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-rw-r--r--DESCRIPTION6
-rw-r--r--R/mkinfit.R28
-rw-r--r--inst/GUI/README1
-rw-r--r--inst/unitTests/runit.mkinfit.R56
-rw-r--r--man/endpoints.Rd33
-rw-r--r--man/ilr.Rd2
-rw-r--r--man/schaefer07_complex_case.Rd2
-rw-r--r--vignettes/mkin.Rnw6
-rw-r--r--vignettes/mkin.pdfbin178902 -> 180535 bytes
9 files changed, 86 insertions, 48 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index bce90d0a..b1cad781 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: 0.9-03
-Date: 2012-05-16
+Version: 0.9-04
+Date: 2012-06-26
Author: Johannes Ranke, Katrin Lindenberger, René Lehmann
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Description: Calculation routines based on the FOCUS Kinetics Report (2006).
@@ -18,4 +18,4 @@ License: GPL
LazyLoad: yes
LazyData: yes
Encoding: UTF-8
-URL: http://cran.r-project.org, http://r-forge.r-project.org/projects/kinfit
+URL: http://cran.r-project.org, http://kinfit.r-forge.r-project.org
diff --git a/R/mkinfit.R b/R/mkinfit.R
index d3ee5e7b..3100b30f 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -228,21 +228,25 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, ...) {
param <- cbind(param, se)
dimnames(param) <- list(pnames, c("Estimate", "Std. Error"))
+ bparam <- as.matrix(object$parms.all)
+ dimnames(bparam) <- list(pnames, c("Estimate"))
+
ans <- list(
- version = as.character(packageVersion("mkin")),
- Rversion = paste(R.version$major, R.version$minor, sep="."),
+ version = as.character(packageVersion("mkin")),
+ Rversion = paste(R.version$major, R.version$minor, sep="."),
date.fit = object$date,
date.summary = date(),
use_of_ff = object$mkinmod$use_of_ff,
- residuals = object$residuals,
- residualVariance = resvar,
- sigma = sqrt(resvar),
- modVariance = modVariance,
- df = c(p, rdf), cov.unscaled = covar,
- cov.scaled = covar * resvar,
- info = object$info, niter = object$iterations,
- stopmess = message,
- par = param)
+ residuals = object$residuals,
+ residualVariance = resvar,
+ sigma = sqrt(resvar),
+ modVariance = modVariance,
+ df = c(p, rdf), cov.unscaled = covar,
+ cov.scaled = covar * resvar,
+ info = object$info, niter = object$iterations,
+ stopmess = message,
+ par = param,
+ bpar = bparam)
ans$diffs <- object$mkinmod$diffs
if(data) ans$data <- object$data
@@ -285,7 +289,7 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), .
printCoefmat(x$par, digits = digits, ...)
cat("\nBacktransformed parameters:\n")
- print(as.data.frame(list(Estimate = x$parms.all)))
+ printCoefmat(x$bpar, digits = digits, ...)
cat("\nResidual standard error:",
format(signif(x$sigma, digits)), "on", rdf, "degrees of freedom\n")
diff --git a/inst/GUI/README b/inst/GUI/README
new file mode 100644
index 00000000..aa83ea6c
--- /dev/null
+++ b/inst/GUI/README
@@ -0,0 +1 @@
+These code fragments do not provide a GUI for mkin. They are purely experimental.
diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R
index e2fc8c3f..26007e78 100644
--- a/inst/unitTests/runit.mkinfit.R
+++ b/inst/unitTests/runit.mkinfit.R
@@ -30,11 +30,11 @@ test.FOCUS_2006_SFO <- function()
median.A.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F, dataset == "A",
c(M0, k, DT50, DT90)), "median"))
- fit.A.SFO.1.r <- as.numeric(c(fit.A.SFO.1$parms.all, fit.A.SFO.1$distimes))
+ fit.A.SFO.1.r <- as.numeric(c(fit.A.SFO.1$parms.all, endpoints(fit.A.SFO.1)$distimes))
dev.A.SFO.1 <- abs(round(100 * ((median.A.SFO - fit.A.SFO.1.r)/median.A.SFO), digits=1))
checkIdentical(dev.A.SFO.1 < 1, rep(TRUE, length(dev.A.SFO.1)))
- fit.A.SFO.2.r <- as.numeric(c(fit.A.SFO.2$parms.all, fit.A.SFO.2$distimes))
+ fit.A.SFO.2.r <- as.numeric(c(fit.A.SFO.2$parms.all, endpoints(fit.A.SFO.2)$distimes))
dev.A.SFO.2 <- abs(round(100 * ((median.A.SFO - fit.A.SFO.2.r)/median.A.SFO), digits=1))
checkIdentical(dev.A.SFO.2 < 1, rep(TRUE, length(dev.A.SFO.2)))
@@ -44,11 +44,11 @@ test.FOCUS_2006_SFO <- function()
median.C.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F, dataset == "C",
c(M0, k, DT50, DT90)), "median"))
- fit.C.SFO.1.r <- as.numeric(c(fit.C.SFO.1$parms.all, fit.C.SFO.1$distimes))
+ fit.C.SFO.1.r <- as.numeric(c(fit.C.SFO.1$parms.all, endpoints(fit.C.SFO.1)$distimes))
dev.C.SFO.1 <- abs(round(100 * ((median.C.SFO - fit.C.SFO.1.r)/median.C.SFO), digits=1))
checkIdentical(dev.C.SFO.1 < 1, rep(TRUE, length(dev.C.SFO.1)))
- fit.C.SFO.2.r <- as.numeric(c(fit.C.SFO.2$parms.all, fit.C.SFO.2$distimes))
+ fit.C.SFO.2.r <- as.numeric(c(fit.C.SFO.2$parms.all, endpoints(fit.C.SFO.2)$distimes))
dev.C.SFO.2 <- abs(round(100 * ((median.C.SFO - fit.C.SFO.2.r)/median.C.SFO), digits=1))
checkIdentical(dev.C.SFO.2 < 1, rep(TRUE, length(dev.C.SFO.2)))
} # }}}
@@ -66,7 +66,7 @@ test.FOCUS_2006_FOMC <- function()
median.A.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "A",
c(M0, alpha, beta, DT50, DT90)), "median"))
- fit.A.FOMC.r <- as.numeric(c(fit.A.FOMC$parms.all, fit.A.FOMC$distimes))
+ fit.A.FOMC.r <- as.numeric(c(fit.A.FOMC$parms.all, endpoints(fit.A.FOMC)$distimes))
dev.A.FOMC <- abs(round(100 * ((median.A.FOMC - fit.A.FOMC.r)/median.A.FOMC), digits=1))
dev.A.FOMC <- dev.A.FOMC[c(1, 4, 5)]
checkIdentical(dev.A.FOMC < 1, rep(TRUE, length(dev.A.FOMC)))
@@ -77,7 +77,7 @@ test.FOCUS_2006_FOMC <- function()
median.B.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "B",
c(M0, alpha, beta, DT50, DT90)), "median"))
- fit.B.FOMC.r <- as.numeric(c(fit.B.FOMC$parms.all, fit.B.FOMC$distimes))
+ fit.B.FOMC.r <- as.numeric(c(fit.B.FOMC$parms.all, endpoints(fit.B.FOMC)$distimes))
dev.B.FOMC <- abs(round(100 * ((median.B.FOMC - fit.B.FOMC.r)/median.B.FOMC), digits=1))
dev.B.FOMC <- dev.B.FOMC[c(1, 4, 5)]
checkIdentical(dev.B.FOMC < 1, rep(TRUE, length(dev.B.FOMC)))
@@ -88,7 +88,7 @@ test.FOCUS_2006_FOMC <- function()
median.C.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "C",
