genspline {MBNMAtime}

Generates spline basis matrices for fitting to time-course function

Description

Generates spline basis matrices for fitting to time-course function

Usage

genspline(
  x,
  spline = "bs",
  knots = 1,
  degree = 1,
  max.time = max(x),
  boundaries = NULL
)

Arguments

x

A numeric vector indicating all time points available in the dataset

spline

Indicates the type of spline function. Can be either a piecewise linear spline ("ls"), natural cubic spline ("ns") or B-spline ("bs").

knots

The number/location of knots. If a single integer is given it indicates the number of knots (they will be equally spaced across the range of time-points). If a numeric vector is given it indicates the quantiles of the knots as a proportion of the maximum study follow-up in the dataset. For example, if the maximum follow-up time in the dataset is 10 months, knots=c(0.1,0.5) would indicate knots should be fitted at 1 and 5 months follow-up.

degree

a positive integer giving the degree of the polynomial from which the spline function is composed (e.g. degree=3 represents a cubic spline).

max.time

A number indicating the maximum time between which to calculate the spline function.

boundaries

A positive numeric vector of length 2 that represents the time-points at which to anchor the B-spline or natural cubic spline basis matrix. This allows data to extend beyond the boundary knots, or for the basis parameters to not depend on x. The default (boundaries=NULL)is the range of x.

Value

A spline basis matrix with number of rows equal to length(x) and the number of columns equal to the number of coefficients in the spline.

Examples

x <- 0:100

genspline(x)

# Generate a quadratic B-spline with 1 equally spaced internal knot
genspline(x, spline="bs", knots=2, degree=2)

# Generate a natural spline with 2 knots at selected quantiles
genspline(x, spline="ns", knots=c(0.1, 0.5))

# Generate a piecewise linear spline with 3 equally spaced knots
genspline(x, spline="ls", knots=3)