From 1852bbe91096dbd4c36e381c3adbd5594e4f3e5c Mon Sep 17 00:00:00 2001 From: jranke Date: Mon, 18 Feb 2013 14:11:41 +0000 Subject: More work on the examples vignette git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@65 edb9625f-4e0d-4859-8d74-9fd3b1da38cb --- DESCRIPTION | 4 +- R/mkinmod.R | 24 ++++--- vignettes/examples.Rnw | 190 ++++++++++++++++++++++++++++++++++++++++++++++++- vignettes/examples.pdf | Bin 184227 -> 176985 bytes 4 files changed, 207 insertions(+), 11 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4b9e6635..8db0fc85 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 Description: Calculation routines based on the FOCUS Kinetics Report (2006). diff --git a/R/mkinmod.R b/R/mkinmod.R index 5d8271a2..adfd9ea3 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 784eddfc..6d75e4ae 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 + +<>= +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). + +<>= +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: + +<>= +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. + +<>= +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. + +<>= +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. + +<>= +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. + +<>= +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. + +<>= +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. + +<>= +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. + +<>= +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. + +<>= +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) +@ + +<>= +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 index ff71a42c..92375460 100644 Binary files a/vignettes/examples.pdf and b/vignettes/examples.pdf differ -- cgit v1.2.1