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authorJohannes Ranke <jranke@uni-bremen.de>2020-05-15 07:33:27 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-05-15 07:33:27 +0200
commited68dee95554c43b150836106ff4036660989b47 (patch)
treedd7facefda5c53e8997b8d2cc2a0797ef8cdd620 /R
parenta1d7c14feadd175674b3cd8b5d7051bafba5bc3e (diff)
Use markdown links in mkinfit documentation
Diffstat (limited to 'R')
-rw-r--r--R/mkinfit.R48
1 files changed, 24 insertions, 24 deletions
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}}.

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