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-rw-r--r--man/HS.solution.Rd23
-rw-r--r--man/SFORB.solution.Rd16
-rw-r--r--man/create_deg_func.Rd26
-rw-r--r--man/logistic.solution.Rd52
-rw-r--r--man/mkinmod.Rd2
-rw-r--r--man/mkinpredict.Rd22
-rw-r--r--man/nlme.Rd6
7 files changed, 86 insertions, 61 deletions
diff --git a/man/HS.solution.Rd b/man/HS.solution.Rd
index 343f83f0..f72df23b 100644
--- a/man/HS.solution.Rd
+++ b/man/HS.solution.Rd
@@ -7,10 +7,21 @@
HS.solution(t, parent_0, k1, k2, tb)
}
\arguments{
+\item{t}{Time.}
+
+\item{parent_0}{Starting value for the response variable at time zero.}
+
+\item{k1}{First kinetic constant.}
+
+\item{k2}{Second kinetic constant.}
+
\item{tb}{Break point. Before this time, exponential decline according to
\code{k1} is calculated, after this time, exponential decline proceeds
according to \code{k2}.}
}
+\value{
+The value of the response variable at time \code{t}.
+}
\description{
Function describing two exponential decline functions with a break point
between them.
@@ -20,6 +31,18 @@ between them.
plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))
}
+\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+ Version 1.1, 18 December 2014
+ \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+}
\seealso{
Other parent solutions:
\code{\link{DFOP.solution}()},
diff --git a/man/SFORB.solution.Rd b/man/SFORB.solution.Rd
index c70ce13b..98a8c684 100644
--- a/man/SFORB.solution.Rd
+++ b/man/SFORB.solution.Rd
@@ -7,6 +7,10 @@
SFORB.solution(t, parent_0, k_12, k_21, k_1output)
}
\arguments{
+\item{t}{Time.}
+
+\item{parent_0}{Starting value for the response variable at time zero.}
+
\item{k_12}{Kinetic constant describing transfer from free to bound.}
\item{k_21}{Kinetic constant describing transfer from bound to free.}
@@ -30,6 +34,18 @@ and no substance in the bound fraction.
\dontrun{plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)}
}
+\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+ Version 1.1, 18 December 2014
+ \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+}
\seealso{
Other parent solutions:
\code{\link{DFOP.solution}()},
diff --git a/man/create_deg_func.Rd b/man/create_deg_func.Rd
new file mode 100644
index 00000000..2eefdb80
--- /dev/null
+++ b/man/create_deg_func.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/create_deg_func.R
+\name{create_deg_func}
+\alias{create_deg_func}
+\title{Create degradation functions for known analytical solutions}
+\usage{
+create_deg_func(spec, use_of_ff = c("min", "max"))
+}
+\arguments{
+\item{spec}{List of model specifications as contained in mkinmod objects}
+
+\item{use_of_ff}{Minimum or maximum use of formation fractions}
+}
+\value{
+Degradation function to be attached to mkinmod objects
+}
+\description{
+Create degradation functions for known analytical solutions
+}
+\examples{
+
+SFO_SFO <- mkinmod(
+ parent = mkinsub("SFO", "m1"),
+ m1 = mkinsub("SFO"))
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+}
diff --git a/man/logistic.solution.Rd b/man/logistic.solution.Rd
index 589ee8ec..33b3d44a 100644
--- a/man/logistic.solution.Rd
+++ b/man/logistic.solution.Rd
@@ -1,12 +1,10 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/logistic.solution.R, R/parent_solutions.R
+% Please edit documentation in R/parent_solutions.R
\name{logistic.solution}
\alias{logistic.solution}
\title{Logistic kinetics}
\usage{
logistic.solution(t, parent_0, kmax, k0, r)
-
-logistic.solution(t, parent_0, kmax, k0, r)
}
\arguments{
\item{t}{Time.}
@@ -18,8 +16,6 @@ logistic.solution(t, parent_0, kmax, k0, r)
\item{k0}{Minumum rate constant effective at time zero.}
\item{r}{Growth rate of the increase in the rate constant.}
-
-\item{parent.0}{Starting value for the response variable at time zero.}
}
\value{
The value of the response variable at time \code{t}.
@@ -27,16 +23,10 @@ The value of the response variable at time \code{t}.
