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-rw-r--r--NEWS.md6
-rw-r--r--R/IORE.solution.R4
-rw-r--r--R/endpoints.R28
-rw-r--r--R/mkinerrmin.R194
-rw-r--r--R/mkinfit.R4
-rw-r--r--R/mkinmod.R54
-rw-r--r--R/mkinparplot.R8
-rw-r--r--R/mkinpredict.R10
-rw-r--r--R/transform_odeparms.R14
-rw-r--r--README.md3
-rw-r--r--man/FOMC.solution.Rd2
-rw-r--r--man/IORE.solution.Rd34
-rw-r--r--man/mkinmod.Rd27
-rw-r--r--man/mkinpredict.Rd19
-rw-r--r--vignettes/FOCUS_L.html167
-rw-r--r--vignettes/FOCUS_Z.pdfbin212996 -> 217963 bytes
-rw-r--r--vignettes/mkin.pdfbin160326 -> 160429 bytes
17 files changed, 360 insertions, 214 deletions
diff --git a/NEWS.md b/NEWS.md
index 3c0d72de..edee4c86 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+# CHANGES in mkin VERSION 0.9-32
+
+## NEW FEATURES
+
+- Add the possibility to fit indeterminate order rate equation (IORE) models using an analytical solution (parent only) or a numeric solution. Paths from IORE compounds to metabolites are supported when using of formation fractions (use_of_ff = 'max'). Note that the numerical solution (method.ode = 'deSolve') of the IORE differential equations sometimes fails due to numerical problems.
+
# CHANGES in mkin VERSION 0.9-31
## BUG FIXES
diff --git a/R/IORE.solution.R b/R/IORE.solution.R
new file mode 100644
index 00000000..9546ce56
--- /dev/null
+++ b/R/IORE.solution.R
@@ -0,0 +1,4 @@
+IORE.solution <- function(t, parent.0, k.iore, N)
+{
+ parent = (parent.0^(1 - N) - (1 - N) * k.iore * t)^(1/(1 - N))
+}
diff --git a/R/endpoints.R b/R/endpoints.R
index 676831a0..ae9aa3ec 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -1,11 +1,11 @@
endpoints <- function(fit) {
# Calculate dissipation times DT50 and DT90 and formation
# fractions as well as SFORB eigenvalues from optimised parameters
- # Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from HS and DFOP,
- # as well as from Eigenvalues b1 and b2 of any SFORB models
+ # Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from
+ # HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models
ep <- list()
obs_vars <- fit$obs_vars
- parms.all <- fit$bparms.ode
+ parms.all <- c(fit$bparms.optim, fit$bparms.fixed)
ep$ff <- vector()
ep$SFORB <- vector()
ep$distimes <- data.frame(DT50 = rep(NA, length(obs_vars)),
@@ -49,6 +49,28 @@ endpoints <- function(fit) {
DT50_back = DT90 / (log(10)/log(2)) # Backcalculated DT50 as recommended in FOCUS 2011
ep$distimes[obs_var, c("DT50back")] = DT50_back
}
+ if (type == "IORE") {
+ k_names = grep(paste("k.iore", obs_var, sep="_"), names(parms.all), value=TRUE)
+ k_tot = sum(parms.all[k_names])
+ # From the NAFTA kinetics guidance, p. 5
+ n = parms.all[paste("N", obs_var, sep = "_")]
+ k = k_tot
+ # Use the initial concentration of the parent compound
+ source_name = fit$mkinmod$map[[1]][[1]]
+ c0 = parms.all[paste(source_name, "0", sep = "_")]
+ alpha = 1 / (n - 1)
+ beta = (c0^(1 - n))/(k * (n - 1))
+ DT50 = beta * (2^(1/alpha) - 1)
+ DT90 = beta * (10^(1/alpha) - 1)
+ DT50_back = DT90 / (log(10)/log(2)) # Backcalculated DT50 as recommended in FOCUS 2011
+ ep$distimes[obs_var, c("DT50back")] = DT50_back
+ if (fit$mkinmod$use_of_ff == "min") {
+ for (k_name in k_names)
+ {
+ ep$ff[[sub("k_", "", k_name)]] = parms.all[[k_name]] / k_tot
+ }
+ }
+ }
if (type == "DFOP") {
k1 = parms.all["k1"]
k2 = parms.all["k2"]
diff --git a/R/mkinerrmin.R b/R/mkinerrmin.R
index 9ebac6a4..4137d33a 100644
--- a/R/mkinerrmin.R
+++ b/R/mkinerrmin.R
@@ -1,94 +1,100 @@
-# Copyright (C) 2010-2014 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/>
-if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "value_mean"))
-
-mkinerrmin <- function(fit, alpha = 0.05)
-{
- parms.optim <- fit$par
-
- kinerrmin <- function(errdata, n.parms) {
- means.mean <- mean(errdata$value_mean, na.rm = TRUE)
- df = length(errdata$value_mean) - n.parms
-
- err.min <- sqrt((1 / qchisq(1 - alpha, df)) *
- sum((errdata$value_mean - errdata$value_pred)^2)/(means.mean^2))