c(M0, alpha, beta, DT50, DT90)), "median"))
- fit.C.FOMC.r <- as.numeric(c(fit.C.FOMC$parms.all, fit.C.FOMC$distimes))
+ fit.C.FOMC.r <- as.numeric(c(fit.C.FOMC$parms.all, endpoints(fit.C.FOMC)$distimes))
dev.C.FOMC <- abs(round(100 * ((median.C.FOMC - fit.C.FOMC.r)/median.C.FOMC), digits=1))
dev.C.FOMC <- dev.C.FOMC[c(1, 4, 5)]
checkIdentical(dev.C.FOMC < 1, rep(TRUE, length(dev.C.FOMC)))
@@ -106,7 +106,7 @@ test.FOCUS_2006_DFOP <- function()
median.A.DFOP <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "A",
c(M0, k1, k2, f, DT50, DT90)), "median"))
- fit.A.DFOP.r <- as.numeric(c(fit.A.DFOP$parms.all, fit.A.DFOP$distimes))
+ fit.A.DFOP.r <- as.numeric(c(fit.A.DFOP$parms.all, endpoints(fit.A.DFOP)$distimes))
dev.A.DFOP <- abs(round(100 * ((median.A.DFOP - fit.A.DFOP.r)/median.A.DFOP), digits=1))
# about 6.7% deviation for parameter f, the others are < 0.1%
checkIdentical(dev.A.DFOP < c(1, 1, 1, 10, 1, 1), rep(TRUE, length(dev.A.DFOP)))
@@ -117,7 +117,7 @@ test.FOCUS_2006_DFOP <- function()
median.B.DFOP <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "B",
c(M0, k1, k2, f, DT50, DT90)), "median"))
- fit.B.DFOP.r <- as.numeric(c(fit.B.DFOP$parms.all, fit.B.DFOP$distimes))
+ fit.B.DFOP.r <- as.numeric(c(fit.B.DFOP$parms.all, endpoints(fit.B.DFOP)$distimes))
dev.B.DFOP <- abs(round(100 * ((median.B.DFOP - fit.B.DFOP.r)/median.B.DFOP), digits=1))
# about 0.6% deviation for parameter f, the others are <= 0.1%
checkIdentical(dev.B.DFOP < 1, rep(TRUE, length(dev.B.DFOP)))
@@ -135,7 +135,7 @@ test.FOCUS_2006_HS <- function()
median.A.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "A",
c(M0, k1, k2, tb, DT50, DT90)), "median"))
- fit.A.HS.r <- as.numeric(c(fit.A.HS$parms.all, fit.A.HS$distimes))
+ fit.A.HS.r <- as.numeric(c(fit.A.HS$parms.all, endpoints(fit.A.HS)$distimes))
dev.A.HS <- abs(round(100 * ((median.A.HS - fit.A.HS.r)/median.A.HS), digits=1))
# about 6.7% deviation for parameter f, the others are < 0.1%
checkIdentical(dev.A.HS < 1, rep(TRUE, length(dev.A.HS)))
@@ -146,7 +146,7 @@ test.FOCUS_2006_HS <- function()
median.B.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "B",
c(M0, k1, k2, tb, DT50, DT90)), "median"))
- fit.B.HS.r <- as.numeric(c(fit.B.HS$parms.all, fit.B.HS$distimes))
+ fit.B.HS.r <- as.numeric(c(fit.B.HS$parms.all, endpoints(fit.B.HS)$distimes))
dev.B.HS <- abs(round(100 * ((median.B.HS - fit.B.HS.r)/median.B.HS), digits=1))
# < 10% deviation for M0, k1, DT50 and DT90, others are problematic
dev.B.HS <- dev.B.HS[c(1, 2, 5, 6)]
@@ -158,7 +158,7 @@ test.FOCUS_2006_HS <- function()
median.C.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "C",
c(M0, k1, k2, tb, DT50, DT90)), "median"))
- fit.A.HS.r <- as.numeric(c(fit.A.HS$parms.all, fit.A.HS$distimes))
+ fit.A.HS.r <- as.numeric(c(fit.A.HS$parms.all, endpoints(fit.A.HS)$distimes))
dev.A.HS <- abs(round(100 * ((median.A.HS - fit.A.HS.r)/median.A.HS), digits=1))
