diff options
| -rw-r--r-- | DESCRIPTION | 4 | ||||
| -rw-r--r-- | R/mkinmod.R | 24 | ||||
| -rw-r--r-- | vignettes/examples.Rnw | 190 | ||||
| -rw-r--r-- | vignettes/examples.pdf | bin | 184227 -> 176985 bytes |
4 files changed, 207 insertions, 11 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 4b9e663..8db0fc8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,8 +2,8 @@ Package: mkin Type: Package Title: Routines for fitting kinetic models with one or more state variables to chemical degradation data -Version: 0.9-11 -Date: 2013-02-17 +Version: 0.9-12 +Date: 2013-02-18 Author: Johannes Ranke, Katrin Lindenberger, René Lehmann Maintainer: Johannes Ranke <jranke@uni-bremen.de> Description: Calculation routines based on the FOCUS Kinetics Report (2006). diff --git a/R/mkinmod.R b/R/mkinmod.R index 5d8271a..adfd9ea 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -22,6 +22,12 @@ mkinmod <- function(..., use_of_ff = "min") {
spec <- list(...)
obs_vars <- names(spec)
+
+ # Check if any of the names of the observed variables contains any other
+ for (obs_var in obs_vars) {
+ if (length(grep(obs_var, obs_vars)) > 1) stop("Sorry, variable names can not contain each other")
+ }
+
if (!use_of_ff %in% c("min", "max"))
stop("The use of formation fractions 'use_of_ff' can only be 'min' or 'max'")
@@ -43,7 +49,7 @@ mkinmod <- function(..., use_of_ff = "min") "Only constant formation fractions over time are implemented.",
"Depending on the reason for the time dependence of degradation",
"this may be unrealistic. You may want to consider using the",
- "SFORB model",
+ "SFORB model",
sep="\n")
warning(message)
} else message <- "ok"
@@ -84,12 +90,11 @@ mkinmod <- function(..., use_of_ff = "min") {
# Get the name of the box(es) we are working on for the decline term(s)
box_1 = map[[varname]][[1]] # This is the only box unless type is SFORB
+ # Turn on sink if this is not explicitly excluded by the user by
+ # specifying sink=FALSE
+ if(is.null(spec[[varname]]$sink)) spec[[varname]]$sink <- TRUE
if(spec[[varname]]$type %in% c("SFO", "SFORB")) { # {{{ Add SFO or SFORB decline term
if (use_of_ff == "min") { # Minimum use of formation fractions
- # Turn on sink if this is not explicitly excluded by the user by
- # specifying sink=FALSE
- if(is.null(spec[[varname]]$sink)) spec[[varname]]$sink <- TRUE
-
if(spec[[varname]]$sink) {
# If sink is required, add first-order sink term
k_compound_sink <- paste("k", box_1, "sink", sep="_")
@@ -103,7 +108,7 @@ mkinmod <- function(..., use_of_ff = "min") parms <- c(parms, k_compound)
decline_term <- paste(k_compound, "*", box_1)
}
- }#}}}
+ } #}}}
if(spec[[varname]]$type == "FOMC") { # {{{ Add FOMC decline term
# From p. 53 of the FOCUS kinetics report
decline_term <- paste("(alpha/beta) * ((time/beta) + 1)^-1 *", box_1)
@@ -132,7 +137,7 @@ mkinmod <- function(..., use_of_ff = "min") reversible_binding_term_2 <- paste("+", k_free_bound, "*", box_1, "-",
k_bound_free, "*", box_2)
} else { # Use formation fractions also for the free compartment
- stop("The maximum use of formation fractions is not supported for SFORB models")
+ stop("The maximum use of formation fractions is not supported for SFORB models")