-
- return(list(err.min = err.min, n.optim = n.parms, df = df))
- }
-
- means <- aggregate(value ~ time + name, data = fit$observed, mean, na.rm=TRUE)
- errdata <- merge(means, fit$predicted, by = c("time", "name"),
- suffixes = c("_mean", "_pred"))
- errdata <- errdata[order(errdata$time, errdata$name), ]
-
- # Any value that is set to exactly zero is not really an observed value
- # Remove those at time 0 - those are caused by the FOCUS recommendation
- # to set metabolites occurring at time 0 to 0
- errdata <- subset(errdata, !(time == 0 & value_mean == 0))
-
- n.optim.overall <- length(parms.optim)
-
- errmin.overall <- kinerrmin(errdata, n.optim.overall)
- errmin <- data.frame(err.min = errmin.overall$err.min,
- n.optim = errmin.overall$n.optim, df = errmin.overall$df)
- rownames(errmin) <- "All data"
-
- # The degrees of freedom are counted according to FOCUS kinetics (2011, p. 164)
- for (obs_var in fit$obs_vars)
- {
- errdata.var <- subset(errdata, name == obs_var)
-
- # Check if initial value is optimised
- n.initials.optim <- length(grep(paste(obs_var, ".*", "_0", sep=""), names(parms.optim)))
-
- # Rate constants are attributed to the source variable
- n.k.optim <- length(grep(paste("^k", obs_var, sep="_"), names(parms.optim)))
- n.k.optim <- n.k.optim + length(grep(paste("^log_k", obs_var, sep="_"),
- names(parms.optim)))
-
- n.ff.optim <- 0
- # Formation fractions are attributed to the target variable, so look
- # for source compartments with formation fractions
- for (source_var in fit$obs_vars) {
- for (target_var in fit$mkinmod$spec[[source_var]]$to) {
- if (obs_var == target_var) {
- n.ff.optim <- n.ff.optim +
- length(grep(paste("^f", source_var, sep = "_"),
- names(parms.optim)))
- }
- }
- }
-
- n.optim <- n.k.optim + n.initials.optim + n.ff.optim
-
- # FOMC, DFOP and HS parameters are only counted if we are looking at the
- # first variable in the model which is always the source variable
- if (obs_var == fit$obs_vars[[1]]) {
- special_parms = c("alpha", "log_alpha", "beta", "log_beta",
- "k1", "log_k1", "k2", "log_k2",
- "g", "g_ilr", "tb", "log_tb")
- n.optim <- n.optim + length(intersect(special_parms, names(parms.optim)))
- }
-
- # Calculate and add a line to the results
- errmin.tmp <- kinerrmin(errdata.var, n.optim)
- errmin[obs_var, c("err.min", "n.optim", "df")] <- errmin.tmp
- }
-
- return(errmin)
-}
+# Copyright (C) 2010-2014 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/>
+if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "value_mean"))
+
+mkinerrmin <- function(fit, alpha = 0.05)
+{
+ parms.optim <- fit$par
+
+ kinerrmin <- function(errdata, n.parms) {
+ means.mean <- mean(errdata$value_mean, na.rm = TRUE)
+ df = length(errdata$value_mean) - n.parms
+
+ err.min <- sqrt((1 / qchisq(1 - alpha, df)) *
+ sum((errdata$value_mean - errdata$value_pred)^2)/(means.mean^2))
+
+ return(list(err.min = err.min, n.optim = n.parms, df = df))
+ }
+
+ means <- aggregate(value ~ time + name, data = fit$observed, mean, na.rm=TRUE)
+ errdata <- merge(means, fit$predicted, by = c("time", "name"),
+ suffixes = c("_mean", "_pred"))
+ errdata <- errdata[order(errdata$time, errdata$name), ]
+
+ # Any value that is set to exactly zero is not really an observed value
+ # Remove those at time 0 - those are caused by the FOCUS recommendation
+ # to set metabolites occurring at time 0 to 0
+ errdata <- subset(errdata, !(time == 0 & value_mean == 0))
+
+ n.optim.overall <- length(parms.optim)
+
+ errmin.overall <- kinerrmin(errdata, n.optim.overall)
+ errmin <- data.frame(err.min = errmin.overall$err.min,
+ n.optim = errmin.overall$n.optim, df = errmin.overall$df)
+ rownames(errmin) <- "All data"
+
+ # The degrees of freedom are counted according to FOCUS kinetics (2011, p. 164)
+ for (obs_var in fit$obs_vars)
+ {
+ errdata.var <- subset(errdata, name == obs_var)
+
+ # Check if initial value is optimised
