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-rw-r--r--R/mkinfit.R33
-rw-r--r--R/mkinpredict.R22
-rw-r--r--TODO3
-rw-r--r--data/FOCUS_2006_DFOP_ref_A_to_B.rdabin0 -> 723 bytes
-rw-r--r--data/FOCUS_2006_FOMC_ref_A_to_F.rdabin0 -> 1227 bytes
-rw-r--r--data/FOCUS_2006_HS_ref_A_to_F.rdabin0 -> 1360 bytes
-rw-r--r--data/FOCUS_2006_SFO_ref_A_to_F.rdabin0 -> 1097 bytes
-rw-r--r--inst/unitTests/runit.mkinfit.R257
-rw-r--r--inst/unitTests/runit.mkinmod.R134
-rw-r--r--man/FOCUS_2006_DFOP_ref_A_to_B.Rd39
-rw-r--r--man/FOCUS_2006_FOMC_ref_A_to_F.Rd38
-rw-r--r--man/FOCUS_2006_HS_ref_A_to_F.Rd39
-rw-r--r--man/FOCUS_2006_SFO_ref_A_to_F.Rd37
-rw-r--r--man/mkinfit.Rd8
-rw-r--r--vignettes/mkin.Rnw4
15 files changed, 443 insertions, 171 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R
index cf58a7d2..6e455e18 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -30,6 +30,7 @@ mkinfit <- function(mkinmod, observed,
plot = FALSE, quiet = FALSE,
err = NULL, weight = "none", scaleVar = FALSE,
atol = 1e-6, n.outtimes = 100,
+ trace_parms = FALSE,
...)
{
# Get the names of the state variables in the model
@@ -112,7 +113,7 @@ mkinfit <- function(mkinmod, observed,
assign("calls", calls+1, inherits=TRUE) # Increase the model solution counter
# Trace parameter values if quiet is off
- if(!quiet) cat(P, "\n")
+ if(trace_parms) cat(P, "\n")
# Time points at which observed data are available
# Make sure we include time 0, so initial values for state variables are for time 0
@@ -216,10 +217,12 @@ mkinfit <- function(mkinmod, observed,
}
fit$errmin <- errmin
- # Calculate dissipation times DT50 and DT90 from parameters
+ # Calculate dissipation times DT50 and DT90 and, if necessary, formation fractions
+ # from optimised parameters
parms.all = backtransform_odeparms(c(fit$par, parms.fixed), mod_vars)
fit$distimes <- data.frame(DT50 = rep(NA, length(obs_vars)), DT90 = rep(NA, length(obs_vars)),
row.names = obs_vars)
+ fit$ff <- vector()
fit$SFORB <- vector()
for (obs_var in obs_vars) {
type = names(mkinmod$map[[obs_var]])[1]
@@ -230,7 +233,7 @@ mkinfit <- function(mkinmod, observed,
DT90 = log(10)/k_tot
for (k_name in k_names)
{
- fit$ff[[sub("^k_", "", k_name)]] = parms.all[[k_name]] / k_tot
+ fit$ff[[sub("k_", "", k_name)]] = parms.all[[k_name]] / k_tot
}
}
if (type == "FOMC") {
@@ -290,10 +293,12 @@ mkinfit <- function(mkinmod, observed,
f_90 <- function(t) (SFORB_fraction(t) - 0.1)^2
DT90.o <- optimize(f_90, c(0.01, max_DT))$minimum
if (abs(DT90.o - max_DT) < 0.01) DT90 = NA else DT90 = DT90.o
+
for (k_out_name in k_out_names)
{
- fit$ff[[sub("^k_", "", k_out_name)]] = parms.all[[k_out_name]] / k_1output
+ fit$ff[[sub("k_", "", k_out_name)]] = parms.all[[k_out_name]] / k_1output
}
+
# Return the eigenvalues for comparison with DFOP rate constants
fit$SFORB[[paste(obs_var, "b1", sep="_")]] = b1
fit$SFORB[[paste(obs_var, "b2", sep="_")]] = b2
@@ -310,6 +315,7 @@ mkinfit <- function(mkinmod, observed,
fit$atol <- atol
fit$parms.all <- parms.all # Return all backtransformed parameters for summary
fit$odeparms.final <- parms.all[mkinmod$parms] # Return ode parameters for further fitting
+ fit$date <- date()
class(fit) <- c("mkinfit", "modFit")
return(fit)
@@ -337,7 +343,12 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, ...) {
