smoothdens: Build the design and penalty matrices for smooth density estimation

Description

This high-level function can be used to prepare objects needed to estimate mixture models of smooth densities using P-Splines.

Usage

smoothdens(
  x,
  par,
  type = "real",
  k = 25,
  knots = NULL,
  degree = 3,
  diff_order = 2,
  pow = 0.5,
  npoints = 10000
)

Value

For one data stream, an object of class "smoothdens": a list containing the design matrix Z, the penalty matrix S, the initial coefficients coef, the prediction design matrix Z_predict, the prediction grid xseq, details for the basis expansion basis, and the function density(beta). For several data streams, a named list of such objects.

Arguments

x

data vector for one data stream, or named data frame or list of several data streams

par

list of initial means and sds ("real", "positive") or means and concentrations ("circular", called kappa or concentration), one value per state. For several data streams, a named list of such lists.

type

type of each data stream, either "real" for data on the reals, "positive" for data on the positive reals or "circular" for angular data.

k

number of basis functions for each data stream

knots

optional vector of knots (including the boundary knots) to be used for basis construction, for several data streams a named list of such vectors. If not provided, the knots are placed equidistantly for "real" and "circular" and using polynomial spacing for "positive".

For "real" and "positive" k - degree + 1 knots are needed, for "circular" k + 1 knots are needed.

degree

degree of the B-spline basis functions for each data stream, defaults to cubic B-splines

diff_order

order of differencing used for the P-Spline penalty matrix for each data stream. Defaults to second-order differences.

pow

power for polynomial knot spacing, only used for type = "positive"

npoints

number of points used in the numerical integration for normalizing the B-spline basis functions

type, k, degree, diff_order, pow and npoints can be of length 1 or one per data stream (named or in the order of x).

Details

Under the hood, make_matrices_dens is used for the actual construction of the design and penalty matrices.

You can provide one or multiple data streams of different types (real, positive, circular) and specify initial means and standard deviations/ concentrations for each data stream. This information is then converted into suitable spline coefficients. smoothdens then constructs the design and penalty matrices for standardised B-splines basis functions (integrating to one) for each data stream. For types "real" and "circular" the knots are placed equidistant in the range of the data, for type "positive" the knots are placed using polynomial spacing.

The last spline coefficient of each state is fixed at zero for identifiability, hence coef has k - 1 columns. density(beta) takes care of this: it maps the coefficient matrix to the allprobs matrix, with rows of missing observations equal to one.

Examples

Run this code

## one data stream, mixture of two normals
x = c(rnorm(100, 0, 1), rnorm(100, 5, 1))
dens = smoothdens(x, par = list(mean = c(0, 5), sd = c(1, 1)))

Z = dens$Z # design matrix
S = dens$S # penalty matrix
beta = dens$coef # initial coefficients
allprobs = dens$density(beta) # use this in the likelihood function

## 3 data streams
data = data.frame(x1 = rnorm(100, mean = 0, sd = 1),
                  x2 = rgamma2(100, mean = 5, sd = 3),
                  x3 = rvm(100, mu = 0, kappa = 2))

par = list(x1 = list(mean = 0, sd = 1),
           x2 = list(mean = 5, sd = 3),
           x3 = list(mean = 0, kappa = 2))

dens = smoothdens(data, par, type = c("real", "positive", "circular"))

# objects for x1
Z1 = dens$x1$Z
allprobs = dens$x1$density(dens$x1$coef) *
  dens$x2$density(dens$x2$coef) *
  dens$x3$density(dens$x3$coef)