+ n.initials.optim <- length(grep(paste(obs_var, ".*", "_0", sep=""), names(parms.optim)))
+
+ # Rate constants and IORE exponents are attributed to the source variable
+ n.k.optim <- length(grep(paste("^k", obs_var, sep="_"), names(parms.optim)))
+ n.k.optim <- n.k.optim + length(grep(paste("^log_k", obs_var, sep="_"),
+ names(parms.optim)))
+ n.k.iore.optim <- length(grep(paste("^k.iore", obs_var, sep="_"), names(parms.optim)))
+ n.k.iore.optim <- n.k.iore.optim + length(grep(paste("^log_k.iore", obs_var,
+ sep = "_"),
+ names(parms.optim)))
+
+ n.N.optim <- length(grep(paste("^N", obs_var, sep="_"), names(parms.optim)))
+
+ n.ff.optim <- 0
+ # Formation fractions are attributed to the target variable, so look
+ # for source compartments with formation fractions
+ for (source_var in fit$obs_vars) {
+ for (target_var in fit$mkinmod$spec[[source_var]]$to) {
+ if (obs_var == target_var) {
+ n.ff.optim <- n.ff.optim +
+ length(grep(paste("^f", source_var, sep = "_"),
+ names(parms.optim)))
+ }
+ }
+ }
+
+ n.optim <- sum(n.initials.optim, n.k.optim, n.k.iore.optim, n.N.optim, n.ff.optim)
+
+ # FOMC, DFOP and HS parameters are only counted if we are looking at the
+ # first variable in the model which is always the source variable
+ if (obs_var == fit$obs_vars[[1]]) {
+ special_parms = c("alpha", "log_alpha", "beta", "log_beta",
+ "k1", "log_k1", "k2", "log_k2",
+ "g", "g_ilr", "tb", "log_tb")
+ n.optim <- n.optim + length(intersect(special_parms, names(parms.optim)))
+ }
+
+ # Calculate and add a line to the dataframe holding the results
+ errmin.tmp <- kinerrmin(errdata.var, n.optim)
+ errmin[obs_var, c("err.min", "n.optim", "df")] <- errmin.tmp
+ }
+
+ return(errmin)
+}
diff --git a/R/mkinfit.R b/R/mkinfit.R
index c6e13b97..46121c6d 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -90,13 +90,15 @@ mkinfit <- function(mkinmod, observed,
defaultpar.names <- setdiff(mkinmod$parms, names(parms.ini))
for (parmname in defaultpar.names) {
# Default values for rate constants, depending on the parameterisation
- if (substr(parmname, 1, 2) == "k_") {
+ if (grepl("^k", parmname)) {
parms.ini[parmname] = 0.1 + k_salt
k_salt = k_salt + 1e-4
}
# Default values for rate constants for reversible binding
if (grepl("free_bound$", parmname)) parms.ini[parmname] = 0.1
if (grepl("bound_free$", parmname)) parms.ini[parmname] = 0.02
+ # Default values for IORE exponents
+ if (grepl("^N", parmname)) parms.ini[parmname] = 1
# Default values for the FOMC, DFOP and HS models
if (parmname == "alpha") parms.ini[parmname] = 1
if (parmname == "beta") parms.ini[parmname] = 10
diff --git a/R/mkinmod.R b/R/mkinmod.R
index eb290719..8b86303f 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2010-2013 Johannes Ranke {{{
+# Copyright (C) 2010-2014 Johannes Ranke {{{
# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
@@ -33,38 +33,39 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
stop("The use of formation fractions 'use_of_ff' can only be 'min' or 'max'")
# The returned model will be a list of character vectors, containing {{{
- # differential equations, parameter names and a mapping from model variables
- # to observed variables. If possible, a matrix representation of the
- # differential equations is included
+ # differential equations (if supported), parameter names and a mapping from
+ # model variables to observed variables. If possible, a matrix representation
+ # of the differential equations is included
parms <- vector()
- diffs <- vector()
- map <- list()
# }}}
- # Do not return a coefficient matrix mat when FOMC, DFOP or HS are used for
- # the parent compound {{{
- if(spec[[1]]$type %in% c("FOMC", "DFOP", "HS")) {
+ # Do not return a coefficient matrix mat when FOMC, IORE, DFOP or HS is used for the parent {{{
+ if(spec[[1]]$type %in% c("FOMC", "IORE", "DFOP", "HS")) {
mat = FALSE
} else mat = TRUE
#}}}
# Establish a list of differential equations as well as a map from observed {{{
# compartments to differential equations
+ diffs <- vector()