param <- cbind(param, se)
dimnames(param) <- list(pnames, c("Estimate", "Std. Error"))
- ans <- list(residuals = object$residuals,
+ ans <- list(
+ version = as.character(packageVersion("mkin")),
+ Rversion = paste(R.version$major, R.version$minor, sep="."),
+ date.fit = object$date,
+ date.summary = date(),
+ residuals = object$residuals,
residualVariance = resvar,
sigma = sqrt(resvar),
modVariance = modVariance,
@@ -354,6 +365,7 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, ...) {
ans$fixed <- object$fixed
ans$errmin <- object$errmin
ans$parms.all <- object$parms.all
+ ans$ff <- object$ff
if(distimes) ans$distimes <- object$distimes
if(length(object$SFORB) != 0) ans$SFORB <- object$SFORB
class(ans) <- c("summary.mkinfit", "summary.modFit")
@@ -362,6 +374,11 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, ...) {
# Expanded from print.summary.modFit
print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), ...) {
+ cat("mkin version: ", x$version, "\n")
+ cat("R version: ", x$Rversion, "\n")
+ cat("Date of fit: ", x$date.fit, "\n")
+ cat("Date of summary:", x$date.summary, "\n")
+
cat("\nEquations:\n")
print(noquote(as.character(x[["diffs"]])))
df <- x$df
@@ -393,6 +410,12 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), .
print(x$distimes, digits=digits,...)
}
+ printff <- !is.null(x$ff)
+ if(printff){
+ cat("\nEstimated formation fractions:\n")
+ print(data.frame(ff = x$ff), digits=digits,...)
+ }
+
printSFORB <- !is.null(x$SFORB)
if(printSFORB){
cat("\nEstimated Eigenvalues of SFORB model(s):\n")
diff --git a/R/mkinpredict.R b/R/mkinpredict.R
index 2b7e51d5..be43b0e4 100644
--- a/R/mkinpredict.R
+++ b/R/mkinpredict.R
@@ -1,3 +1,23 @@
+# $Id$
+
+# Copyright (C) 2010-2012 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# 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/>
+
mkinpredict <- function(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve", map_output = TRUE, atol = 1e-6, ...) {
# Get the names of the state variables in the model
@@ -35,7 +55,7 @@ mkinpredict <- function(mkinmod, odeparms, odeini, outtimes, solution_type = "de
evalparse(parent.name),
evalparse(paste("k", parent.name, "bound", sep="_")),
evalparse(paste("k", sub("free", "bound", parent.name), "free", sep="_")),
- evalparse(paste("k", parent.name, sep="_")))
+ evalparse(paste("k", parent.name, "sink", sep="_")))
)
out <- cbind(outtimes, o)
dimnames(out) <- list(outtimes, c("time", sub("_free", "", parent.name)))
diff --git a/TODO b/TODO
index a49957d2..a7503bda 100644
--- a/TODO
+++ b/TODO
@@ -1,10 +1,9 @@
Must have:
- Fix remaining problem with the schaefer complex test data (test.R)
-- Fix parent only SFORB model (see vignette)
-- Fix unit tests for mkinmod
- Adapt mkinplot function
Nice to have:
+- Make unit tests for mkinpredict, comparing different solution types
- Calculate confidence intervals for parameters assuming normal distribution
- Calculate confidence intervals for DT50 and DT90 values when only one parameter is involved
- Add unit tests for mkinfit
diff --git a/data/FOCUS_2006_DFOP_ref_A_to_B.rda b/data/FOCUS_2006_DFOP_ref_A_to_B.rda
new file mode 100644
index 00000000..8b9dc9f8
--- /dev/null
+++ b/data/FOCUS_2006_DFOP_ref_A_to_B.rda
Binary files differ
