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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-19 15:41:24 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-19 15:41:24 +0100
commitdb9ae6a0c9cecb92048fde6f06af1da183c09b5f (patch)
treef0ea97545549c71bd7aa3d13afed422fd402f0e6 /man
parent6441a9f35d66f2c4d38c0036f99cd8f509d76f3b (diff)
Depend on parallel, doc improvements
By depending on parallel instead of importing it, functions to set up and stop a cluster are always available when mkin is loaded. The use of multicore processing in mmkin on Windows is now documented in the help file, which brings mkin closer to a version 1.0 #9.
Diffstat (limited to 'man')
-rw-r--r--man/mkinmod.Rd57
-rw-r--r--man/mkinsub.Rd52
-rw-r--r--man/mmkin.Rd11
-rw-r--r--man/print.mkinmod.Rd26
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)
-
-}

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