+ map <- list()
for (varname in obs_vars)
{
# Check the type component of the compartment specification {{{
if(is.null(spec[[varname]]$type)) stop(
"Every part of the model specification must be a list containing a type component")
- if(!spec[[varname]]$type %in% c("SFO", "FOMC", "DFOP", "HS", "SFORB")) stop(
- "Available types are SFO, FOMC, DFOP, HS and SFORB only")
+ if(!spec[[varname]]$type %in% c("SFO", "FOMC", "IORE", "DFOP", "HS", "SFORB")) stop(
+ "Available types are SFO, FOMC, IORE, DFOP, HS and SFORB only")
if(spec[[varname]]$type %in% c("FOMC", "DFOP", "HS") & match(varname, obs_vars) != 1) {
stop(paste("Types FOMC, DFOP and HS are only implemented for the first compartment,",
"which is assumed to be the source compartment"))
- } #}}}
+ }
+ #}}}
# New (sub)compartments (boxes) needed for the model type {{{
new_boxes <- switch(spec[[varname]]$type,
SFO = varname,
FOMC = varname,
+ IORE = varname,
DFOP = varname,
HS = varname,
SFORB = paste(varname, c("free", "bound"), sep = "_")
@@ -85,20 +86,40 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
# 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]]$type %in% c("SFO", "SFORB")) { # {{{ Add SFO or SFORB decline term
+ if(spec[[varname]]$type %in% c("SFO", "IORE", "SFORB")) { # {{{ Add decline term
if (use_of_ff == "min") { # Minimum use of formation fractions
if(spec[[varname]]$sink) {
- # If sink is required, add first-order sink term
+ if(spec[[varname]]$type == "IORE" && length(spec[[varname]]$to) > 0) {
+ stop("Transformation reactions from compounds modelled with IORE\n",
+ "are only supported with formation fractions (use_of_ff = 'max')")
+ }
+ # If sink is required, add first-order/IORE sink term
k_compound_sink <- paste("k", box_1, "sink", sep = "_")
+ if(spec[[varname]]$type == "IORE") {
+ k_compound_sink <- paste("k.iore", box_1, "sink", sep = "_")
+ }
parms <- c(parms, k_compound_sink)
decline_term <- paste(k_compound_sink, "*", box_1)
+ if(spec[[varname]]$type == "IORE") {
+ N <- paste("N", box_1, sep = "_")
+ parms <- c(parms, N)
+ decline_term <- paste0(decline_term, "^", N)
+ }
} else { # otherwise no decline term needed here
decline_term = "0"
}
} else {
k_compound <- paste("k", box_1, sep = "_")
+ if(spec[[varname]]$type == "IORE") {
+ k_compound <- paste("k.iore", box_1, sep = "_")
+ }
parms <- c(parms, k_compound)
decline_term <- paste(k_compound, "*", box_1)
+ if(spec[[varname]]$type == "IORE") {
+ N <- paste("N", box_1, sep = "_")
+ parms <- c(parms, N)
+ decline_term <- paste0(decline_term, "^", N)
+ }
}
} #}}}
if(spec[[varname]]$type == "FOMC") { # {{{ Add FOMC decline term
@@ -157,9 +178,10 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
for (target in to) {
target_box <- switch(spec[[target]]$type,
SFO = target,
+ IORE = target,
SFORB = paste(target, "free", sep = "_"))
- if (use_of_ff == "min" && spec[[varname]]$type %in% c("SFO",
- "SFORB")) {
+ if (use_of_ff == "min" && spec[[varname]]$type %in% c("SFO", "SFORB"))
+ {
k_from_to <- paste("k", origin_box, target_box, sep = "_")
parms <- c(parms, k_from_to)
diffs[[origin_box]] <- paste(diffs[[origin_box]], "-",
diff --git a/R/mkinparplot.R b/R/mkinparplot.R
index 683a8b24..4abecab9 100644
--- a/R/mkinparplot.R
+++ b/R/mkinparplot.R
@@ -19,11 +19,13 @@ mkinparplot <- function(object) {
state.optim = rownames(subset(object$start, type == "state"))
deparms.optim = rownames(subset(object$start, type == "deparm"))
fractions.optim = grep("^f_", deparms.optim, value = TRUE)
+ N.optim = grep("^N_", deparms.optim, value = TRUE)
if ("g" %in% deparms.optim) fractions.optim <- c("g", fractions.optim)
- rates.optim.unsorted = setdiff(deparms.optim, fractions.optim)
+ rates.optim.unsorted = setdiff(deparms.optim, union(fractions.optim, N.optim))
rates.optim <- rownames(object$start[rates.optim.unsorted, ])
n.plot <- c(state.optim = length(state.optim),
rates.optim = length(rates.optim),