diff --git a/data/FOCUS_2006_FOMC_ref_A_to_F.rda b/data/FOCUS_2006_FOMC_ref_A_to_F.rda
new file mode 100644
index 00000000..246a53fa
--- /dev/null
+++ b/data/FOCUS_2006_FOMC_ref_A_to_F.rda
Binary files differ
diff --git a/data/FOCUS_2006_HS_ref_A_to_F.rda b/data/FOCUS_2006_HS_ref_A_to_F.rda
new file mode 100644
index 00000000..1e3b3864
--- /dev/null
+++ b/data/FOCUS_2006_HS_ref_A_to_F.rda
Binary files differ
diff --git a/data/FOCUS_2006_SFO_ref_A_to_F.rda b/data/FOCUS_2006_SFO_ref_A_to_F.rda
new file mode 100644
index 00000000..411c5368
--- /dev/null
+++ b/data/FOCUS_2006_SFO_ref_A_to_F.rda
Binary files differ
diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R
index 2a026ce0..a06e4ff1 100644
--- a/inst/unitTests/runit.mkinfit.R
+++ b/inst/unitTests/runit.mkinfit.R
@@ -18,36 +18,243 @@
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>
+# Test SFO model to a relative tolerance of 1% # {{{
+test.FOCUS_2006_SFO <- function()
+{
+ SFO.1 <- mkinmod(parent = list(type = "SFO"))
+ SFO.2 <- mkinmod(parent = list(type = "SFO"), use_of_ff = "max")
+
+ fit.A.SFO.1 <- mkinfit(SFO.1, FOCUS_2006_A, quiet=TRUE)
+ fit.A.SFO.2 <- mkinfit(SFO.2, FOCUS_2006_A, quiet=TRUE)
+
+ 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))
+ 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))
+ 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)))
+
+ fit.C.SFO.1 <- mkinfit(SFO.1, FOCUS_2006_C, quiet=TRUE)
+ fit.C.SFO.2 <- mkinfit(SFO.2, FOCUS_2006_C, quiet=TRUE)
+
+ 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))
+ 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))
+ 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)))
+} # }}}
+
+# Test FOMC model to a relative tolerance of 1% {{{
+# See kinfit vignette for a discussion of FOMC fits to FOCUS_2006_A
+# In this case, only M0, DT50 and DT90 are checked
+test.FOCUS_2006_FOMC <- function()
+{
+ FOMC <- mkinmod(parent = list(type = "FOMC"))
+
+ # FOCUS_2006_A (compare kinfit vignette for discussion)
+ fit.A.FOMC <- mkinfit(FOMC, FOCUS_2006_A, quiet=TRUE)
+
+ 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))
+ 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)))
+
+ # FOCUS_2006_B
+ fit.B.FOMC <- mkinfit(FOMC, FOCUS_2006_B, quiet=TRUE)
+
+ 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))
+ 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)))
+
+ # FOCUS_2006_C
+ fit.C.FOMC <- mkinfit(FOMC, FOCUS_2006_C, quiet=TRUE)
+
+ 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))
+ 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)))
+} # }}}
+
+# Test DFOP model, tolerance of 1% with the exception of f parameter for A {{{
+test.FOCUS_2006_DFOP <- function()
+{
+ DFOP <- mkinmod(parent = list(type = "DFOP"))
+
+ # FOCUS_2006_A
+ fit.A.DFOP <- mkinfit(DFOP, FOCUS_2006_A, quiet=TRUE)
+ fit.A.DFOP <- mkinfit(DFOP, FOCUS_2006_A, quiet=TRUE, plot=TRUE)
+
+ 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))
+ 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)))
+
+ # FOCUS_2006_B
+ fit.B.DFOP <- mkinfit(DFOP, FOCUS_2006_B, quiet=TRUE)
+
+ 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))
+ 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)))
+} # }}}
+
+# Test HS model to a relative tolerance of 1% excluding Mathematica values {{{
+# as they are unreliable
+test.FOCUS_2006_HS <- function()