# deviation <= 0.1%
checkIdentical(dev.A.HS < 1, rep(TRUE, length(dev.A.HS)))
@@ -178,9 +178,9 @@ test.FOCUS_2006_SFORB <- function()
fit.A.SFORB.1.r <- as.numeric(c(
parent_0 = fit.A.SFORB.1$parms.all[[1]],
- k1 = fit.A.SFORB.1$SFORB[[1]],
- k2 = fit.A.SFORB.1$SFORB[[2]],
- fit.A.SFORB.1$distimes))
+ k1 = endpoints(fit.A.SFORB.1)$SFORB[[1]],
+ k2 = endpoints(fit.A.SFORB.1)$SFORB[[2]],
+ endpoints(fit.A.SFORB.1)$distimes))
dev.A.SFORB.1 <- abs(round(100 * ((median.A.SFORB - fit.A.SFORB.1.r)/median.A.SFORB), digits=1))
# The first Eigenvalue is a lot different from k1 in the DFOP fit
# The explanation is that the dataset is simply SFO
@@ -189,9 +189,9 @@ test.FOCUS_2006_SFORB <- function()
fit.A.SFORB.2.r <- as.numeric(c(
parent_0 = fit.A.SFORB.2$parms.all[[1]],
- k1 = fit.A.SFORB.2$SFORB[[1]],
- k2 = fit.A.SFORB.2$SFORB[[2]],
- fit.A.SFORB.2$distimes))
+ k1 = endpoints(fit.A.SFORB.2)$SFORB[[1]],
+ k2 = endpoints(fit.A.SFORB.2)$SFORB[[2]],
+ endpoints(fit.A.SFORB.2)$distimes))
dev.A.SFORB.2 <- abs(round(100 * ((median.A.SFORB - fit.A.SFORB.2.r)/median.A.SFORB), digits=1))
# The first Eigenvalue is a lot different from k1 in the DFOP fit
# The explanation is that the dataset is simply SFO
@@ -207,17 +207,17 @@ test.FOCUS_2006_SFORB <- function()
fit.B.SFORB.1.r <- as.numeric(c(
parent_0 = fit.B.SFORB.1$parms.all[[1]],
- k1 = fit.B.SFORB.1$SFORB[[1]],
- k2 = fit.B.SFORB.1$SFORB[[2]],
- fit.B.SFORB.1$distimes))
+ k1 = endpoints(fit.B.SFORB.1)$SFORB[[1]],
+ k2 = endpoints(fit.B.SFORB.1)$SFORB[[2]],
+ endpoints(fit.B.SFORB.1)$distimes))
dev.B.SFORB.1 <- abs(round(100 * ((median.B.SFORB - fit.B.SFORB.1.r)/median.B.SFORB), digits=1))
checkIdentical(dev.B.SFORB.1 < 1, rep(TRUE, length(dev.B.SFORB.1)))
fit.B.SFORB.2.r <- as.numeric(c(
parent_0 = fit.B.SFORB.2$parms.all[[1]],
- k1 = fit.B.SFORB.2$SFORB[[1]],
- k2 = fit.B.SFORB.2$SFORB[[2]],
- fit.B.SFORB.2$distimes))
+ k1 = endpoints(fit.B.SFORB.2)$SFORB[[1]],
+ k2 = endpoints(fit.B.SFORB.2)$SFORB[[2]],
+ endpoints(fit.B.SFORB.2)$distimes))
dev.B.SFORB.2 <- abs(round(100 * ((median.B.SFORB - fit.B.SFORB.2.r)/median.B.SFORB), digits=1))
checkIdentical(dev.B.SFORB.2 < 1, rep(TRUE, length(dev.B.SFORB.2)))
} # }}}
@@ -244,10 +244,10 @@ test.FOCUS_2006_D_SFO_SFO <- function()
FOCUS_2006_D_results_schaefer07_means <- c(
parent_0 = 99.65, DT50_parent = 7.04, DT50_m1 = 131.34)
- r.1.e <- c(fit.1.e$parms.all[[1]], fit.1.e$distimes[[1]])
- r.1.d <- c(fit.1.d$parms.all[[1]], fit.1.d$distimes[[1]])
- r.2.e <- c(fit.2.e$parms.all[[1]], fit.2.e$distimes[[1]])
- r.2.d <- c(fit.2.d$parms.all[[1]], fit.2.d$distimes[[1]])
+ r.1.e <- c(fit.1.e$parms.all[[1]], endpoints(fit.1.e)$distimes[[1]])
+ r.1.d <- c(fit.1.d$parms.all[[1]], endpoints(fit.1.d)$distimes[[1]])
+ r.2.e <- c(fit.2.e$parms.all[[1]], endpoints(fit.2.e)$distimes[[1]])
+ r.2.d <- c(fit.2.d$parms.all[[1]], endpoints(fit.2.d)$distimes[[1]])
dev.1.e <- 100 * (r.1.e - FOCUS_2006_D_results_schaefer07_means)/r.1.e