+ N.optim = length(N.optim),
fractions.optim = length(fractions.optim))
n.plot <- n.plot[n.plot > 0]
@@ -42,6 +44,8 @@ mkinparplot <- function(object) {
na.rm = TRUE, finite = TRUE),
rates.optim = range(c(0, unlist(values)),
na.rm = TRUE, finite = TRUE),
+ N.optim = range(c(0, 1, unlist(values)),
+ na.rm = TRUE, finite = TRUE),
fractions.optim = range(c(0, 1, unlist(values)),
na.rm = TRUE, finite = TRUE))
stripchart(values["Estimate", ][length(parnames):1],
@@ -49,7 +53,7 @@ mkinparplot <- function(object) {
ylim = c(0.5, length(get(type)) + 0.5),
yaxt = "n")
if (type %in% c("rates.optim", "fractions.optim")) abline(v = 0, lty = 2)
- if (type %in% c("fractions.optim")) abline(v = 1, lty = 2)
+ if (type %in% c("N.optim", "fractions.optim")) abline(v = 1, lty = 2)
position <- ifelse(values["Estimate", ] < mean(xlim), "right", "left")
text(ifelse(position == "left", min(xlim), max(xlim)),
length(parnames):1, parnames,
diff --git a/R/mkinpredict.R b/R/mkinpredict.R
index 14efc568..da013d50 100644
--- a/R/mkinpredict.R
+++ b/R/mkinpredict.R
@@ -50,6 +50,12 @@ mkinpredict <- function(mkinmod, odeparms, odeini,
FOMC = FOMC.solution(outtimes,
evalparse(parent.name),
evalparse("alpha"), evalparse("beta")),
+ IORE = IORE.solution(outtimes,
+ evalparse(parent.name),
+ ifelse(mkinmod$use_of_ff == "min",
+ evalparse(paste("k.iore", parent.name, "sink", sep="_")),
+ evalparse(paste("k.iore", parent.name, sep="_"))),
+ evalparse("N_parent")),
DFOP = DFOP.solution(outtimes,
evalparse(parent.name),
evalparse("k1"), evalparse("k2"),
@@ -103,6 +109,10 @@ mkinpredict <- function(mkinmod, odeparms, odeini,
rtol = rtol,
...
)
+ if (sum(is.na(out)) > 0) {
+ stop("Differential equations were not integrated for all output times because\n",
+ "NaN values occurred in output from ode()")
+ }
}
if (map_output) {
# Output transformation for models with unobserved compartments like SFORB
diff --git a/R/transform_odeparms.R b/R/transform_odeparms.R
index 912a5c0a..a36b7eae 100644
--- a/R/transform_odeparms.R
+++ b/R/transform_odeparms.R
@@ -33,6 +33,8 @@ transform_odeparms <- function(parms, mkinmod,
# Log transformation for rate constants if requested
k <- parms[grep("^k_", names(parms))]
+ k.iore <- parms[grep("^k.iore_", names(parms))]
+ k <- c(k, k.iore)
if (length(k) > 0) {
if(transform_rates) {
transparms[paste0("log_", names(k))] <- log(k)
@@ -40,6 +42,10 @@ transform_odeparms <- function(parms, mkinmod,
else transparms[names(k)] <- k
}
+ # Do not transform exponents in IORE models
+ N <- parms[grep("^N", names(parms))]
+ transparms[names(N)] <- N
+
# Go through state variables and apply isometric logratio transformation to
# formation fractions if requested
mod_vars = names(spec)
@@ -98,8 +104,10 @@ backtransform_odeparms <- function(transparms, mkinmod,
# Exponential transformation for rate constants
if(transform_rates) {
trans_k <- transparms[grep("^log_k_", names(transparms))]
+ trans_k.iore <- transparms[grep("^log_k.iore_", names(transparms))]
+ trans_k = c(trans_k, trans_k.iore)
if (length(trans_k) > 0) {
- k_names <- gsub("^log_k_", "k_", names(trans_k))
+ k_names <- gsub("^log_k", "k", names(trans_k))
parms[k_names] <- exp(trans_k)
}
} else {
@@ -107,6 +115,10 @@ backtransform_odeparms <- function(transparms, mkinmod,
parms[names(trans_k)] <- trans_k
}
+ # Do not transform exponents in IORE models
+ N <- transparms[grep("^N", names(transparms))]
+ parms[names(N)] <- N
+
# Go through state variables and apply inverse isometric logratio transformation
mod_vars = names(spec)
for (box in mod_vars) {
diff --git a/README.md b/README.md
index e171180f..6b128ec3 100644
--- a/README.md
+++ b/README.md
@@ -114,6 +114,9 @@ or the package vignettes referenced from the
`reweight = "obs"` to your call to `mkinfit` and a separate variance
componenent for each of the observed variables will be optimised
in a second stage after the primary optimisation algorithm has converged.
