findPath: Find best subset of points for follow-up experiments
In ezer/NITPicker: Finds the Best Subset of Points to Sample

findPath is the main function of the NITPicker package– it finds the best subset of points to sample from a time course (or spatial axis, along a single axis), based on a set of example curves.

1 2	findPath(tp, y, training, numSubSamples, multiple = F, spline = 1, resampleTraining = T, iter = 20, knots = 100, numPerts = 1000)

`tp`	A numerical vector of time points (or spatial coordinates along a single axis)
`y`	A numerical vector of measurements (of the control)– this can be set to `rep(0, length(tp))` for calculating the shape of the curves only
`training`	Unless multiple is true, this is a numerical matrix of training data, where the rows represent different samples, columns represent different time points (or points on a single spatial axis), and the values correspond to measurements. If multiple is true, this is a list of numerical matrices, each representing a different class of curves (for instance, different genes).
`numSubSamples`	integer that represents the number of time points that will be subsampled
`multiple`	A boolean that designates whether training is a matrix or a list of matrices
`spline`	A positive integer representing the spline used to interpolate between knots when generating perturbations. Note that this does NOT designate the spline used when calculating the L2-error.
`resampleTraining`	A boolean designating whether the exact training data should be used (False) or whether a probability distribution of curves should be generated and training curves resampled (True).
`knots`	A positive integer– for time warping to work optimally, the points must be evenly sampled. This determines how many points do we evenly sample before conducting time warping
`iterations`	A positive integer, representing the maximum number of iterations employed during time warping (see time_warping in fdasrvf library)
`numPert`	a positive integer, representing the number of sampled curves to output.

An integer vector of the indices of the time points selected to be subsampled. The actual time points can be found by tp[output]. The length of this vector should be numSubSamples.

ezer/NITPicker documentation built on May 12, 2019, 7:18 p.m.