From 8bdb4cd437a9d4663e542f95869e8692aa38dadb Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 7 May 2020 08:59:29 +0200 Subject: Static documentation rebuilt by pkgdown --- man/DFOP.solution.Rd | 21 ++++++++++++++--- man/FOMC.solution.Rd | 16 ++++++++++--- man/HS.solution.Rd | 30 +++++++++--------------- man/IORE.solution.Rd | 17 ++++++++++---- man/SFO.solution.Rd | 23 ++++++++++++++---- man/SFORB.solution.Rd | 23 +++++++++--------- man/logistic.solution.Rd | 61 +++++++++++++++++++++++++++++++++++++++++++++--- 7 files changed, 143 insertions(+), 48 deletions(-) (limited to 'man') diff --git a/man/DFOP.solution.Rd b/man/DFOP.solution.Rd index b145984a..8ada60c5 100644 --- a/man/DFOP.solution.Rd +++ b/man/DFOP.solution.Rd @@ -1,15 +1,15 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/DFOP.solution.R +% Please edit documentation in R/parent_solutions.R \name{DFOP.solution} \alias{DFOP.solution} \title{Double First-Order in Parallel kinetics} \usage{ -DFOP.solution(t, parent.0, k1, k2, g) +DFOP.solution(t, parent_0, k1, k2, g) } \arguments{ \item{t}{Time.} -\item{parent.0}{Starting value for the response variable at time zero.} +\item{parent_0}{Starting value for the response variable at time zero.} \item{k1}{First kinetic constant.} @@ -36,4 +36,19 @@ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence 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{FOMC.solution}()}, +\code{\link{HS.solution}()}, +\code{\link{IORE.solution}()}, +\code{\link{SFO.solution}()}, +\code{\link{SFORB.solution}()}, +\code{\link{logistic.solution}()} } +\concept{parent solutions} diff --git a/man/FOMC.solution.Rd b/man/FOMC.solution.Rd index 54430dd1..d326f13a 100644 --- a/man/FOMC.solution.Rd +++ b/man/FOMC.solution.Rd @@ -1,15 +1,15 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/FOMC.solution.R +% Please edit documentation in R/parent_solutions.R \name{FOMC.solution} \alias{FOMC.solution} \title{First-Order Multi-Compartment kinetics} \usage{ -FOMC.solution(t, parent.0, alpha, beta) +FOMC.solution(t, parent_0, alpha, beta) } \arguments{ \item{t}{Time.} -\item{parent.0}{Starting value for the response variable at time zero.} +\item{parent_0}{Starting value for the response variable at time zero.} \item{alpha}{Shape parameter determined by coefficient of variation of rate constant values.} @@ -49,3 +49,13 @@ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence A new model based on spatial variability. \emph{Environmental Science and Technology} \bold{24}, 1032-1038 } +\seealso{ +Other parent solutions: +\code{\link{DFOP.solution}()}, +\code{\link{HS.solution}()}, +\code{\link{IORE.solution}()}, +\code{\link{SFO.solution}()}, +\code{\link{SFORB.solution}()}, +\code{\link{logistic.solution}()} +} +\concept{parent solutions} diff --git a/man/HS.solution.Rd b/man/HS.solution.Rd index ba96b139..343f83f0 100644 --- a/man/HS.solution.Rd +++ b/man/HS.solution.Rd @@ -1,27 +1,16 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/HS.solution.R +% Please edit documentation in R/parent_solutions.R \name{HS.solution} \alias{HS.solution} \title{Hockey-Stick kinetics} \usage{ -HS.solution(t, parent.0, k1, k2, tb) +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. @@ -31,10 +20,13 @@ 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} +\seealso{ +Other parent solutions: +\code{\link{DFOP.solution}()}, +\code{\link{FOMC.solution}()}, +\code{\link{IORE.solution}()}, +\code{\link{SFO.solution}()}, +\code{\link{SFORB.solution}()}, +\code{\link{logistic.solution}()} } +\concept{parent solutions} diff --git a/man/IORE.solution.Rd b/man/IORE.solution.Rd index ad2df3df..e1f1be1a 100644 --- a/man/IORE.solution.Rd +++ b/man/IORE.solution.Rd @@ -1,15 +1,15 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/IORE.solution.R +% Please edit documentation in R/parent_solutions.R \name{IORE.solution} \alias{IORE.solution} \title{Indeterminate order rate equation kinetics} \usage{ -IORE.solution(t, parent.0, k__iore, N) +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{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.