+* When a metabolite decline phase is not described well by SFO kinetics,
+ either IORE kinetics or SFORB kinetics can be used for the metabolite,
+ adding one respectively two parameters to the system.
## GUI
diff --git a/man/FOMC.solution.Rd b/man/FOMC.solution.Rd
index d04d34e1..f4a26e41 100644
--- a/man/FOMC.solution.Rd
+++ b/man/FOMC.solution.Rd
@@ -44,6 +44,6 @@ FOMC.solution(t, parent.0, alpha, beta)
Technology} \bold{24}, 1032-1038
}
\examples{
- \dontrun{plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2)}
+ \dontrun{plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100))}
}
\keyword{ manip }
diff --git a/man/IORE.solution.Rd b/man/IORE.solution.Rd
new file mode 100644
index 00000000..65dac9a7
--- /dev/null
+++ b/man/IORE.solution.Rd
@@ -0,0 +1,34 @@
+\name{IORE.solution}
+\Rdversion{1.1}
+\alias{IORE.solution}
+\title{ Indeterminate order rate equation kinetics }
+\description{
+ Function describing exponential decline from a defined starting value, with
+ a concentration dependent rate constant.
+}
+\usage{
+ IORE.solution(t, parent.0, k.iore, N)
+}
+\arguments{
+ \item{t}{ Time. }
+ \item{parent.0}{ Starting value for the response variable at time zero. }
+ \item{k.iore}{ Rate constant. Note that this depends on the concentration units used. }
+ \item{N}{ Exponent describing the nonlinearity of the rate equation }
+}
+\note{
+ The solution of the IORE kinetic model reduces to the
+ \code{\link{SFO.solution}} if N = 1.
+}
+\value{
+ The value of the response variable at time \code{t}.
+}
+\references{
+ NAFTA Technical Working Group on Pesticides (not dated) Guidance for
+ Evaluating and Calculating Degradation Kinetics in Environmental
+ Media
+}
+\examples{
+ \dontrun{plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2,
+ ylim = c(0, 100))}
+}
+\keyword{ manip }
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
index 76127c58..e6749ded 100644
--- a/man/mkinmod.Rd
+++ b/man/mkinmod.Rd
@@ -4,9 +4,13 @@
Function to set up a kinetic model with one or more state variables.
}
\description{
- The function takes a specification, consisting of a list of the observed variables
- in the data. Each observed variable is again represented by a list, specifying the
- kinetic model type and reaction or transfer to other observed compartments.
+ The function usually takes several expressions, each assigning a compound name to
+ a list, specifying the kinetic model type and reaction or transfer to other
+ observed compartments. Instead of specifying several expressions, a list
+ of lists can be given in the speclist argument.
+
+ For the definition of model types and their parameters, the equations given
+ in the FOCUS and NAFTA guidance documents are used.
