diff options
| -rw-r--r-- | NAMESPACE | 12 | ||||
| -rw-r--r-- | R/mkinmod.R | 77 | ||||
| -rw-r--r-- | man/mkinmod.Rd | 21 |
3 files changed, 57 insertions, 53 deletions
@@ -1 +1,11 @@ -export(mkinmod, mkinpredict, mkinfit, mkinplot, mkin_long_to_wide, mkin_wide_to_long, ilr, invilr, transform_odeparms, backtransform_odeparms) +# Default NAMESPACE created by R +# Remove the previous line if you edit this file + +# Export all names +exportPattern(".") + +# Import all packages listed as Imports or Depends +import( + FME, + deSolve +) diff --git a/R/mkinmod.R b/R/mkinmod.R index d4ff75b..37f96ce 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -1,6 +1,6 @@ # $Id$
-# Copyright (C) 2010-2012 Johannes Ranke
+# Copyright (C) 2010-2012 Johannes Ranke#{{{
# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
@@ -16,20 +16,23 @@ # details.
# You should have received a copy of the GNU General Public License along with
-# this program. If not, see <http://www.gnu.org/licenses/>
+# this program. If not, see <http://www.gnu.org/licenses/>#}}}
mkinmod <- function(...)
{
spec <- list(...)
obs_vars <- names(spec)
- # The returned model will be a list of character vectors, containing
+ # The returned model will be a list of character vectors, containing#{{{
# differential equations, parameter names and a mapping from model variables
# to observed variables. If possible, a matrix representation of the
# differential equations is included
parms <- vector()
diffs <- vector()
- map <- list()
+ map <- list()#}}}
+
+ # Give a warning when a model with time dependent degradation uses formation#{{{
+ # fractions
if(spec[[1]]$type %in% c("FOMC", "DFOP", "HS")) {
mat = FALSE
if(!is.null(spec[[1]]$to)) {
@@ -40,12 +43,13 @@ mkinmod <- function(...) sep="\n")
warning(message)
} else message <- "ok"
- } else mat = TRUE
+ } else mat = TRUE#}}}
- # Establish list of differential equations
- # as well as map from observed compartments to differential equations
+ # Establish list of differential equations as well as map from observed#{{{
+ # compartments to differential equations
for (varname in obs_vars)
{
+ # Check the type component of the compartment specification#{{{
if(is.null(spec[[varname]]$type)) stop(
"Every argument to mkinmod must be a list containing a type component")
if(!spec[[varname]]$type %in% c("SFO", "FOMC", "DFOP", "HS", "SFORB")) stop(
@@ -53,9 +57,8 @@ mkinmod <- function(...) if(spec[[varname]]$type %in% c("FOMC", "DFOP", "HS") & match(varname, obs_vars) != 1) {
stop(paste("Types FOMC, DFOP and HS are only implemented for the first compartment,",
"which is assumed to be the source compartment"))
- }
-
- # New (sub)compartments (boxes) needed for the model type
+ }#}}}
+ # New (sub)compartments (boxes) needed for the model type#{{{
new_boxes <- switch(spec[[varname]]$type,
SFO = varname,
FOMC = varname,
@@ -64,51 +67,44 @@ mkinmod <- function(...) SFORB = paste(varname, c("free", "bound"), sep="_")
)
map[[varname]] <- new_boxes
- names(map[[varname]]) <- rep(spec[[varname]]$type, length(new_boxes))
-
- # Start a new differential equation for each new box
+ names(map[[varname]]) <- rep(spec[[varname]]$type, length(new_boxes))#}}}
+ # Start a new differential equation for each new box#{{{
new_diffs <- paste("d_", new_boxes, " =", sep="")
names(new_diffs) <- new_boxes
- diffs <- c(diffs, new_diffs)
- }
+ diffs <- c(diffs, new_diffs)#}}}
+ }#}}}
- # Create content of differential equations and build parameter list
+ # Create content of differential equations and build parameter list#{{{
for (varname in obs_vars)
{
- # Add first-order term to first (or only) box for SFO and SFORB
+ # Add first-order term to first (or only) box for SFO and SFORB#{{{
box_1 = map[[varname]][[1]] # This is the only box unless type is SFORB
if(spec[[varname]]$type %in% c("SFO", "SFORB")) {
k_compound <- paste("k", box_1, sep="_")
origin_term <- paste(k_compound, "*", box_1)
parms <- c(parms, k_compound)
- }
-
-
- # Construct and add FOMC term and add FOMC parameters if needed
