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  • Description of lfex1
    terms of events per unit time instead of the default statistical density estimation alpha 0 6 specifies the width of the sliding windows as a fraction of the total spikes xlim gives the limits of the observation interval Correct specification of this is critical to avoid introducing bias at end points The lfband fit line adds confidence bands based on pointwise 95 coverage to the plot The spike time data is from Hemant Bokil CROSS REFERENCE INFORMATION This function calls This function is called by SOURCE CODE 0001 Local Estimation a spike firing rate in spikes per unit time 0002 0003 The estimation procedure approximates the log of the spike firing 0004 rate by a quadratic polynomial within a sliding window 0005 0006 The first argument to locfit is a column vector of the spike times 0007 family rate specifies that the output of the density estimate should 0008 be in terms of events per unit time instead of the default statistical 0009 density estimation 0010 0011 alpha 0 6 specifies the width of the sliding windows as a fraction of 0012 the total spikes 0013 0014 xlim gives the limits of the observation interval Correct specification 0015 of this

    Original URL path: http://www.chronux.org/Documentation/chronux/locfit/Neuro/lfex1.html (2015-03-27)
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  • Description of psth
    the number 0025 of spikes falling under the kernel is the same on 0026 average but is time dependent Reagions rich 0027 in data therefore have their kernel width reduced 0028 0029 Outputs 0030 0031 R rate 0032 t times 0033 E errors standard error 0034 0035 if nargin 1 error I need data end 0036 data padNaN data create a zero padded data matrix from input structural array 0037 sz size data 0038 transposes data so that the longer dimension is assumed to be time 0039 Procedure used to bring input data into form compatible with that required 0040 for Murray s routine 0041 if sz 1 sz 2 data data end 0042 if nargin 2 sig 0 05 end 0043 if nargin 3 plt r end 0044 if nargin 5 err 2 end 0045 0046 if isempty sig sig 0 05 end 0047 if isempty plt plt r end 0048 if isempty err err 2 end 0049 0050 adapt 0 0051 if sig 0 adapt 1 sig sig end 0052 0053 to avoid end effects increase time interval by the width 0054 of the kernel otherwise rate is too low near edges 0055 0056 if nargin 4 0057 T 1 min data 1 0058 T 2 max max data 0059 else 0060 T 1 T 1 4 sig 0061 T 2 T 2 4 sig 0062 end 0063 0064 calculate NT and ND and filter out times of interest 0065 0066 NT length data 1 0067 if NT 4 err 2 0068 disp Using Poisson errorbars as number of trials is too small for bootstrap 0069 err 1 0070 end 0071 0072 m 1 0073 D zeros size data 0074 ND zeros 1 NT 0075 for n 1 NT 0076 indx find isnan data n data n T 1 data n T 2 0077 ND n length indx 0078 D n 1 ND n data n indx 0079 m m ND n 0080 end 0081 N tot m 0082 N max max ND 0083 D D 1 N max 0084 0085 if the kernel density is such that there are on average 0086 one or less spikes under the kernel then the units are probably wrong 0087 0088 L N tot NT T 2 T 1 0089 if 2 L NT sig 1 L 0 1 0090 disp Spikes very low density are the units right is the kernel width sensible 0091 disp Total events num2str fix 100 N tot 100 sig 0092 num2str fix 1000 sig ms T num2str fix 100 T 100 events sig 0093 num2str fix 100 N tot sig T 2 T 1 100 0094 end 0095 0096 Smear each spike out 0097 std dev is sqrt rate integral over kernal 2 trials 0098 for Gaussian integral over Kernal 2 is 1 2 sig srqt pi 0099 0100 if nargin 6 0101 N pts fix 5 T 2 T 1 sig 0102 t linspace T 1 T 2 N pts 0103 else 0104 N