}
\usage{
mkinmod(..., use_of_ff = "min", speclist = NULL)
@@ -15,7 +19,8 @@ mkinmod(..., use_of_ff = "min", speclist = NULL)
\item{...}{
For each observed variable, a list has to be specified as an argument, containing
at least a component \code{type}, specifying the type of kinetics to use
- for the variable. Currently, single first order kinetics "SFO" or
+ for the variable. Currently, single first order kinetics "SFO",
+ indeterminate order rate equation kinetics "IORE", or
single first order with reversible binding "SFORB" are implemented for all
variables, while
"FOMC", "DFOP" and "HS" can additionally be chosen for the first
@@ -46,7 +51,19 @@ mkinmod(..., use_of_ff = "min", speclist = NULL)
\item{map}{ A list containing named character vectors for each observed variable, specifying
the modelling variables by which it is represented. }
\item{use_of_ff}{ The content of \code{use_of_ff} is passed on in this list component. }
- \item{coefmat}{ The coefficient matrix, if the system of differential equations can be represented by one. }
+ \item{coefmat}{ The coefficient matrix, if the system of differential equations can be
+ represented by one. }
+}
+\references{
+ 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}
+
+ NAFTA Technical Working Group on Pesticides (not dated) Guidance for
+ Evaluating and Calculating Degradation Kinetics in Environmental
+ Media
}
\author{
Johannes Ranke
diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index 97db90e3..7d8979e4 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -65,21 +65,25 @@
}
\examples{
SFO <- mkinmod(degradinol = list(type = "SFO"))
+ # Compare solution types
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
solution_type = "analytical")
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+ solution_type = "deSolve")
+ mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
solution_type = "eigen")
- mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 1:20,
- solution_type = "analytical")[20,]
- mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
- atol = 1e-20)[20,]
- # The integration method does not make a lot of difference
+ # Compare integration methods to analytical solution
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
- atol = 1e-20, method = "ode45")[20,]
+ solution_type = "analytical")[21,]
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
- atol = 1e-20, method = "rk4")[20,]
+ method = "lsoda")[21,]
+ mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+ method = "ode45")[21,]
+ mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+ method = "rk4")[21,]
+ # rk4 is not as precise here
# The number of output times used to make a lot of difference until the
# default for atol was adjusted
@@ -87,5 +91,6 @@
seq(0, 20, by = 0.1))[201,]
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
seq(0, 20, by = 0.01))[2001,]
+
}
\keyword{ manip }
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index bb02ec3e..bae659fd 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -1,53 +1,11 @@
<!DOCTYPE html>
+<!-- saved from url=(0014)about:internet -->
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<title>Example evaluation of FOCUS Laboratory Data L1 to L3</title>
-<!-- Styles for R syntax highlighter -->
-<style type="text/css">
- pre .operator,
- pre .paren {
- color: rgb(104, 118, 135)
- }
-
- pre .literal {
- color: rgb(88, 72, 246)
- }
-
- pre .number {
- color: rgb(0, 0, 205);
- }
-
- pre .comment {
- color: rgb(76, 136, 107);
- }
-
- pre .keyword {
- color: rgb(0, 0, 255);
- }
-
- pre .identifier {
- color: rgb(0, 0, 0);
- }
-
- pre .string {
- color: rgb(3, 106, 7);
- }
-</style>
-
-<!-- R syntax highlighter -->
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+ }
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+ }
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@@ -223,10 +222,10 @@ FOCUS report.</p>
summary(m.L1.SFO)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:20 2014
-## Date of summary: Mon Jul 14 20:32:20 2014
+## Date of fit: Mon Jul 14 19:59:26 2014
+## Date of summary: Mon Jul 14 19:59:26 2014
##
## Equations:
## [1] d_parent = - k_parent_sink * parent
@@ -309,14 +308,14 @@ summary(m.L1.SFO)
<pre><code class="r">plot(m.L1.SFO)
</code></pre>
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alt="plot of chunk unnamed-chunk-5"/> </p>
+<p><img src="data:image/png;base64,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alt="plot of chunk unnamed-chunk-5"/> </p>
<p>The residual plot can be easily obtained by</p>
<pre><code class="r">mkinresplot(m.L1.SFO, ylab = &quot;Observed&quot;, xlab = &quot;Time&quot;)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-6"/> </p>
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alt="plot of chunk unnamed-chunk-6"/> </p>
<p>For comparison, the FOMC model is fitted as well, and the chi<sup>2</sup> error level
is checked.</p>
@@ -325,10 +324,10 @@ is checked.</p>
summary(m.L1.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:20 2014
-## Date of summary: Mon Jul 14 20:32:20 2014
+## Date of fit: Mon Jul 14 19:59:26 2014
+## Date of summary: Mon Jul 14 19:59:26 2014