# The problems were: Calculation of dissipation times did not work in this case
# and the coefficient matrix is not generated correctly by the code present
# in this file in this case
@@ -167,6 +172,9 @@ mkinmod <- function(..., use_of_ff = "min") diffs[[target_box]] <- paste(diffs[[target_box]], "+",
k_from_to, "*", origin_box)
} else {
+ if (!spec[[varname]]$sink) {
+ stop("Turning off the sink when using formation fractions is not supported")
+ }
fraction_to_target = paste("f", origin_box, "to", target, sep="_")
parms <- c(parms, fraction_to_target)
diffs[[target_box]] <- paste(diffs[[target_box]], "+",
@@ -240,4 +248,4 @@ mkinmod <- function(..., use_of_ff = "min") class(model) <- "mkinmod"
return(model)
}
-# vim: set foldmethod=marker:
+# vim: set foldmethod=marker ts=2 sw=2 expandtab:
diff --git a/vignettes/examples.Rnw b/vignettes/examples.Rnw index 784eddf..6d75e4a 100644 --- a/vignettes/examples.Rnw +++ b/vignettes/examples.Rnw @@ -47,7 +47,6 @@ University of Bremen\\ \textbf{Key words}: Kinetics, FOCUS, nonlinear optimisation
\section{Kinetic evaluations for parent compounds}
-\label{intro}
These examples are also evaluated in a parallel vignette of the
\Rpackage{kinfit} package \citep{pkg:kinfit}. The datasets are from Appendix 3,
@@ -282,5 +281,194 @@ model. However, the difference appears negligible. \bibliographystyle{plainnat}
\bibliography{references}
+\section{Kinetic evaluations for parent and metabolites}
+
+\subsection{Laboratory Data for example compound Z}
+
+The following code defines the example dataset from Appendix 7 to the FOCUS kinetics
+report, p.350
+
+<<FOCUS_2006_Z_data, echo=TRUE, eval=TRUE>>=
+LOD = 0.5
+FOCUS_2006_Z = data.frame(
+ t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21, 42, 61, 96, 124),
+ Z0 = c(100, 81.7, 70.4, 51.1, 41.2, 6.6, 4.6, 3.9, 4.6, 4.3, 6.8, 2.9, 3.5,
+ 5.3, 4.4, 1.2, 0.7),
+ Z1 = c(0, 18.3, 29.6, 46.3, 55.1, 65.7, 39.1, 36, 15.3, 5.6, 1.1, 1.6, 0.6,
+ 0.5 * LOD, NA, NA, NA),
+ Z2 = c(0, NA, 0.5 * LOD, 2.6, 3.8, 15.3, 37.2, 31.7, 35.6, 14.5, 0.8, 2.1,
+ 1.9, 0.5 * LOD, NA, NA, NA),
+ Z3 = c(0, NA, NA, NA, NA, 0.5 * LOD, 9.2, 13.1, 22.3, 28.4, 32.5, 25.2, 17.2,
+ 4.8, 4.5, 2.8, 4.4))
+
+FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z)
+@
+
+The next step is to set up the models used for the kinetic analysis. As the
+simultaneous fit of parent and the first metabolite is usually straightforward,
+Step 1 (SFO for parent only) is skipped here. We start with the model 2a,
+with formation and decline of metabolite Z1 and the pathway from parent
+directly to sink included (default in mkin).
+
+<<FOCUS_2006_Z_fits_1, echo=TRUE, fig=TRUE>>=
+debug(mkinmod)
+Z.2a <- mkinmod(Z0 = list(type = "SFO", to = "Z1"),
+ Z1 = list(type = "SFO"))
+m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin)
+summary(m.Z.2a, data = FALSE)
+plot(m.Z.2a)
+@
+
+As obvious from the summary, the kinetic rate constant from parent compound Z to sink
+is negligible. Accordingly, the exact magnitude of the fitted parameter
+\texttt{log k\_Z\_sink} is ill-defined and the covariance matrix is not returned.
+This suggests, in agreement to the analysis in the FOCUS kinetics report, to simplify
+the model by removing the pathway to sink.
