diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/mkinmod.Rd | 57 | ||||
| -rw-r--r-- | man/mkinsub.Rd | 52 | ||||
| -rw-r--r-- | man/mmkin.Rd | 11 | ||||
| -rw-r--r-- | man/print.mkinmod.Rd | 26 |
4 files changed, 61 insertions, 85 deletions
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd index 98623201..e5b1c8f3 100644 --- a/man/mkinmod.Rd +++ b/man/mkinmod.Rd @@ -1,7 +1,9 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/mkinmod.R +% Please edit documentation in R/mkinmod.R, R/mkinsub.R \name{mkinmod} \alias{mkinmod} +\alias{print.mkinmod} +\alias{mkinsub} \title{Function to set up a kinetic model with one or more state variables} \usage{ mkinmod( @@ -11,6 +13,10 @@ mkinmod( quiet = FALSE, verbose = FALSE ) + +\method{print}{mkinmod}(x, ...) + +mkinsub(submodel, to = NULL, sink = TRUE, full_name = NA) } \arguments{ \item{...}{For each observed variable, a list as obtained by \code{\link[=mkinsub]{mkinsub()}} @@ -25,13 +31,14 @@ variables to which a transfer is to be assumed in the model. If the argument \code{use_of_ff} is set to "min" (default) and the model for the compartment is "SFO" or "SFORB", an additional \code{\link[=mkinsub]{mkinsub()}} argument can be \code{sink = FALSE}, effectively -fixing the flux to sink to zero.} +fixing the flux to sink to zero. +In print.mkinmod, this argument is currently not used.} \item{use_of_ff}{Specification of the use of formation fractions in the -model equations and, if applicable, the coefficient matrix. If "min", a -minimum use of formation fractions is made in order to avoid fitting the -product of formation fractions and rate constants. If "max", formation -fractions are always used.} +model equations and, if applicable, the coefficient matrix. If "max", +formation fractions are always used (default). If "min", a minimum use of +formation fractions is made, i.e. each pathway to a metabolite has its +own rate constant.} \item{speclist}{The specification of the observed variables and their submodel types and pathways can be given as a single list using this @@ -41,6 +48,22 @@ argument. Default is NULL.} \item{verbose}{If \code{TRUE}, passed to \code{\link[inline:cfunction]{inline::cfunction()}} if applicable to give detailed information about the C function being built.} + +\item{x}{An \code{\link{mkinmod}} object.} + +\item{submodel}{Character vector of length one to specify the submodel type. +See \code{\link{mkinmod}} for the list of allowed submodel names.} + +\item{to}{Vector of the names of the state variable to which a +transformation shall be included in the model.} + +\item{sink}{Should a pathway to sink be included in the model in addition to +the pathways to other state variables?} + +\item{full_name}{An optional name to be used e.g. for plotting fits +performed with the model. You can use non-ASCII characters here, but then +your R code will not be portable, \emph{i.e.} may produce unintended plot +results on other operating systems or system configurations.} } \value{ A list of class \code{mkinmod} for use with \code{\link[=mkinfit]{mkinfit()}}, @@ -68,11 +91,19 @@ represented by one. If generated, a compiled function calculating the derivatives as returned by cfunction. } + +A list for use with \code{\link{mkinmod}}. } \description{ This function is usually called using a call to \code{\link[=mkinsub]{mkinsub()}} for each observed variable, specifying the corresponding submodel as well as outgoing pathways (see examples). + +Print mkinmod objects in a way that the user finds his way to get to its +components. + +This is a convenience function to set up the lists used as arguments for +\code{\link{mkinmod}}. } \details{ For the definition of model types and their parameters, the equations given @@ -103,6 +134,11 @@ SFO_SFO <- mkinmod( m1 = mkinsub("SFO")) \dontrun{ +# Now supplying full names used for plotting + SFO_SFO.2 <- mkinmod( + parent = mkinsub("SFO", "m1", full_name = "Test compound"), + m1 = mkinsub("SFO", full_name = "Metabolite M1")) + # The above model used to be specified like this, before the advent of mkinsub() SFO_SFO <- mkinmod( parent = list(type = "SFO", to = "m1"), @@ -123,13 +159,20 @@ m_synth_DFOP_par <- mkinmod( parent = mkinsub("DFOP", c("M1", "M2")), M1 = mkinsub("SFO"), M2 = mkinsub("SFO"), - use_of_ff = "max", quiet = TRUE) + quiet = TRUE) fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, synthetic_data_for_UBA_2014[[12]]$data, quiet = TRUE) } + + m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"), + M1 = list(type = "SFO", to = "M2"), + M2 = list(type = "SFO"), use_of_ff = "max") + + print(m_synth_SFO_lin) + } \references{ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence diff --git a/man/mkinsub.Rd b/man/mkinsub.Rd deleted file mode 100644 index 81615a00..00000000 --- a/man/mkinsub.Rd +++ /dev/null @@ -1,52 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/mkinsub.R -\name{mkinsub} -\alias{mkinsub} -\title{Function to set up a kinetic submodel for one state variable} -\usage{ -mkinsub(submodel, to = NULL, sink = TRUE, full_name = NA) -} -\arguments{ -\item{submodel}{Character vector of length one to specify the submodel type. -See \code{\link{mkinmod}} for the list of allowed submodel names.} - -\item{to}{Vector of the names of the state variable to which a -transformation shall be included in the model.} - -\item{sink}{Should a pathway to sink be included in the model in addition to -the pathways to other state variables?} - -\item{full_name}{An optional name to be used e.g. for plotting fits -performed with the model. You can use non-ASCII characters here, but then -your R code will not be portable, \emph{i.e.} may produce unintended plot -results on other operating systems or system configurations.} -} -\value{ -A list for use with \code{\link{mkinmod}}. -} -\description{ -This is a convenience function to set up the lists used as arguments for -\code{\link{mkinmod}}. -} -\examples{ - -# One parent compound, one metabolite, both single first order. -SFO_SFO <- mkinmod( - parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO")) - -# The same model using mkinsub -SFO_SFO.2 <- mkinmod( - parent = mkinsub("SFO", "m1"), - m1 = mkinsub("SFO")) - -\dontrun{ - # Now supplying full names - SFO_SFO.2 <- mkinmod( - parent = mkinsub("SFO", "m1", full_name = "Test compound"), - m1 = mkinsub("SFO", full_name = "Metabolite M1")) - } -} -\author{ -Johannes Ranke -} diff --git a/man/mmkin.Rd b/man/mmkin.Rd index 80360cd7..9b836242 100644 --- a/man/mmkin.Rd +++ b/man/mmkin.Rd @@ -76,6 +76,17 @@ plot_sep(fits.0[[1, 1]]) # Plotting with mmkin (single brackets, extracting an mmkin object) does not # allow to plot the observed variables separately plot(fits.0[1, 1]) + +# On Windows, we can use multiple cores by making a cluster using the parallel +# package, which gets loaded with mkin, and passing it to mmkin, e.g. +cl <- makePSOCKcluster(12) +f <- mmkin(c("SFO", "FOMC", "DFOP"), + list(A = FOCUS_2006_A, B = FOCUS_2006_B, C = FOCUS_2006_C, D = FOCUS_2006_D), + cluster = cl, quiet = TRUE) +print(f) +# We get false convergence for the FOMC fit to FOCUS_2006_A because this +# dataset is really SFO, and the FOMC fit is overparameterised +stopCluster(cl) } } diff --git a/man/print.mkinmod.Rd b/man/print.mkinmod.Rd deleted file mode 100644 index 4e44cde6..00000000 --- a/man/print.mkinmod.Rd +++ /dev/null @@ -1,26 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/mkinmod.R -\name{print.mkinmod} -\alias{print.mkinmod} -\title{Print mkinmod objects} -\usage{ -\method{print}{mkinmod}(x, ...) -} -\arguments{ -\item{x}{An \code{\link{mkinmod}} object.} - -\item{\dots}{Not used.} -} -\description{ -Print mkinmod objects in a way that the user finds his way to get to its -components. -} -\examples{ - - m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"), - M1 = list(type = "SFO", to = "M2"), - M2 = list(type = "SFO"), use_of_ff = "max") - - print(m_synth_SFO_lin) - -} |