+{
+ HS <- mkinmod(parent = list(type = "HS"))
+
+ # FOCUS_2006_A
+ fit.A.HS <- mkinfit(HS, FOCUS_2006_A, quiet=TRUE)
+
+ 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))
+ 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)))
+
+ # FOCUS_2006_B
+ fit.B.HS <- mkinfit(HS, FOCUS_2006_B, quiet=TRUE)
+
+ 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))
+ 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)]
+ checkIdentical(dev.B.HS < 10, rep(TRUE, length(dev.B.HS)))
+
+ # FOCUS_2006_C
+ fit.C.HS <- mkinfit(HS, FOCUS_2006_C, quiet=TRUE)
+
+ 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))
+ 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)))
+} # }}}
+
+# Test SFORB model against DFOP solutions to a relative tolerance of 1% # {{{
+test.FOCUS_2006_SFORB <- function()
+{
+ SFORB <- mkinmod(parent = list(type = "SFORB"))
+
+ # FOCUS_2006_A
+ fit.A.SFORB.1 <- mkinfit(SFORB, FOCUS_2006_A, quiet=TRUE)
+ fit.A.SFORB.2 <- mkinfit(SFORB, FOCUS_2006_A, solution_type = "deSolve", quiet=TRUE)
+
+ median.A.SFORB <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "A",
+ c(M0, k1, k2, DT50, DT90)), "median"))
+
+ 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))
+ 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
+ dev.A.SFORB.1 <- dev.A.SFORB.1[c(1, 3, 4, 5)]
+ checkIdentical(dev.A.SFORB.1 < 1, rep(TRUE, length(dev.A.SFORB.1)))
+
+ 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))
+ 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
+ dev.A.SFORB.2 <- dev.A.SFORB.2[c(1, 3, 4, 5)]
+ checkIdentical(dev.A.SFORB.2 < 1, rep(TRUE, length(dev.A.SFORB.2)))
+
+ # FOCUS_2006_B
+ fit.B.SFORB.1 <- mkinfit(SFORB, FOCUS_2006_B, quiet=TRUE)
+ fit.B.SFORB.2 <- mkinfit(SFORB, FOCUS_2006_B, solution_type = "deSolve", quiet=TRUE)
+
+ median.B.SFORB <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "B",
+ c(M0, k1, k2, DT50, DT90)), "median"))
+
+ 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))
+ 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))
+ 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)))
+} # }}}
+
+# Test eigenvalue based fit to Schaefer 2007 data against solution from conference paper {{{
test.mkinfit.schaefer07_complex_example <- function()
{
schaefer07_complex_model <- mkinmod(
- parent = list(type = "SFO", to = c("A1", "B1", "C1")),
+ parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),
A1 = list(type = "SFO", to = "A2"),
B1 = list(type = "SFO"),
C1 = list(type = "SFO"),
A2 = list(type = "SFO"))
-# Commented out because it takes too much time and is currently not used (see below)
-# fit <- mkinfit(schaefer07_complex_model,
-# mkin_wide_to_long(schaefer07_complex_case, time = "time"))
-# r <- schaefer07_complex_results
-# r$mkin <- c(
-# fit$parms.all["k_parent"],
-# fit$distimes["parent", "DT50"],
-# fit$parms.all["f_parent_to_A1"],
-# fit$parms.all["k_A1"],
-# fit$distimes["A1", "DT50"],
-# fit$parms.all["f_parent_to_B1"],
-# fit$parms.all["k_B1"],
-# fit$distimes["B1", "DT50"],
-# fit$parms.all["f_parent_to_C1"],
-# fit$parms.all["k_C1"],
-# fit$distimes["C1", "DT50"],
-# fit$parms.all["f_A1_to_A2"],
-# fit$parms.all["k_A2"],
-# fit$distimes["A2", "DT50"])
-# r$means <- (r$KinGUI + r$ModelMaker)/2
-# r$mkin.deviation <- abs(round(100 * ((r$mkin - r$means)/r$means), digits=1))