+
+A similar result can be obtained when formation fractions are used in the model formulation:
+
+<<FOCUS_2006_Z_fits_2, echo=TRUE, fig=TRUE>>=
+Z.2a.ff <- mkinmod(Z0 = list(type = "SFO", to = "Z1"),
+ Z1 = list(type = "SFO"), use_of_ff = "max")
+
+m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin)
+summary(m.Z.2a.ff, data = FALSE)
+plot(m.Z.2a.ff)
+@
+
+Here, the ilr transformed formation fraction fitted in the model takes a very large value,
+and the backtransformed formation fraction from parent Z to Z1 is practically unity. Again,
+the covariance matrix is not returned as the model is overparameterised.
+
+The simplified model is obtained by setting the list component \texttt{sink} to
+\texttt{FALSE}. This model definition is not supported when formation fractions
+are used.
+
+<<FOCUS_2006_Z_fits_3, echo=TRUE, fig=TRUE>>=
+Z.3 <- mkinmod(Z0 = list(type = "SFO", to = "Z1", sink = FALSE),
+ Z1 = list(type = "SFO"))
+m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin)
+m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, parms.ini = c(k_Z0_Z1 = 0.5))
+m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, solution_type = "deSolve")
+summary(m.Z.2b, data = FALSE)
+plot(m.Z.2b)
+@
+
+The first attempt to fit the model fails, as the default solution type chosen
+by mkinfit is based on eigenvalues, and the system defined by the starting
+parameters is identified as being singular to the solver. This is caused by the
+fact that the rate constants for both state variables are the same using the
+default starting paramters. Setting a different starting value for one of the
+parameters overcomes this. Alternatively, the \Rpackage{deSolve} based model
+solution can be chosen, at the cost of a bit more computing time.
+
+<<FOCUS_2006_Z_fits_4, echo=TRUE, fig=TRUE>>=
+Z.4a <- mkinmod(Z0 = list(type = "SFO", to = "Z1", sink = FALSE),
+ Z1 = list(type = "SFO", to = "Z2"),
+ Z2 = list(type = "SFO"))
+m.Z.4a <- mkinfit(Z.4a, FOCUS_2006_Z_mkin, parms.ini = c(k_Z0_Z1 = 0.5))
+summary(m.Z.4a, data = FALSE)
+plot(m.Z.4a)
+@
+
+As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as
+well. While this step appears questionable on the basis of the above results, it
+is followed here for the purpose of comparison. Also, in the FOCUS report, it is
+assumed that there is additional empirical evidence that Z1 quickly and exclusively
+hydrolyses to Z2. Again, in order to avoid a singular system when using default starting
+parameters, the starting parameter for the pathway without sink term has to be adapted.
+
+<<FOCUS_2006_Z_fits_4, echo=TRUE, fig=TRUE>>=
+Z.5 <- mkinmod(Z0 = list(type = "SFO", to = "Z1", sink = FALSE),
+ Z1 = list(type = "SFO", to = "Z2", sink = FALSE),
+ Z2 = list(type = "SFO"))
+m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin,
+ parms.ini = c(k_Z0_Z1 = 0.5, k_Z1_Z2 = 0.2))
+summary(m.Z.5, data = FALSE)
+plot(m.Z.5)
+@
+
+Finally, metabolite Z3 is added to the model.
+
+<<FOCUS_2006_Z_fits_5, echo=TRUE, fig=TRUE>>=
+Z.FOCUS <- mkinmod(Z0 = list(type = "SFO", to = "Z1", sink = FALSE),
+ Z1 = list(type = "SFO", to = "Z2", sink = FALSE),
+ Z2 = list(type = "SFO", to = "Z3"),
+ Z3 = list(type = "SFO"))
+m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin,
+ parms.ini = c(k_Z0_Z1 = 0.5, k_Z1_Z2 = 0.2, k_Z2_Z3 = 0.3))
+summary(m.Z.FOCUS, data = FALSE)
+plot(m.Z.FOCUS)
+@
+
+As the FOCUS report states, there is a certain tailing of the time course of metabolite
+Z3. Also, the time course of the parent compound is not fitted very well using the
+SFO model, as residues at a certain low level remain.
