computept: Computes a persistence terrace of point cloud data.
In pterrace: Persistence Terrace for Topological Data Analysis

Description Usage Arguments Value Examples

Computes a persistence terrace of point cloud data for given smoothing parameters. For the detailed explanation of the parameters data, sp, fun, lim, by, lib, sublevel, see the R package TDA. A parallel option is available to reduce computation time.

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computept(data, sp, fun = kde, lim = NULL, by = NULL,
  maxdimension = max(NCOL(data)), lib = "Dionysus", sublevel = FALSE,
  par = FALSE, ncore = NULL)

`data`	a matrix of n by d, a point cloud of n points in d dimensions.
`sp`	a vector of smoothing parameter values to be used in the persistence terrace.
`fun`	a smoothing function. The default is the Gaussian kernel density estimator.
`lim`	a 2 by d matrix specifying the range of space to compute. The default value is `NULL`.
`by`	a numeric value or vector that specifies the grid. The default value is `NULL`.
`maxdimension`	a integer of specifying the maximum dimension of persistence terrace to compute.
`lib`	a library to compute persistent homology. The default is "Dionysus".
`sublevel`	a logical value selecting whether persistent homology is computed to super-level sets (`FALSE`) or sub-level sets (`TRUE`). The default value is `FALSE`.
`par`	if `TRUE`, the user can compute the persistence terrace in parallel using multiple cores. The default value is FALSE.
`ncore`	an integer selecting the number of cores to use when parallel computing option is selected. The default value is `NULL`.

The function computept returns a list of the computed persistence terraces up to given dimension. For each dimension, the computed persistence terrace includes the following components:

`x`	The vector of the smoothing parameters used in computation. The x-axis of the persistence terrace.
`y`	The vector of filtration where the Betti number changes. The y-axis of the persistence terrace.
`z`	The matrix of Betti numbers.

# load three circle data
data(three_circle_dat)

# input variables
Xlim <- c(-4,12)
Ylim <- c(-4,9)
lim <- cbind(Xlim, Ylim)
by <- 0.2
spseq <- seq(0.01,1.5,length.out = 10)

# compute persistence terrace
threecirclept <- computept(three_circle_dat,sp=spseq,lim=lim,by=by)

## Not run: 
# compute persistence terrace with parallel option
spseq <- seq(0.01,1.5,length.out = 30)
threecirclept <- computept(three_circle_dat,sp=spseq,lim=lim,by=by,par=TRUE)

## End(Not run)