ClusterLhnData: A function for fitting Shahar's LHN data to the...

In sfrechter/physplit.analysis: Packaged and versioned Analysis functions for Shahar's cells

Description

In the following, T: the number of time bins, S: the number of odors, N: the number of cells, K: the number of clusters.

Usage

ClusterLhnData(Data, numClusters = 3, kalpha = 10, thalpha = 3/20,
  sdv0 = 0.1, taua = 1, taul0 = 0.5, minIters = 0, numIters = 10000,
  dt = 1e-05, seed = 0, initMode = "random", iclust = NULL,
  verbose = TRUE, timer = "OFF", slopeRatioToStop = 100,
  numSlopePoints = 20, checkToStopEvery = 100, keepHistory = NULL,
  keepHistoryAt = NULL, maxPreFitIters = 1)

Arguments

Data	FIXME - what should the input data look like?!
numClusters	The number of clusters to use.
kalpha	The shape parameter for the gamma prior on alpha.
thalpha	The scale parameter for the gamma prior on alpha
sdv0	The standard deviation of the gaussian prior on membrane potential offset.
taua	The rate constant for the exponential prior on the drive parameters
taul0	The rate constant for the exponential prior on l0.
minIters	The minumum number of iterations.
numIters	The maximum number of iterations.
dt	The time constant of the updates.
seed	The random seed to use.
initMode	The initialization mode for the clustering. Can be "random", "kmeans", or "kmeans++".
iclust	An initial clustering assignment, if any.
verbose	If TRUE will print out the progress of the algorithm and other diagonstic information.
timer	If "ON" will time different blocks of the code.
slopeRatioToStop	The ratio of the rate of change of the objective at the end to the start above which to terminate.
numSlopePoints	How many points to take to compute the slope of the objective
checkToStopEvery	How often to compute the stopping ratio.
keepHistory	A least of strings containing the variables to track.
keepHistoryAt	A list of iterations at which to record history. If NULL defaults to all.
maxPreFitIters	The maximum number of iterations to pre fit the cell-specific parameters to the clusters. If set to 0 will not prefit the parameters.

Value

A list consisting of

seed	The random seed used.
a	A 2 x S x K array containing the learned drive parameters
al	A N x 1 vector containing the learned alpha values
v0	A N x 1 vector containing the learned v0 parameters
l0	A N x 1 vector containing the learned l0 parameters
qnk	A N x K matrix of the cluster responsibilities for each data point.
L	A T x S x N x K array containing the final lambda values
Lclust	A T x S x N array containing the final lambda value for the most likely cluster for each fit.
numIters	The actual number of iterations that ran.
F	A numIters x 1 array containing the objective function as function of the number of iterations.
clust	A N x 1 vector of cluster assignments.
pclust	A N x 1 vector of the probabilities of the cluster chosen.
dclust	A N x 1 vector of distances to its cluster center.
exitMode	A string with the exit mode of the algorithm: "ITERS" if it hit the maximum number of iterations, "SLOPE_RATIO" if it exited early due to the slope ratio.
history	A list containing the values of the tracked variables for the specified iterations.
misc	A miscellaneous list to hold other variables, used mainly for debugging.

sfrechter/physplit.analysis documentation built on May 29, 2019, 8:02 p.m.