##
## Equations:
## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
@@ -417,10 +416,10 @@ FOCUS_2006_L2_mkin &lt;- mkin_wide_to_long(FOCUS_2006_L2)
summary(m.L2.SFO)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:20 2014
-## Date of summary: Mon Jul 14 20:32:20 2014
+## Date of fit: Mon Jul 14 19:59:27 2014
+## Date of summary: Mon Jul 14 19:59:27 2014
##
## Equations:
## [1] d_parent = - k_parent_sink * parent
@@ -500,7 +499,7 @@ plot(m.L2.SFO)
mkinresplot(m.L2.SFO)
</code></pre>
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alt="plot of chunk unnamed-chunk-10"/> </p>
<p>In the FOCUS kinetics report, it is stated that there is no apparent systematic
error observed from the residual plot up to the measured DT90 (approximately at
@@ -521,15 +520,15 @@ plot(m.L2.FOMC)
mkinresplot(m.L2.FOMC)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-11"/> </p>
<pre><code class="r">summary(m.L2.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:21 2014
-## Date of summary: Mon Jul 14 20:32:21 2014
+## Date of fit: Mon Jul 14 19:59:28 2014
+## Date of summary: Mon Jul 14 19:59:28 2014
##
## Equations:
## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
@@ -594,7 +593,7 @@ experimental error has to be assumed in order to explain the data.</p>
plot(m.L2.DFOP)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-12"/> </p>
<p>Here, the default starting parameters for the DFOP model obviously do not lead
to a reasonable solution. Therefore the fit is repeated with different starting
@@ -606,15 +605,15 @@ parameters.</p>
plot(m.L2.DFOP)
</code></pre>
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alt="plot of chunk unnamed-chunk-13"/> </p>
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alt="plot of chunk unnamed-chunk-13"/> </p>
<pre><code class="r">summary(m.L2.DFOP, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:23 2014
-## Date of summary: Mon Jul 14 20:32:23 2014
+## Date of fit: Mon Jul 14 19:59:28 2014
+## Date of summary: Mon Jul 14 19:59:28 2014
##
## Equations:
## [1] d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * parent
@@ -692,15 +691,15 @@ FOCUS_2006_L3_mkin &lt;- mkin_wide_to_long(FOCUS_2006_L3)
plot(m.L3.SFO)
</code></pre>
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alt="plot of chunk unnamed-chunk-15"/> </p>
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alt="plot of chunk unnamed-chunk-15"/> </p>
<pre><code class="r">summary(m.L3.SFO)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:23 2014
-## Date of summary: Mon Jul 14 20:32:23 2014
+## Date of fit: Mon Jul 14 19:59:29 2014
+## Date of summary: Mon Jul 14 19:59:29 2014
##
## Equations:
## [1] d_parent = - k_parent_sink * parent
@@ -777,15 +776,15 @@ does not fit very well. </p>
plot(m.L3.FOMC)
</code></pre>
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alt="plot of chunk unnamed-chunk-16"/> </p>
+<p><img 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alt="plot of chunk unnamed-chunk-16"/> </p>
<pre><code class="r">summary(m.L3.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:24 2014
-## Date of summary: Mon Jul 14 20:32:24 2014
+## Date of fit: Mon Jul 14 19:59:29 2014
+## Date of summary: Mon Jul 14 19:59:29 2014
##
## Equations:
## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
@@ -849,15 +848,15 @@ considerably:</p>
plot(m.L3.DFOP)
</code></pre>
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alt="plot of chunk unnamed-chunk-17"/> </p>
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alt="plot of chunk unnamed-chunk-17"/> </p>
<pre><code class="r">summary(m.L3.DFOP, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:24 2014
-## Date of summary: Mon Jul 14 20:32:24 2014
+## Date of fit: Mon Jul 14 19:59:30 2014
+## Date of summary: Mon Jul 14 19:59:30 2014
##
## Equations:
## [1] d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * parent
@@ -939,15 +938,15 @@ FOCUS_2006_L4_mkin &lt;- mkin_wide_to_long(FOCUS_2006_L4)
plot(m.L4.SFO)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-19"/> </p>
<pre><code class="r">summary(m.L4.SFO, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:27 2014
-## Date of summary: Mon Jul 14 20:32:27 2014
+## Date of fit: Mon Jul 14 19:59:30 2014
+## Date of summary: Mon Jul 14 19:59:30 2014
##
## Equations:
## [1] d_parent = - k_parent_sink * parent
@@ -1013,15 +1012,15 @@ fits very well. </p>
plot(m.L4.FOMC)
</code></pre>
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alt="plot of chunk unnamed-chunk-20"/> </p>
<pre><code class="r">summary(m.L4.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:28 2014
-## Date of summary: Mon Jul 14 20:32:28 2014
+## Date of fit: Mon Jul 14 19:59:31 2014
+## Date of summary: Mon Jul 14 19:59:31 2014
##
## Equations:
## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 559504cc..a3f0ce1e 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
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diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index f06d38f9..991e54d3 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf
Binary files differ

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