+
+Therefore, an additional model is offered here, using the single first-order
+reversible binding (SFORB) model for metabolite Z3. However, the $\chi^2$ error
+level is higher for metabolite Z3 using this model, the covariance matrix is
+not returned, and graphically the fit is not significantly improved. Therefore,
+this appears to be a case of overparamterisation.
+
+<<FOCUS_2006_Z_fits_6, echo=TRUE, fig=TRUE>>=
+Z.mkin.1 <- mkinmod(Z0 = list(type = "SFO", to = "Z1", sink = FALSE),
+ Z1 = list(type = "SFO", to = "Z2", sink = FALSE),
+ Z2 = list(type = "SFO", to = "Z3"),
+ Z3 = list(type = "SFORB"))
+m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin,
+ parms.ini = c(k_Z0_Z1 = 0.5, k_Z1_Z2 = 0.3, k_Z2_Z3 = 0.2))
+summary(m.Z.mkin.1, data = FALSE)
+plot(m.Z.mkin.1)
+@
+
+On the other hand, the model fit for the parent compound can be improved by
+using the SFORB model.
+
+<<FOCUS_2006_Z_fits_6, echo=TRUE, fig=TRUE>>=
+Z.mkin.2 <- mkinmod(Z0 = list(type = "SFORB", to = "Z1", sink = FALSE),
+ Z1 = list(type = "SFO"))
+m.Z.mkin.2 <- mkinfit(Z.mkin.2, FOCUS_2006_Z_mkin)
+summary(m.Z.mkin.2, data = FALSE)
+plot(m.Z.mkin.2)
+@
+
+The sink is for Z1 is turned off again, for the same reasons as in the original analysis.
+Then, metabolite Z2 is added.
+
+<<FOCUS_2006_Z_fits_6, echo=TRUE, fig=TRUE>>=
+Z.mkin.3 <- mkinmod(Z0 = list(type = "SFORB", to = "Z1", sink = FALSE),
+ Z1 = list(type = "SFO", to = "Z2"),
+ Z2 = list(type = "SFO"))
+m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin)
+summary(m.Z.mkin.3, data = FALSE)
+plot(m.Z.mkin.3)
+@
+
+Finally, Z3 is added as well. This model appears overparameterised (no
+covariance matrix returned) if the sink for Z1 is left in the model.
+
+<<FOCUS_2006_Z_fits_6, echo=TRUE, fig=TRUE>>=
+Z.mkin.4 <- mkinmod(Z0 = list(type = "SFORB", to = "Z1", sink = FALSE),
+ Z1 = list(type = "SFO", to = "Z2", sink = FALSE),
+ Z2 = list(type = "SFO", to = "Z3"),
+ Z3 = list(type = "SFO"))
+m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin,
+ parms.ini = c(k_Z1_Z2 = 0.05))
+summary(m.Z.mkin.4, data = FALSE)
+plot(m.Z.mkin.4)
+@
+
+<<FOCUS_2006_Z_fits_6, echo=TRUE, fig=TRUE>>=
+Z.mkin.5 <- mkinmod(Z0 = list(type = "SFORB", to = "Z1", sink = FALSE),
+ Z1 = list(type = "SFO", to = "Z2", sink = FALSE),
+ Z2 = list(type = "SFO", to = "Z3"),
+ Z3 = list(type = "SFORB"))
+m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin)
+summary(m.Z.mkin.5, data = FALSE)
+plot(m.Z.mkin.5)
+@
+
+
\end{document}
% vim: set foldmethod=syntax:
diff --git a/vignettes/examples.pdf b/vignettes/examples.pdf Binary files differindex ff71a42..9237546 100644 --- a/vignettes/examples.pdf +++ b/vignettes/examples.pdf |