\description{
Function describing exponential decline from a defined starting value, with
an increasing rate constant, supposedly caused by microbial growth
-
-Function describing exponential decline from a defined starting value, with
-an increasing rate constant, supposedly caused by microbial growth
}
\note{
The solution of the logistic model reduces to the
\code{\link{SFO.solution}} if \code{k0} is equal to \code{kmax}.
-
-The solution of the logistic model reduces to the
- \code{\link{SFO.solution}} if \code{k0} is equal to \code{kmax}.
}
\examples{
@@ -74,43 +64,13 @@ The solution of the logistic model reduces to the
summary(m)$bpar
endpoints(m)$distimes
-
- # Reproduce the plot on page 57 of FOCUS (2014)
- plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.2),
- from = 0, to = 100, ylim = c(0, 100),
- xlab = "Time", ylab = "Residue")
- plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.4),
- from = 0, to = 100, add = TRUE, lty = 2, col = 2)
- plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.8),
- from = 0, to = 100, add = TRUE, lty = 3, col = 3)
- plot(function(x) logistic.solution(x, 100, 0.08, 0.001, 0.2),
- from = 0, to = 100, add = TRUE, lty = 4, col = 4)
- plot(function(x) logistic.solution(x, 100, 0.08, 0.08, 0.2),
- from = 0, to = 100, add = TRUE, lty = 5, col = 5)
- legend("topright", inset = 0.05,
- legend = paste0("k0 = ", c(0.0001, 0.0001, 0.0001, 0.001, 0.08),
- ", r = ", c(0.2, 0.4, 0.8, 0.2, 0.2)),
- lty = 1:5, col = 1:5)
-
- # Fit with synthetic data
- logistic <- mkinmod(parent = mkinsub("logistic"))
-
- sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
- parms_logistic <- c(kmax = 0.08, k0 = 0.0001, r = 0.2)
- d_logistic <- mkinpredict(logistic,
- parms_logistic, c(parent = 100),
- sampling_times)
- d_2_1 <- add_err(d_logistic,
- sdfunc = function(x) sigma_twocomp(x, 0.5, 0.07),
- n = 1, reps = 2, digits = 5, LOD = 0.1, seed = 123456)[[1]]
-
- m <- mkinfit("logistic", d_2_1, quiet = TRUE)
- plot_sep(m)
- summary(m)$bpar
- endpoints(m)$distimes
-
}
\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence
and Degradation Kinetics from Environmental Fate Studies on Pesticides in
EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
index 020917b9..2ba917d6 100644
--- a/man/mkinmod.Rd
+++ b/man/mkinmod.Rd
@@ -6,7 +6,7 @@
\usage{
mkinmod(
...,
- use_of_ff = "min",
+ use_of_ff = "max",
speclist = NULL,
quiet = FALSE,
verbose = FALSE
diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index 366d5b83..f7e4acfc 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -102,36 +102,36 @@ kinetic parameters and initial values for the state variables.
SFO <- mkinmod(degradinol = mkinsub("SFO"))
# Compare solution types
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
solution_type = "analytical")
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
solution_type = "deSolve")
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
solution_type = "deSolve", use_compiled = FALSE)
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
solution_type = "eigen")
# Compare integration methods to analytical solution
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
solution_type = "analytical")[21,]
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
method = "lsoda")[21,]
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
method = "ode45")[21,]
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 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
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100),
seq(0, 20, by = 0.1))[201,]
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100),
seq(0, 20, by = 0.01))[2001,]
# Check compiled model versions - they are faster than the eigenvalue based solutions!
SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),
- m1 = list(type = "SFO"))
+ m1 = list(type = "SFO"), use_of_ff = "min")
if(require(rbenchmark)) {
benchmark(
eigen = mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
diff --git a/man/nlme.Rd b/man/nlme.Rd
index 4a668ac0..a9e368dd 100644
--- a/man/nlme.Rd
+++ b/man/nlme.Rd
@@ -37,15 +37,15 @@ datasets.
sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
m_SFO <- mkinmod(parent = mkinsub("SFO"))
d_SFO_1 <- mkinpredict(m_SFO,
- c(k_parent_sink = 0.1),
+ c(k_parent = 0.1),
c(parent = 98), sampling_times)
d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time")
d_SFO_2 <- mkinpredict(m_SFO,
- c(k_parent_sink = 0.05),
+ c(k_parent = 0.05),
c(parent = 102), sampling_times)
d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time")
d_SFO_3 <- mkinpredict(m_SFO,
- c(k_parent_sink = 0.02),
+ c(k_parent = 0.02),
c(parent = 103), sampling_times)
d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time")

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