NEURON Sample Entropy demo readme
"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 architecturespecific directory containing
"special", a script to start NEURON and load the compiledin
libraries. For example, on x86 64bit 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 timeseries 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
standarddeviation, 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):438444, 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 timeseries analysis using approximate entropy and
sample entropy by Richman, JS and Moorman, JR American Journal of
Physiology Heart and Circulatory Physiology 278(6):H2039H2049,
2000.
For questions/comments, email Sam Neymotin: samn at neurosim dot
downstate dot edu