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/pointtimes/psth.html (2015-03-27)
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  • Description of JointDist
    0003 JOINTDIST 0004 Usage P bins JointDist x y nbins 0005 0006 This function calculates the joint distribution of the variables x and y 0007 It is simply a normalized histogram using hist3 nbins can take any form 0008 of bins that hist3 can take but no other hist3 options 0009 0010 Written by Dan Valente 0011 October 2007 0012 0013 ensure x and y are both column matrices 0014

    Original URL path: http://www.chronux.org/Documentation/chronux/fly_track/FAnalyze/functions/JointDist.html (2015-03-27)
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  • Description of fig2_2
    Figure 2 2 Using different smoothing parameters CROSS REFERENCE INFORMATION This function calls This function is called by runbook SOURCE CODE 0001 Local Regression and Likelihood Figure 2 2 0002 0003 Using different smoothing parameters 0004 0005 load ethanol 0006

    Original URL path: http://www.chronux.org/Documentation/chronux/locfit/Book/fig2_2.html (2015-03-27)
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  • Description of lfex2
    bandwidth here is critical The data shows on off behavior exhibiting periods of mainly successes and mainly failures respectively Large values of alpha will smooth out this behavior while small values will be too sensitive to random variability Values of 0 15 to 0 2 seem reasonable for this example AIC is based on asymptotic approximations and seems unreliable here formal model selection needs more investigation Data is from Keith Purpura CROSS REFERENCE INFORMATION This function calls This function is called by SOURCE CODE 0001 Model the success probability of successive trials of a monkey 0002 performing a task 0003 0004 The y variable is a vector of 0 1 with 1 denoting success on 0005 the trial 0 failure The fitting procedure uses logistic 0006 regression within sliding windows specified by the family binomial 0007 arguments 0008 0009 Choosing the bandwidth here is critical The data shows on off behavior 0010 exhibiting periods of mainly successes and mainly failures respectively 0011 Large values of alpha will smooth out this behavior while small values 0012 will be too sensitive to random variability Values of 0 15 to 0 2 seem 0013 reasonable for this example 0014 0015 AIC is based

    Original URL path: http://www.chronux.org/Documentation/chronux/locfit/Neuro/lfex2.html (2015-03-27)
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  • Description of quadcof
    eigenvectors This function is called by SOURCE CODE 0001 function A sumV quadcof N NW order 0002 Helper function to calculate the nonstationary quadratic inverse matrix 0003 Usage A sumV quadcof N NW order 0004 N number of samples 0005 NW Time bandwidth product 0006 order order number of coefficients upto 4NW 0007 0008 Outputs 0009 0010 A quadratic inverse coefficient matrix 0011 sumV sum of the quadratic inverse eigenvectors

    Original URL path: http://www.chronux.org/Documentation/chronux/spectral_analysis/continuous/quadcof.html (2015-03-27)
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  • Description of ProbDist1D
    other hist options CROSS REFERENCE INFORMATION This function calls This function is called by SOURCE CODE 0001 function P bins ProbDist1D x nbins 0002 0003 PROBDIST1D 0004 Usage P bins ProbDist1D x nbins 0005 0006 This function calculates the discrete probability distribution for a 0007 variable that is in a one dimensional phase space It is simply a 0008 normalized histogram using hist so nbins can take any form that

    Original URL path: http://www.chronux.org/Documentation/chronux/fly_track/FAnalyze/functions/ProbDist1D.html (2015-03-27)
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  • Description of fig2_3
    Using different smoothing parameters CROSS REFERENCE INFORMATION This function calls This function is called by runbook SOURCE CODE 0001 Local Regression and Likelihood Figure 2 3 0002 0003 Using different smoothing parameters 0004 0005 load ethanol 0006 0007 alp 0 2 0 4 0 6 0 8 0008 f a b c d 0009 for i 1 4 0010 figure Name sprintf figure2 3 c Changing smoothing parameters f i

    Original URL path: http://www.chronux.org/Documentation/chronux/locfit/Book/fig2_3.html (2015-03-27)
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