+ }#}}}
+ # Construct and add FOMC term and add FOMC parameters if needed#{{{
if(spec[[varname]]$type == "FOMC") {
# From p. 53 of the FOCUS kinetics report
origin_term <- paste("(alpha/beta) * ((time/beta) + 1)^-1 *", box_1)
parms <- c(parms, "alpha", "beta")
- }
-
- # Construct and add DFOP term and add DFOP parameters if needed
+ } #}}}
+ # Construct and add DFOP term and add DFOP parameters if needed#{{{
if(spec[[varname]]$type == "DFOP") {
# From p. 57 of the FOCUS kinetics report
origin_term <- paste("((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) *", box_1)
parms <- c(parms, "k1", "k2", "g")
- }
-
- # Construct and add HS term and add HS parameters if needed
+ } #}}}
+ # Construct and add HS term and add HS parameters if needed#{{{
if(spec[[varname]]$type == "HS") {
# From p. 55 of the FOCUS kinetics report
origin_term <- paste("ifelse(time <= tb, k1, k2)", "*", box_1)
parms <- c(parms, "k1", "k2", "tb")
- }
-
- # Add origin decline term to box 1 (usually the only box, unless type is SFORB)
- diffs[[box_1]] <- paste(diffs[[box_1]], "-", origin_term)
-
- # Add reversible binding for SFORB models
+ } #}}}
+ # Add origin decline term to box 1 (usually the only box, unless type is SFORB)#{{{
+ diffs[[box_1]] <- paste(diffs[[box_1]], "-", origin_term)#}}}
+ # Add reversible binding for SFORB models#{{{
if(spec[[varname]]$type == "SFORB") {
box_2 = map[[varname]][[2]]
k_free_bound <- paste("k", varname, "free", "bound", sep="_")
@@ -120,9 +116,8 @@ mkinmod <- function(...) k_bound_free, "*", box_2)
diffs[[box_2]] <- paste(diffs[[box_2]], reversible_binding_term_2)
parms <- c(parms, k_free_bound, k_bound_free)
- }
-
- # Transfer between compartments
+ } #}}}
+ # Transfer between compartments#{{{
to <- spec[[varname]]$to
if(!is.null(to)) {
# Name of box from which transfer takes place
@@ -138,11 +133,12 @@ mkinmod <- function(...) fraction_to_target, "*", origin_term)
parms <- c(parms, fraction_to_target)
}
- }
- }
+ }#}}}
+ }#}}}
+
model <- list(diffs = diffs, parms = parms, map = map)
- # Create coefficient matrix if appropriate
+ # Create coefficient matrix if appropriate#{{{
if (mat) {
boxes <- names(diffs)
n <- length(boxes)
@@ -165,8 +161,9 @@ mkinmod <- function(...) }
}
model$coefmat <- m
- }
+ }#}}}
class(model) <- "mkinmod"
return(model)
}
+# vim: set foldmethod=marker:
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd index 7c11735..16ad38a 100644 --- a/man/mkinmod.Rd +++ b/man/mkinmod.Rd @@ -19,12 +19,10 @@ mkinmod(...) single first order with reversible binding "SFORB" are implemented for all
variables, while
"FOMC", "DFOP" and "HS" can additionally be chosen for the first
- variable which is assumed to be the source compartment. Optional components
- of each argument are \code{to}, a
- vector of names of variables to which a transfer is to be assumed in the
- model, and \code{sink}, a logical specifying if transformation to
- unspecified compounds (sink) is to be assumed in the model (defaults to
- \code{TRUE})
+ variable which is assumed to be the source compartment.
+ Additionally, each component of the list can include a character vector \code{to},
+ specifying names of variables to which a transfer is to be assumed in the
+ model.
}
}
\value{
@@ -37,17 +35,16 @@ mkinmod(...) \item{coefmat}{ The coefficient matrix, if the system of differential equations can be represented by one. }
}
\author{
- Johannes Ranke <jranke@{harlan.com,uni-bremen.de}>
+ Johannes Ranke
}
\examples{
-# There are different ways to specify the SFO model
-SFO.1 <- mkinmod(parent = list(type = "SFO", to = NULL, sink = TRUE))
-SFO.2 <- mkinmod(parent = list(type = "SFO"))
-all.equal(SFO.1, SFO.2)
+# Specify the SFO model
+SFO <- mkinmod(parent = list(type = "SFO"))
# One parent compound, one metabolite, both single first order.
SFO_SFO <- mkinmod(
- parent = list(type = "SFO", to = "m1", sink = TRUE),
+ parent = list(type = "SFO", to = "m1"),
m1 = list(type = "SFO"))
+
}
\keyword{ models }
|