tsce: Exact solution of the Two-Stage Clonal Expansion Model

Description

For piecewise constant parameters tsce(t,parameterList) returns the exact hazard and logarithm of the survival function of the Two-Stage Clonal Expansion Model. All arguments are matrices. Evaluation is performed separately for each row.

Usage

tsce(t, parameterList)

Value

Returns a list. Besides the parameters of the parameterList, it contains two named components: hazard the exact hazard and lnSurvival the logarithm of the survival function of the Two-Stage Clonal Expansion Model.

Arguments

t

Each element in a row of t defines the endpoint of a time interval. The first time interval starts at time 0. The last element is the time point for which hazard and survival function are evaluated. Elements in a row have to be in monotonously increasing order. In order to achieve a different number of time intervals for different rows, rows may start with an arbitrary number of zeros (i.e. time intervals of length zero).

parameterList

List of Matrices. Each list member has to be named. Allowed names are Nnu0, alpha, gamma, and nu1. Matrices Nnu0 and nu1 must be provided. If alpha or gamma are missing, they are assumed to be zero. For each matrix it has to hold that the number of columns must be equal to the ones in t. The number of rows can either equal to the number of rows in t, or only one row is provided, which then is applied to all rows of t.

Values in matrices Nnu0, alpha, gamma, nu1 correspond to parameters for each time interval, see the figure and explanations in the package vignette. Here, Nnu0 is the product of \(N\) and \(\nu_0\) and \(\gamma\) is defined by \(\alpha-\beta\).

Details

Schematic depiction of the TSCE model. See the package vignette for details.

Examples

Run this code

t <-matrix(data=c(10,20,65,10,20,70),nrow=2,byrow=TRUE)
Nnu0 <- matrix(c(0.3,0.7,1),nrow = 1)
alpha<- matrix(1,nrow=1,ncol=3)
gamma<- matrix(c(0.13,0.13,0.13, 0.15,0.15,0.15),nrow=2,byrow=TRUE)
nu1  <- matrix(1e-6,nrow=1,ncol=3)
pars = list(Nnu0=Nnu0, alpha=alpha,gamma=gamma,nu1=nu1) 

tsce(t,pars)