- # Commented out the check as mkin is fitting a different model
- #checkIdentical(r$mkin.deviation < 10, rep(TRUE, length(r$mkin.deviation)))
-}
+ fit <- mkinfit(schaefer07_complex_model,
+ mkin_wide_to_long(schaefer07_complex_case, time = "time"))
+ s <- summary(fit)
+ r <- schaefer07_complex_results
+ attach(as.list(fit$parms.all))
+ k_parent <- sum(k_parent_A1, k_parent_B1, k_parent_C1)
+ r$mkin <- c(
+ k_parent,
+ s$distimes["parent", "DT50"],
+ s$ff["parent_A1"],
+ sum(k_A1_sink, k_A1_A2),
+ s$distimes["A1", "DT50"],
+ s$ff["parent_B1"],
+ k_B1_sink,
+ s$distimes["B1", "DT50"],
+ s$ff["parent_C1"],
+ k_C1_sink,
+ s$distimes["C1", "DT50"],
+ s$ff["A1_A2"],
+ k_A2_sink,
+ s$distimes["A2", "DT50"])
+ r$means <- (r$KinGUI + r$ModelMaker)/2
+ r$mkin.deviation <- abs(round(100 * ((r$mkin - r$means)/r$means), digits=1))
+ checkIdentical(r$mkin.deviation < 10, rep(TRUE, length(r$mkin.deviation)))
+} # }}}
+# vim: set foldmethod=marker ts=2 sw=2 expandtab:
diff --git a/inst/unitTests/runit.mkinmod.R b/inst/unitTests/runit.mkinmod.R
deleted file mode 100644
index 38b07cd5..00000000
--- a/inst/unitTests/runit.mkinmod.R
+++ /dev/null
@@ -1,134 +0,0 @@
-# $Id: runit.mkinmod.R 64 2010-09-01 13:33:51Z jranke $
-
-# Copyright (C) 2010-2012 Johannes Ranke
-# Contact: jranke@uni-bremen.de
-
-# This file is part of the R package mkin
-
-# mkin is free software: you can redistribute it and/or modify it under the
-# terms of the GNU General Public License as published by the Free Software
-# Foundation, either version 3 of the License, or (at your option) any later
-# version.
-
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
-# 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/>
-
-test.mkinmod.SFO <- function()
-{
- SFO.diffs <- c(
- parent = "d_parent = - k_parent * parent"
- )
- SFO.parms <- c("k_parent")
- SFO.map <- list(parent = c(SFO = "parent"))
- SFO.coefmat <- matrix("- k_parent", dimnames = list("parent", "parent"))
- SFO <- list(diffs = SFO.diffs, parms = SFO.parms, map = SFO.map,
- coefmat = SFO.coefmat)
- class(SFO) <- "mkinmod"
- SFO.mkinmod <- mkinmod(
- parent = list(type = "SFO")
- )
- checkIdentical(SFO, SFO.mkinmod)
-}
-
-test.mkinmod.SFORB <- function()
-{
- SFORB.diffs <- c(
- parent_free = paste(
- "d_parent_free = - k_parent_free * parent_free",
- "- k_parent_free_bound * parent_free",
- "+ k_parent_bound_free * parent_bound"),
- parent_bound = paste(
- "d_parent_bound =",
- "+ k_parent_free_bound * parent_free",
- "- k_parent_bound_free * parent_bound")
- )
- SFORB.parms <- c("k_parent_free", "k_parent_free_bound", "k_parent_bound_free")
- SFORB.map <- list(parent = c(SFORB = "parent_free", SFORB = "parent_bound"))
- vars <- paste("parent", c("free", "bound"), sep="_")
- SFORB.coefmat <- matrix(
- c("- k_parent_free - k_parent_free_bound", "k_parent_bound_free",
- "k_parent_free_bound", "- k_parent_bound_free"), nrow=2, byrow=TRUE,
- dimnames=list(vars, vars))
- SFORB <- list(diffs = SFORB.diffs, parms = SFORB.parms,
- map = SFORB.map, coefmat = SFORB.coefmat)
- class(SFORB) <- "mkinmod"
- SFORB.mkinmod <- mkinmod(
- parent = list(type = "SFORB")
- )
- #checkIdentical(SFORB, SFORB.mkinmod)
-}
-
-test.mkinmod.SFO_SFO <- function()
-{
- SFO_SFO.diffs <- c(
