Nothing
# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#' Numerical solution of the Multi-Stage Clonal Expansion Model
#'
#' This function aims to solve the general multi-stage model
#' with piecewise constant parameters approximatively
#' by integrating the characteristic equations with Euler's method.
#' For sufficiently small time intervalls, this approximation often
#' yields reasonable results.
#' Small time intervals can either be provided explicitly with many columns
#' in argument \code{t}.
#' An alternative is the optional parameter \code{innerSteps}.
#' @param t Each element in a row of \code{t} defines the endpoint of a
#' time interval.
#' The first time interval starts at time \code{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).
#' @param parameterList List of Matrices.
#' Each list member has to be named. Allowed names are \code{Nnu0},
#' \code{alphaX}, \code{gammaX}, and \code{nuX} where \code{X}
#' can be any positive integer value.
#' The number of stages is deduced from \code{nuX}
#' with the highest \code{X}.
#' Matrices \code{Nnu0} and successive \code{nuX} must be provided.
#' Missing other matrices are assumed to be zero.
#' For each matrix it has to hold that the number of columns
#' must be equal to the ones in \code{t}.
#' The number of rows can either equal to the number of rows
#' in \code{t}, or only one row is provided,
#' which then is applied to all rows of \code{t}.
#'
#' Values in matrices \code{Nnu0}, \code{alphaX}, \code{gammaX},
#' \code{nuX} correspond to parameters for each time interval,
#' see the figure and explanations in the package vignette.
#' Here, \code{Nnu0} is the product of \eqn{N}{N} and \eqn{\nu_0}{nu0}
#' and \eqn{\gamma_X}{gammaX} is defined by
#' \eqn{\alpha_X-\beta_X}{alphaX-betaX}.
#' @param innerSteps Positive integer.
#' To improve accuracy, each time interval is internally
#' divided into \code{innerSteps} time intervals of equal length.
#' Defaults to 1000.
#' Note, however, that even in the limit of infinite innerSteps,
#' there will always be a finite discrepancy to the exact result.
#' @return The output list contains all used arguments of the
#' \code{parameterList} and vectors of the model results for
#' hazard and logarithm of the survival function
#' for each row of the input.
#' @details
#' \figure{MSCE.jpg}{Schematic depiction of the MSCE model.
#' See the package vignette for details.}
#' @examples
#' t <-matrix(data=c(10,20,65,10,20,70),nrow=2,byrow=TRUE)
#' Nnu0 <- matrix(c(0.3,0.7,1),nrow = 1)
#' nu1 <- matrix(1e-6,nrow=1,ncol=3)
#' alpha1<- matrix(1,nrow=1,ncol=3)
#' gamma1<- matrix(c(0.13,0.13,0.13, 0.15,0.15,0.15),nrow=2,byrow=TRUE)
#' pars = list(Nnu0=Nnu0, nu1=nu1,alpha1=alpha1,gamma1=gamma1)
#'
#' msce_numerical(t,pars)
#' @seealso \code{\link{tsce}}
#' @export
msce_numerical <- function(t, parameterList, innerSteps = 1000L) {
.Call(`_msce_msce_numerical`, t, parameterList, innerSteps)
}
#' Exact solution of the Two-Stage Clonal Expansion Model
#'
#' For piecewise constant parameters \code{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.
#' @param t Each element in a row of \code{t} defines the endpoint of a
#' time interval.
#' The first time interval starts at time \code{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).
#' @param parameterList List of Matrices.
#' Each list member has to be named. Allowed names are \code{Nnu0},
#' \code{alpha}, \code{gamma}, and \code{nu1}.
#' Matrices \code{Nnu0} and \code{nu1} must be provided.
#' If \code{alpha} or \code{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 \code{t}.
#' The number of rows can either equal to the number of rows in
#' \code{t}, or only one row is provided,
#' which then is applied to all rows of \code{t}.
#'
#' Values in matrices \code{Nnu0}, \code{alpha}, \code{gamma},
#' \code{nu1} correspond to parameters for each time interval,
#' see the figure and explanations in the package vignette.
#' Here, \code{Nnu0} is the product of \eqn{N}{N} and \eqn{\nu_0}{nu0}
#' and \eqn{\gamma}{gamma} is defined by
#' \eqn{\alpha-\beta}{alpha-beta}.
#' @details
#' \figure{TSCE.jpg}{Schematic depiction of the TSCE model.
#' See the package vignette for details.}
#' @examples
#' 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)
#' @seealso \code{\link{msce_numerical}}
#' @export
tsce <- function(t, parameterList) {
.Call(`_msce_tsce`, t, parameterList)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.