written by Sam Neymotin
"Sample Entropy is the negative natural logarithm of an estimate of the conditional probability that subseries (epochs) of length m that match pointwise within a tolerance r also match at the next point."
Files: sampen.mod - has the Sample Entropy (SampEn) Vector function, vsampen vecst.mod, misc.mod, misc.h - support code mosinit.hoc - sets up hoc GUI and starts demo
To compile: nrnivmodl *.mod
This should generate an architecture-specific directory containing "special", a script to start NEURON and load the compiled-in libraries. For example, on x86 64-bit systems, it will make x86_64 directory containing "special"
Then, to run : x86_64/special that will start NEURON To start the demo, use this command from the NEURON prompt: load_file("mosinit.hoc") mosinit.hoc calls vsampen using its default parameters.
Note that mosinit.hoc calls install_sampen() in the beginning, to make sure the Vector function, vsampen is available to NEURON.
vsampen Usage: Vec.vsampen([epoch length,error tolerance,normalize input,compute stdev,output vector]) Vec is a Vector with time-series data all arguments to vsampen are optional epoch length: the number of points to use to match subseries, default:2 error tolerance: the factor * standard deviation of vector to use to consider points in subseries a match, default:0.2 normalize: sets Vector to have mean of 0 and standard deviation of 1 before running sample entropy, default:0 compute stdev:- estimates standard deviation of Sample Entropy measure, default:0 output vector: should have size of 2 and stores SampEn and estimate of standard-deviation, default:empty vsampen returns the sample entropy value, which should be >=0. returns -1 on failure
The code in sampen.mod was used in: Interictal {EEG} Discoordination in a Rat Seizure Model by Neymotin, SA and Lee, H and Fenton, AA and Lytton, WW Journal of Clinical Neurophysiology 27(6):438-444, 2010. The code in sampen.mod is a NEURON Vector function wrapper over code written by Doug Lake. Original C code is available from http://www.physionet.org/physiotools/sampen/ Sample Entropy was first described in: Physiological time-series analysis using approximate entropy and sample entropy by Richman, JS and Moorman, JR American Journal of Physiology- Heart and Circulatory Physiology 278(6):H2039--H2049, 2000.
For questions/comments, email Sam Neymotin: "Neymotin, Samuel (NKI)" <samuel.neymotin at nki.rfmh.org>