survPen: design.matrix – R documentation

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design.matrix

Design matrix for the model needed in Gauss-Legendre quadrature

Description

Builds the design matrix for the whole model when the sum-to-zero constraints are specified. The function is called inside model.cons for Gauss-Legendre quadrature.

Usage

design.matrix(
  formula,
  data.spec,
  Z.smf,
  Z.tensor,
  Z.tint,
  list.smf,
  list.tensor,
  list.tint,
  list.rd
)

Arguments

`formula`	formula object identifying the model
`data.spec`	data frame that represents the environment from which the covariate values and knots are to be calculated
`Z.smf`	List of matrices that represents the sum-to-zero constraint to apply for `smf` splines
`Z.tensor`	List of matrices that represents the sum-to-zero constraint to apply for `tensor` splines
`Z.tint`	List of matrices that represents the sum-to-zero constraint to apply for `tint` splines
`list.smf`	List of all smf.smooth.spec objects contained in the model
`list.tensor`	List of all tensor.smooth.spec objects contained in the model
`list.tint`	List of all tint.smooth.spec objects contained in the model
`list.rd`	List of all rd.smooth.spec objects contained in the model

Value

design matrix for the model

Examples

library(survPen)

# standard spline of time with 4 knots

data <- data.frame(time=seq(0,5,length=100),event=1,t0=0)

form <- ~ smf(time,knots=c(0,1,3,5))

t1 <- eval(substitute(time), data)
t0 <- eval(substitute(t0), data)
event <- eval(substitute(event), data)
	
# Setting up the model
model.c <- model.cons(form,lambda=0,data.spec=data,t1=t1,t1.name="time",
t0=rep(0,100),t0.name="t0",event=event,event.name="event",
expected=NULL,expected.name=NULL,type="overall",n.legendre=20,
cl="survPen(form,data,t1=time,event=event)",beta.ini=NULL)
 
# Retrieving the sum-to-zero constraint matrices and the list of knots
Z.smf <- model.c$Z.smf ; list.smf <- model.c$list.smf

# Calculating the design matrix
design.M <- design.matrix(form,data.spec=data,Z.smf=Z.smf,list.smf=list.smf,
Z.tensor=NULL,Z.tint=NULL,list.tensor=NULL,list.tint=NULL,list.rd=NULL)

survPen

Multidimensional Penalized Splines for Survival and Net Survival Models

v1.5.1

GPL-3 | file LICENSE

Authors

Mathieu Fauvernier [aut, cre], Laurent Roche [aut], Laurent Remontet [aut], Zoe Uhry [ctb], Nadine Bossard [ctb]

Initial release