From 0a3eb0893cb4bd1b12f07a79069d1c7f5e991495 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 25 Oct 2019 00:37:42 +0200 Subject: Use roxygen for functions and methods --- man/mkinpredict.Rd | 133 +++++++++++++++++++++++++++-------------------------- 1 file changed, 69 insertions(+), 64 deletions(-) (limited to 'man/mkinpredict.Rd') diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd index 24b918dc..53f02dea 100644 --- a/man/mkinpredict.Rd +++ b/man/mkinpredict.Rd @@ -1,78 +1,80 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/mkinpredict.R \name{mkinpredict} \alias{mkinpredict} \alias{mkinpredict.mkinmod} \alias{mkinpredict.mkinfit} -\title{ - Produce predictions from a kinetic model using specific parameters -} -\description{ - This function produces a time series for all the observed variables in a - kinetic model as specified by \code{\link{mkinmod}}, using a specific set of - kinetic parameters and initial values for the state variables. -} +\title{Produce predictions from a kinetic model using specific parameters} \usage{ - mkinpredict(x, odeparms, odeini, outtimes = seq(0, 120, by = 0.1), - solution_type = "deSolve", use_compiled = "auto", method.ode = "lsoda", - atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...) +mkinpredict(x, odeparms, odeini, outtimes = seq(0, 120, by = 0.1), + solution_type = "deSolve", use_compiled = "auto", + method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, + map_output = TRUE, ...) + +\method{mkinpredict}{mkinmod}(x, odeparms = c(k_parent_sink = 0.1), + odeini = c(parent = 100), outtimes = seq(0, 120, by = 0.1), + solution_type = "deSolve", use_compiled = "auto", + method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, + map_output = TRUE, ...) + +\method{mkinpredict}{mkinfit}(x, odeparms = x$bparms.ode, + odeini = x$bparms.state, outtimes = seq(0, 120, by = 0.1), + solution_type = "deSolve", use_compiled = "auto", + method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, + map_output = TRUE, ...) } \arguments{ - \item{x}{ - A kinetic model as produced by \code{\link{mkinmod}}, or a kinetic - fit as fitted by \code{\link{mkinfit}}. In the latter case, the fitted - parameters are used for the prediction. - } - \item{odeparms}{ - A numeric vector specifying the parameters used in the kinetic model, which - is generally defined as a set of ordinary differential equations. - } - \item{odeini}{ - A numeric vectory containing the initial values of the state variables of - the model. Note that the state variables can differ from the observed - variables, for example in the case of the SFORB model. - } - \item{outtimes}{ - A numeric vector specifying the time points for which model predictions - should be generated. - } - \item{solution_type}{ - The method that should be used for producing the predictions. This should - generally be "analytical" if there is only one observed variable, and - usually "deSolve" in the case of several observed variables. The third - possibility "eigen" is faster but not applicable to some models e.g. - using FOMC for the parent compound. - } - \item{method.ode}{ - The solution method passed via \code{\link{mkinpredict}} to - \code{\link{ode}} in case the solution type is "deSolve". The default - "lsoda" is performant, but sometimes fails to converge. - } - \item{use_compiled}{ - If set to \code{FALSE}, no compiled version of the \code{\link{mkinmod}} - model is used, even if is present. - } - \item{atol}{ - Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-8, - lower than in \code{\link{lsoda}}. - } - \item{rtol}{ - Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-10, - much lower than in \code{\link{lsoda}}. - } - \item{map_output}{ - Boolean to specify if the output should list values for the observed - variables (default) or for all state variables (if set to FALSE). - } - \item{\dots}{ - Further arguments passed to the ode solver in case such a solver is used. - } +\item{x}{A kinetic model as produced by \code{\link{mkinmod}}, or a kinetic +fit as fitted by \code{\link{mkinfit}}. In the latter case, the fitted +parameters are used for the prediction.} + +\item{odeparms}{A numeric vector specifying the parameters used in the +kinetic model, which is generally defined as a set of ordinary +differential equations.} + +\item{odeini}{A numeric vectory containing the initial values of the state +variables of the model. Note that the state variables can differ from the +observed variables, for example in the case of the SFORB model.} + +\item{outtimes}{A numeric vector specifying the time points for which model +predictions should be generated.} + +\item{solution_type}{The method that should be used for producing the +predictions. This should generally be "analytical" if there is only one +observed variable, and usually "deSolve" in the case of several observed +variables. The third possibility "eigen" is faster but not applicable to +some models e.g. using FOMC for the parent compound.} + +\item{use_compiled}{If set to \code{FALSE}, no compiled version of the +\code{\link{mkinmod}} model is used, even if is present.} + +\item{method.ode}{The solution method passed via \code{\link{mkinpredict}} +to \code{\link{ode}} in case the solution type is "deSolve". The default +"lsoda" is performant, but sometimes fails to converge.} + +\item{atol}{Absolute error tolerance, passed to \code{\link{ode}}. Default +is 1e-8, lower than in \code{\link{lsoda}}.} + +\item{rtol}{Absolute error tolerance, passed to \code{\link{ode}}. Default +is 1e-10, much lower than in \code{\link{lsoda}}.} + +\item{map_output}{Boolean to specify if the output should list values for +the observed variables (default) or for all state variables (if set to +FALSE).} + +\item{\dots}{Further arguments passed to the ode solver in case such a +solver is used.} } \value{ - A matrix in the same format as the output of \code{\link{ode}}. +A matrix in the same format as the output of \code{\link{ode}}. } -\author{ - Johannes Ranke +\description{ +This function produces a time series for all the observed variables in a +kinetic model as specified by \code{\link{mkinmod}}, using a specific set of +kinetic parameters and initial values for the state variables. } \examples{ + SFO <- mkinmod(degradinol = mkinsub("SFO")) # Compare solution types mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, @@ -124,5 +126,8 @@ f <- mkinfit(SFO_SFO, FOCUS_2006_C) head(mkinpredict(f)) } + +} +\author{ +Johannes Ranke } -\keyword{ manip } -- cgit v1.2.1