- parent = "d_parent = - k_parent * parent",
- m1 = "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1"
- )
- SFO_SFO.parms <- c("k_parent", "f_parent_to_m1", "k_m1")
- SFO_SFO.map <- list(parent = c(SFO = "parent"), m1 = c(SFO = "m1"))
- vars <- c("parent", "m1")
- SFO_SFO.coefmat <- matrix(c("- k_parent",
- "0", "f_parent_to_m1 * k_parent", "- k_m1"), nrow=2, byrow=TRUE,
- dimnames=list(vars, vars))
- SFO_SFO <- list(diffs = SFO_SFO.diffs, parms = SFO_SFO.parms,
- map = SFO_SFO.map, coefmat = SFO_SFO.coefmat)
- class(SFO_SFO) <- "mkinmod"
- SFO_SFO.mkinmod <- mkinmod(
- parent = list(type = "SFO", to = "m1"),
- m1 = list(type = "SFO", sink=TRUE)
- )
- checkIdentical(SFO_SFO, SFO_SFO.mkinmod)
-}
-
-test.mkinmod.SFO_SFO2 <- function()
-{
- SFO_SFO2.diffs <- c(
- parent = "d_parent = - k_parent * parent",
- m1 = "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1",
- m2 = "d_m2 = + f_parent_to_m2 * k_parent * parent - k_m2 * m2"
- )
- SFO_SFO2.parms <- c("k_parent", "f_parent_to_m1", "f_parent_to_m2", "k_m1", "k_m2")
- SFO_SFO2.map <- list(parent = c(SFO = "parent"), m1 = c(SFO = "m1"), m2 = c(SFO = "m2"))
- vars <- c("parent", "m1", "m2")
- SFO_SFO2.coefmat <- matrix(
- c("- k_parent", "0", "0",
- "f_parent_to_m1 * k_parent", "- k_m1", "0",
- "f_parent_to_m2 * k_parent", "0", "- k_m2"), nrow=3, byrow=TRUE,
- dimnames=list(vars, vars))
- SFO_SFO2 <- list(diffs = SFO_SFO2.diffs, parms = SFO_SFO2.parms,
- map = SFO_SFO2.map, coefmat = SFO_SFO2.coefmat)
- class(SFO_SFO2) <- "mkinmod"
- SFO_SFO2.mkinmod <- mkinmod(
- parent = list(type = "SFO", to = c("m1", "m2"), sink=TRUE),
- m1 = list(type = "SFO", sink=TRUE),
- m2 = list(type = "SFO", sink=TRUE)
- )
- checkIdentical(SFO_SFO2, SFO_SFO2.mkinmod)
-}
-
-test.mkinmod.FOMC_SFO2 <- function()
-{
- FOMC_SFO2.diffs <- c(
- parent = "d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent",
- m1 = "d_m1 = + f_parent_to_m1 * (alpha/beta) * ((time/beta) + 1)^-1 * parent - k_m1 * m1",
- m2 = "d_m2 = + f_parent_to_m2 * (alpha/beta) * ((time/beta) + 1)^-1 * parent - k_m2 * m2"
- )
- FOMC_SFO2.parms <- c("alpha", "beta", "f_parent_to_m1", "f_parent_to_m2", "k_m1", "k_m2")
- FOMC_SFO2.map <- list(parent = c(FOMC = "parent"),
- m1 = c(SFO = "m1"),
- m2 = c(SFO = "m2"))
- FOMC_SFO2 <- list(diffs = FOMC_SFO2.diffs, parms = FOMC_SFO2.parms,
- map = FOMC_SFO2.map)
- class(FOMC_SFO2) <- "mkinmod"
- FOMC_SFO2.mkinmod <- mkinmod(
- parent = list(type = "FOMC", to = c("m1", "m2"), sink=TRUE),
- m1 = list(type = "SFO"),
- m2 = list(type = "SFO")
- )
- checkIdentical(FOMC_SFO2, FOMC_SFO2.mkinmod)
-}
diff --git a/man/FOCUS_2006_DFOP_ref_A_to_B.Rd b/man/FOCUS_2006_DFOP_ref_A_to_B.Rd
new file mode 100644
index 00000000..88bd4ac6
--- /dev/null
+++ b/man/FOCUS_2006_DFOP_ref_A_to_B.Rd
@@ -0,0 +1,39 @@
+\name{FOCUS_2006_DFOP_ref_A_to_B}
+\Rdversion{1.1}
+\alias{FOCUS_2006_DFOP_ref_A_to_B}
+\docType{data}
+\title{
+Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)
+}
+\description{
+A table with the fitted parameters and the resulting DT50 and DT90 values
+generated with different software packages. Taken directly from FOCUS (2006).
+The results from fitting the data with the Topfit software was removed, as
+the initial concentration of the parent compound was fixed to a value of 100
+in this fit.
