diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/HS.solution.Rd | 23 | ||||
| -rw-r--r-- | man/SFORB.solution.Rd | 16 | ||||
| -rw-r--r-- | man/create_deg_func.Rd | 26 | ||||
| -rw-r--r-- | man/logistic.solution.Rd | 52 | ||||
| -rw-r--r-- | man/mkinmod.Rd | 2 | ||||
| -rw-r--r-- | man/mkinpredict.Rd | 22 | ||||
| -rw-r--r-- | man/nlme.Rd | 6 |
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") |