} @@ -48,4 +48,13 @@ The solution of the IORE kinetic model reduces to the NAFTA Technical Working Group on Pesticides (not dated) Guidance for Evaluating and Calculating Degradation Kinetics in Environmental Media } -\keyword{manip} +\seealso{ +Other parent solutions: +\code{\link{DFOP.solution}()}, +\code{\link{FOMC.solution}()}, +\code{\link{HS.solution}()}, +\code{\link{SFO.solution}()}, +\code{\link{SFORB.solution}()}, +\code{\link{logistic.solution}()} +} +\concept{parent solutions} diff --git a/man/SFO.solution.Rd b/man/SFO.solution.Rd index 03c0dce8..6892cccc 100644 --- a/man/SFO.solution.Rd +++ b/man/SFO.solution.Rd @@ -1,17 +1,17 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/SFO.solution.R +% Please edit documentation in R/parent_solutions.R \name{SFO.solution} \alias{SFO.solution} \title{Single First-Order kinetics} \usage{ -SFO.solution(t, parent.0, k) +SFO.solution(t, parent_0, k) } \arguments{ \item{t}{Time.} -\item{parent.0}{Starting value for the response variable at time zero.} +\item{parent_0}{Starting value for the response variable at time zero.} -\item{k}{Kinetic constant.} +\item{k}{Kinetic rate constant.} } \value{ The value of the response variable at time \code{t}. @@ -30,4 +30,19 @@ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence 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}()}, +\code{\link{FOMC.solution}()}, +\code{\link{HS.solution}()}, +\code{\link{IORE.solution}()}, +\code{\link{SFORB.solution}()}, +\code{\link{logistic.solution}()} } +\concept{parent solutions} diff --git a/man/SFORB.solution.Rd b/man/SFORB.solution.Rd index ce9dce73..c70ce13b 100644 --- a/man/SFORB.solution.Rd +++ b/man/SFORB.solution.Rd @@ -1,16 +1,12 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/SFORB.solution.R +% Please edit documentation in R/parent_solutions.R \name{SFORB.solution} \alias{SFORB.solution} \title{Single First-Order Reversible Binding kinetics} \usage{ -SFORB.solution(t, parent.0, k_12, k_21, k_1output) +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.} @@ -34,10 +30,13 @@ 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} +\seealso{ +Other parent solutions: +\code{\link{DFOP.solution}()}, +\code{\link{FOMC.solution}()}, +\code{\link{HS.solution}()}, +\code{\link{IORE.solution}()}, +\code{\link{SFO.solution}()}, +\code{\link{logistic.solution}()} } +\concept{parent solutions} diff --git a/man/logistic.solution.Rd b/man/logistic.solution.Rd index def776aa..589ee8ec 100644 --- a/man/logistic.solution.Rd +++ b/man/logistic.solution.Rd @@ -1,30 +1,40 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/logistic.solution.R +% Please edit documentation in R/logistic.solution.R, 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) + +logistic.solution(t, parent_0, kmax, k0, r) } \arguments{ \item{t}{Time.} -\item{parent.0}{Starting value for the response variable at time zero.} +\item{parent_0}{Starting value for the response variable at time zero.} \item{kmax}{Maximum rate constant.} \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}. } \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}. } @@ -64,6 +74,41 @@ 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 (2014) \dQuote{Generic guidance for Estimating Persistence @@ -72,3 +117,13 @@ FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence Version 1.1, 18 December 2014 \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } +\seealso{ +Other parent solutions: +\code{\link{DFOP.solution}()}, +\code{\link{FOMC.solution}()}, +\code{\link{HS.solution}()}, +\code{\link{IORE.solution}()}, +\code{\link{SFO.solution}()}, +\code{\link{SFORB.solution}()} +} +\concept{parent solutions} -- cgit v1.2.1