 0001 function S t f Serr mtspecgramc slow data movingwin params 0002 Multi taper time frequency spectrum continuous process 0003 0004 Usage 0005 S t f Serr mtspecgramc data movingwin params 0006 Input 0007 Note units have to be consistent Thus if movingwin is in seconds Fs 0008 has to be in Hz see chronux m for more information 0009 data in form samples x channels trials required 0010 movingwin in the form window winstep i e length of moving 0011 window and step size 0012 Note that units here have 0013 to be consistent with 0014 units of Fs required 0015 params structure with fields tapers pad Fs fpass err trialave 0016 optional 0017 tapers precalculated tapers from dpss or in the one of the following 0018 forms 0019 1 A numeric vector TW K where TW is the 0020 time bandwidth product and K is the number of 0021 tapers to be used less than or equal to 0022 2TW 1 0023 2 A numeric vector W T p where W is the 0024 bandwidth T is the duration of the data and p 0025 is an integer such that 2TW p tapers are used In 0026 this form there is no default i e to specify 0027 the bandwidth you have to specify T and p as 0028 well Note that the units of W and T have to be 0029 consistent if W is in Hz T must be in seconds 0030 and vice versa Note that these units must also 0031 be consistent with the units of params Fs W can 0032 be in Hz if and only if params Fs is in Hz 0033 The default is to use form 1 with TW 3 and K 5 0034 Note that T has to be equal to movingwin 1 0035 0036 pad padding factor for the FFT optional Defaults to 0 0037 e g For N 500 if PAD 0 we pad the FFT 0038 to 512 points if PAD 2 we pad the FFT 0039 to 2048 points etc 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 p or 0

Original URL path: http://www.chronux.org/Documentation/chronux/test/mtspecgramc_slow.html (2015-03-27)

Open archived version from archive - Description of spike-field-coherenceMBL2005

0 100 params trialave 1 0004 movingwin 0 5 0 1 duration of moving window used to evaluate spectrograms 0005 win 2 2 window around events 0006 fignum 2 3 6 9 8 7 4 1 figure numbers for particular directions 0007 for targ 0 7 0008 E targoff find targets targ 0009 datasp createdatamatpt dsp 1 E win 0010 datalfp createdatamatc dlfp 1 E Fs win 0011 C phi

Original URL path: http://www.chronux.org/Documentation/chronux/old/tutorial/spike-field-coherenceMBL2005.html (2015-03-27)

Open archived version from archive - Description of coherencycpt

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 This function is called by coherencysegcpt Multi taper coherency cross spectrum and individual spectra computed by segmenting cohgramcpt Multi taper time frequency coherence cross spectrum and individual spectra SOURCE CODE 0001 function C phi S12 S1 S2 f zerosp confC phistd Cerr coherencycpt data1 data2 params fscorr t 0002 Multi taper coherency cross spectrum and individual spectra continuous data and point process as times 0003 0004 Usage 0005 0006 C phi S12 S1 S2 f zerosp confC phistd Cerr coherencycpt data1 data2 params fscorr t 0007 Input 0008 data1 continuous data in time x trials form required 0009 data2 structure array of spike times with dimension trials 0010 also accepts 1d array of spike times required 0011 params structure with fields tapers pad Fs fpass err trialave 0012 optional 0013 tapers precalculated tapers from dpss or in the one of the following 0014 forms 0015 1 A numeric vector TW K where TW is the 0016 time bandwidth product and K is the number of 0017 tapers to be used less than or equal to 0018 2TW 1 0019 2 A numeric vector W T p where W is the 0020 bandwidth T is the duration of the data and p 0021 is an integer such that 2TW p tapers are used In 0022 this form there is no default i e to specify 0023 the bandwidth you have to specify T and p as 0024 well Note that the units of W and T have to be 0025 consistent if W is in Hz T must be in seconds 0026 and vice versa Note that these units must also 0027 be consistent with the units of params Fs W can 0028 be in Hz if and only if params Fs is in Hz 0029 The default is to use form 1 with TW 3 and K 5 0030 0031 pad padding factor for the FFT optional can take values 1 0 1 2 0032 1 corresponds to no padding 0 corresponds to padding 0033 to the next highest power of 2 etc 0034 e g For N 500 if PAD 1 we do not pad if PAD 0 we pad the FFT 0035 to 512 points if pad 1 we pad to 1024 points etc 0036 Defaults to 0 0037 Fs sampling frequency optional Default 1 0038 fpass frequency band to be used in the calculation in the form 0039 fmin fmax optional 0040 Default all frequencies between 0 and Fs 2 0041 err error calculation 1 p Theoretical error bars 2 p Jackknife error bars 0042 0 p or 0 no error bars optional Default 0 0043 trialave average over trials when 1 don t average when 0 optional Default 0 0044 fscorr finite size corrections 0 don t use finite size corrections or 0045 1 use finite size corrections

Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/hybrid/coherencycpt.html (2015-03-27)

Open archived version from archive - Description of fig7_2

Author Catherine Loader CROSS REFERENCE INFORMATION This function calls This function is called by runbook SOURCE CODE 0001 Local Regression and Likelihood Figure 7 2 0002 0003 Conditional Hazard Rate Estimation 0004 When hazard rate estimation is performed with multiple x variables 0005 the result is an estimate of the conditional hazard rate for the 0006 first variable given the levels of the remaining variables 0007 0008 The surface plot

Original URL path: http://www.chronux.org/Documentation/chronux/locfit/Book/fig7_2.html (2015-03-27)

Open archived version from archive