+}
+\usage{data(FOCUS_2006_DFOP_ref_A_to_B)}
+\format{
+ A data frame containing the following variables.
+ \describe{
+ \item{\code{package}}{a factor giving the name of the software package}
+ \item{\code{M0}}{The fitted initial concentration of the parent compound}
+ \item{\code{f}}{The fitted f parameter}
+ \item{\code{k1}}{The fitted k1 parameter}
+ \item{\code{k2}}{The fitted k2 parameter}
+ \item{\code{DT50}}{The resulting half-life of the parent compound}
+ \item{\code{DT90}}{The resulting DT90 of the parent compound}
+ \item{\code{dataset}}{The FOCUS dataset that was used}
+ }
+}
+\source{
+ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and
+ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+ Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+ \url{http://focus.jrc.ec.europa.eu/dk}
+}
+\examples{
+data(FOCUS_2006_DFOP_ref_A_to_B)
+}
+\keyword{datasets}
diff --git a/man/FOCUS_2006_FOMC_ref_A_to_F.Rd b/man/FOCUS_2006_FOMC_ref_A_to_F.Rd
new file mode 100644
index 00000000..2fcc2db7
--- /dev/null
+++ b/man/FOCUS_2006_FOMC_ref_A_to_F.Rd
@@ -0,0 +1,38 @@
+\name{FOCUS_2006_FOMC_ref_A_to_F}
+\Rdversion{1.1}
+\alias{FOCUS_2006_FOMC_ref_A_to_F}
+\docType{data}
+\title{
+Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)
+}
+\description{
+A table with the fitted parameters and the resulting DT50 and DT90 values
+generated with different software packages. Taken directly from FOCUS (2006).
+The results from fitting the data with the Topfit software was removed, as
+the initial concentration of the parent compound was fixed to a value of 100
+in this fit.
+}
+\usage{data(FOCUS_2006_FOMC_ref_A_to_F)}
+\format{
+ A data frame containing the following variables.
+ \describe{
+ \item{\code{package}}{a factor giving the name of the software package}
+ \item{\code{M0}}{The fitted initial concentration of the parent compound}
+ \item{\code{alpha}}{The fitted alpha parameter}
+ \item{\code{beta}}{The fitted beta parameter}
+ \item{\code{DT50}}{The resulting half-life of the parent compound}
+ \item{\code{DT90}}{The resulting DT90 of the parent compound}
+ \item{\code{dataset}}{The FOCUS dataset that was used}
+ }
+}
+\source{
+ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and
+ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+ Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+ \url{http://focus.jrc.ec.europa.eu/dk}
+}
+\examples{
+data(FOCUS_2006_FOMC_ref_A_to_F)
+}
+\keyword{datasets}
diff --git a/man/FOCUS_2006_HS_ref_A_to_F.Rd b/man/FOCUS_2006_HS_ref_A_to_F.Rd
new file mode 100644
index 00000000..6fc99933
--- /dev/null
+++ b/man/FOCUS_2006_HS_ref_A_to_F.Rd
@@ -0,0 +1,39 @@
+\name{FOCUS_2006_HS_ref_A_to_F}
+\Rdversion{1.1}
+\alias{FOCUS_2006_HS_ref_A_to_F}
+\docType{data}
+\title{
+Results of fitting the HS model to Datasets A to F of FOCUS (2006)
+}
+\description{
+A table with the fitted parameters and the resulting DT50 and DT90 values
+generated with different software packages. Taken directly from FOCUS (2006).
+The results from fitting the data with the Topfit software was removed, as
+the initial concentration of the parent compound was fixed to a value of 100
+in this fit.
+}
+\usage{data(FOCUS_2006_HS_ref_A_to_F)}
+\format{
+ A data frame containing the following variables.
