From ed68dee95554c43b150836106ff4036660989b47 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 15 May 2020 07:33:27 +0200 Subject: Use markdown links in mkinfit documentation --- R/mkinfit.R | 48 ++++++++++++++++++++++++------------------------ 1 file changed, 24 insertions(+), 24 deletions(-) (limited to 'R/mkinfit.R') diff --git a/R/mkinfit.R b/R/mkinfit.R index 8231cd00..393473d1 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -3,9 +3,11 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value")) #' Fit a kinetic model to data with one or more state variables #' #' This function maximises the likelihood of the observed data using the Port -#' algorithm \code{\link{nlminb}}, and the specified initial or fixed +#' algorithm [stats::nlminb()], and the specified initial or fixed #' parameters and starting values. In each step of the optimisation, the -#' kinetic model is solved using the function \code{\link{mkinpredict}}. The +#' kinetic model is solved using the function [mkinpredict()], except +#' if an analytical solution is implemented, in which case the model is solved +#' using the degradation function in the [mkinmod] object. The #' parameters of the selected error model are fitted simultaneously with the #' degradation model parameters, as both of them are arguments of the #' likelihood function. @@ -14,7 +16,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value")) #' order to better satisfy the assumption of a normal distribution of their #' estimators. #' -#' @param mkinmod A list of class \code{\link{mkinmod}}, containing the kinetic +#' @param mkinmod A list of class [mkinmod], containing the kinetic #' model to be fitted to the data, or one of the shorthand names ("SFO", #' "FOMC", "DFOP", "HS", "SFORB", "IORE"). If a shorthand name is given, a #' parent only degradation model is generated for the variable with the @@ -42,7 +44,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value")) #' @param state.ini A named vector of initial values for the state variables of #' the model. In case the observed variables are represented by more than one #' model variable, the names will differ from the names of the observed -#' variables (see \code{map} component of \code{\link{mkinmod}}). The default +#' variables (see \code{map} component of [mkinmod]). The default #' is to set the initial value of the first model variable to the mean of the #' time zero values for the variable with the maximum observed value, and all #' others to 0. If this variable has no time zero observations, its initial @@ -66,20 +68,19 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value")) #' @param solution_type If set to "eigen", the solution of the system of #' differential equations is based on the spectral decomposition of the #' coefficient matrix in cases that this is possible. If set to "deSolve", a -#' numerical ode solver from package \code{\link{deSolve}} is used. If set to -#' "analytical", an analytical solution of the model is used. This is only -#' implemented for relatively simple degradation models. The default is +#' numerical [ode solver from package deSolve][deSolve::ode()] is used. If +#' set to "analytical", an analytical solution of the model is used. This is +#' only implemented for relatively simple degradation models. The default is #' "auto", which uses "analytical" if possible, otherwise "deSolve" if a #' compiler is present, and "eigen" if no compiler is present and the model -#' can be expressed using eigenvalues and eigenvectors. This argument is -#' passed on to the helper function \code{\link{mkinpredict}}. -#' @param method.ode The solution method passed via \code{\link{mkinpredict}} -#' to \code{\link{ode}} in case the solution type is "deSolve". The default +#' can be expressed using eigenvalues and eigenvectors. +#' @param method.ode The solution method passed via [mkinpredict()] +#' to [deSolve::ode()] in case the solution type is "deSolve". The default #' "lsoda" is performant, but sometimes fails to converge. #' @param use_compiled If set to \code{FALSE}, no compiled version of the -#' \code{\link{mkinmod}} model is used in the calls to -#' \code{\link{mkinpredict}} even if a compiled version is present. -#' @param control A list of control arguments passed to \code{\link{nlminb}}. +#' [mkinmod] model is used in the calls to [mkinpredict()] even if a compiled +#' version is present. +#' @param control A list of control arguments passed to [stats::nlminb()]. #' @param transform_rates Boolean specifying if kinetic rate constants should #' be transformed in the model specification used in the fitting for better #' compliance with the assumption of normal distribution of the estimator. If @@ -93,13 +94,14 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value")) #' of the estimator. The default (TRUE) is to do transformations. If TRUE, #' the g parameter of the DFOP and HS models are also transformed, as they #' can also be seen as compositional data. The transformation used for these -#' transformations is the \code{\link{ilr}} transformation. +#' transformations is the [ilr()] transformation. #' @param quiet Suppress printing out the current value of the negative #' log-likelihood after each improvement? -#' @param atol Absolute error tolerance, passed to \code{\link{ode}}. Default -#' is 1e-8, lower than in \code{\link{lsoda}}. -#' @param rtol Absolute error tolerance, passed to \code{\link{ode}}. Default -#' is 1e-10, much lower than in \code{\link{lsoda}}. +#' @param atol Absolute error tolerance, passed to [deSolve::ode()]. Default +#' is 1e-8, which is lower than the default in the [deSolve::lsoda()] +#' function which is used per default. +#' @param rtol Absolute error tolerance, passed to [deSolve::ode()]. Default +#' is 1e-10, much lower than in [deSolve::lsoda()]. #' @param error_model If the error model is "const", a constant standard #' deviation is assumed. #' @@ -147,17 +149,15 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value")) #' @param reweight.max.iter Maximum number of iterations in IRLS fits. #' @param trace_parms Should a trace of the parameter values be listed? #' @param \dots Further arguments that will be passed on to -#' \code{\link{deSolve}}. +#' [deSolve::ode()]. #' @importFrom stats nlminb aggregate dist -#' @return A list with "mkinfit" in the class attribute. A summary can be -#' obtained by \code{\link{summary.mkinfit}}. +#' @return A list with "mkinfit" in the class attribute. #' @note When using the "IORE" submodel for metabolites, fitting with #' "transform_rates = TRUE" (the default) often leads to failures of the #' numerical ODE solver. In this situation it may help to switch off the #' internal rate transformation. #' @author Johannes Ranke -#' @seealso Plotting methods \code{\link{plot.mkinfit}} and -#' \code{\link{mkinparplot}}. +#' @seealso [summary.mkinfit], [plot.mkinfit], [parms] and [lrtest]. #' #' Comparisons of models fitted to the same data can be made using #' \code{\link{AIC}} by virtue of the method \code{\link{logLik.mkinfit}}. -- cgit v1.2.1