checkIdentical(as.numeric(abs(dev.1.e)) < 1, rep(TRUE, 3))
diff --git a/man/endpoints.Rd b/man/endpoints.Rd
new file mode 100644
index 00000000..21316cf2
--- /dev/null
+++ b/man/endpoints.Rd
@@ -0,0 +1,33 @@
+\name{endpoints}
+\alias{endpoints}
+\title{
+Function to calculate endpoints for further use from kinetic models fitted with mkinfit
+}
+\description{
+This function calculates DT50 and DT90 values as well as formation fractions from kinetic models
+fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites,
+the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but
+with the advantage that the SFORB model can also be used for metabolites.
+}
+\usage{
+endpoints(fit, pseudoDT50 = FALSE)
+}
+\arguments{
+ \item{fit}{
+ An object of class \code{\link{mkinfit}}.
+}
+ \item{pseudoDT50}{
+ Should pseudoDT50 values for FOMC, DFOP and SFORB models be reported, as
+ recommended by the FOCUS group? Currently not implemented.
+}
+}
+\note{
+ The function is used internally by \code{\link{summary.mkinfit}}.
+}
+\value{
+ A list with the components mentioned above.
+}
+\author{
+ Johannes Ranke
+}
+\keyword{ manip }
diff --git a/man/ilr.Rd b/man/ilr.Rd
index 8bf7a728..cedb49ca 100644
--- a/man/ilr.Rd
+++ b/man/ilr.Rd
@@ -38,7 +38,7 @@ ilr(c(10, 1, 0.1))
ilr(c(3, 3, 3))
# Almost equal entries give small numbers
ilr(c(0.3, 0.4, 0.3))
-# Only the ration between the numbers counts, not their sum
+# Only the ratio between the numbers counts, not their sum
invilr(ilr(c(0.7, 0.29, 0.01)))
invilr(ilr(2.1 * c(0.7, 0.29, 0.01)))
# Inverse transformation of larger numbers gives unequal elements
diff --git a/man/schaefer07_complex_case.Rd b/man/schaefer07_complex_case.Rd
index f2f024a2..ed4f6941 100644
--- a/man/schaefer07_complex_case.Rd
+++ b/man/schaefer07_complex_case.Rd
@@ -24,7 +24,7 @@
}
The results are a data frame with 14 results for different parameter values
}
-\source{
+\references{
Schäfer D, Mikolasch M, Rainbird P and Harvey B (2007). KinGUI: a new kinetic
software tool for evaluations according to FOCUS degradation kinetics. In: Del
Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII
diff --git a/vignettes/mkin.Rnw b/vignettes/mkin.Rnw
index f674db7e..2965bc5a 100644
--- a/vignettes/mkin.Rnw
+++ b/vignettes/mkin.Rnw
@@ -26,11 +26,11 @@ options(SweaveHooks = list(
\begin{document}
\title{mkin -\\
Routines for fitting kinetic models with one or more state variables to chemical degradation data}
-\author{\textbf{Johannes Ranke} \\
+\author{\textbf{Johannes Ranke} \\[0.5cm]
%EndAName
Eurofins Regulatory AG\\
-Weidenweg 15, CH--4310 Rheinfelden, Switzerland\\{1cm}
-and\\
+Weidenweg 15, CH--4310 Rheinfelden, Switzerland\\[0.5cm]
+and\\[0.5cm]
University of Bremen\\
}
\maketitle
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index f963d1e6..523d7195 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf
Binary files differ

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