+ \describe{
+ \item{\code{package}}{a factor giving the name of the software package}
+ \item{\code{M0}}{The fitted initial concentration of the parent compound}
+ \item{\code{tb}}{The fitted tb parameter}
+ \item{\code{k1}}{The fitted k1 parameter}
+ \item{\code{k2}}{The fitted k2 parameter}
+ \item{\code{DT50}}{The resulting half-life of the parent compound}
+ \item{\code{DT90}}{The resulting DT90 of the parent compound}
+ \item{\code{dataset}}{The FOCUS dataset that was used}
+ }
+}
+\source{
+ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and
+ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+ Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+ \url{http://focus.jrc.ec.europa.eu/dk}
+}
+\examples{
+data(FOCUS_2006_HS_ref_A_to_F)
+}
+\keyword{datasets}
diff --git a/man/FOCUS_2006_SFO_ref_A_to_F.Rd b/man/FOCUS_2006_SFO_ref_A_to_F.Rd
new file mode 100644
index 00000000..19650ed4
--- /dev/null
+++ b/man/FOCUS_2006_SFO_ref_A_to_F.Rd
@@ -0,0 +1,37 @@
+\name{FOCUS_2006_SFO_ref_A_to_F}
+\Rdversion{1.1}
+\alias{FOCUS_2006_SFO_ref_A_to_F}
+\docType{data}
+\title{
+Results of fitting the SFO model to Datasets A to F of FOCUS (2006)
+}
+\description{
+A table with the fitted parameters and the resulting DT50 and DT90 values
+generated with different software packages. Taken directly from FOCUS (2006).
+The results from fitting the data with the Topfit software was removed, as
+the initial concentration of the parent compound was fixed to a value of 100
+in this fit.
+}
+\usage{data(FOCUS_2006_SFO_ref_A_to_F)}
+\format{
+ A data frame containing the following variables.
+ \describe{
+ \item{\code{package}}{a factor giving the name of the software package}
+ \item{\code{M0}}{The fitted initial concentration of the parent compound}
+ \item{\code{k}}{The fitted first-order degradation rate constant}
+ \item{\code{DT50}}{The resulting half-life of the parent compound}
+ \item{\code{DT90}}{The resulting DT90 of the parent compound}
+ \item{\code{dataset}}{The FOCUS dataset that was used}
+ }
+}
+\source{
+ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and
+ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+ Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+ \url{http://focus.jrc.ec.europa.eu/dk}
+}
+\examples{
+data(FOCUS_2006_SFO_ref_A_to_F)
+}
+\keyword{datasets}
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 0c8e48f1..5f70dae9 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -17,7 +17,8 @@ mkinfit(mkinmod, observed,
solution_type = "auto",
plot = FALSE, quiet = FALSE, err = NULL, weight = "none",
scaleVar = FALSE,
- atol = 1e-6, n.outtimes, ...)
+ atol = 1e-6, n.outtimes,
+ trace_parms, ...)
}
\arguments{
\item{mkinmod}{
@@ -92,6 +93,9 @@ mkinfit(mkinmod, observed,
the numerical solver if that is used (see \code{solution} argument.
The default value is 100.
}
+ \item{trace_parms}{
+ Should a trace of the parameter values be listed?
+ }
\item{\dots}{
Further arguments that will be passed to \code{\link{modFit}}.
}
@@ -101,7 +105,7 @@ mkinfit(mkinmod, observed,
A summary can be obtained by \code{\link{summary.mkinfit}}.
}
\author{
- Johannes Ranke <jranke@{harlan.com,uni-bremen.de}>
+ Johannes Ranke <jranke@uni-bremen.de>
}
\examples{
# One parent compound, one metabolite, both single first order.
diff --git a/vignettes/mkin.Rnw b/vignettes/mkin.Rnw
index ee472ba5..f674db7e 100644
--- a/vignettes/mkin.Rnw
+++ b/vignettes/mkin.Rnw
@@ -147,8 +147,8 @@ on the fundamental system of the coefficient matrix, as proposed by
<<model_fitting, echo=TRUE>>=
SFO.fit <- mkinfit(SFO, FOCUS_2006_C)
summary(SFO.fit)
-#SFORB.fit <- mkinfit(SFORB, FOCUS_2006_C)
-#summary(SFORB.fit)
+SFORB.fit <- mkinfit(SFORB, FOCUS_2006_C)
+summary(SFORB.fit)
SFO_SFO.fit <- mkinfit(SFO_SFO, FOCUS_2006_D, plot=TRUE)
summary(SFO_SFO.fit, data=FALSE)
SFORB_SFO.fit <- mkinfit(SFORB_SFO, FOCUS_2006_D, plot=TRUE)

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