diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/DFOP.solution.R | 27 | ||||
| -rw-r--r-- | R/FOMC.solution.R | 36 | ||||
| -rw-r--r-- | R/HS.solution.R | 29 | ||||
| -rw-r--r-- | R/IORE.solution.R | 37 | ||||
| -rw-r--r-- | R/SFO.solution.R | 22 | ||||
| -rw-r--r-- | R/SFORB.solution.R | 35 | ||||
| -rw-r--r-- | R/parent_solutions.R | 231 |
7 files changed, 231 insertions, 186 deletions
diff --git a/R/DFOP.solution.R b/R/DFOP.solution.R deleted file mode 100644 index 608e7e18..00000000 --- a/R/DFOP.solution.R +++ /dev/null @@ -1,27 +0,0 @@ -#' Double First-Order in Parallel kinetics -#' -#' Function describing decline from a defined starting value using the sum of -#' two exponential decline functions. -#' -#' @param t Time. -#' @param parent.0 Starting value for the response variable at time zero. -#' @param k1 First kinetic constant. -#' @param k2 Second kinetic constant. -#' @param g Fraction of the starting value declining according to the first -#' kinetic constant. -#' @return The value of the response variable at time \code{t}. -#' @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} -#' @examples -#' -#' plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim = c(0,100)) -#' -#' @export -DFOP.solution <- function(t, parent.0, k1, k2, g) -{ - parent = g * parent.0 * exp(-k1 * t) + - (1 - g) * parent.0 * exp(-k2 * t) -} diff --git a/R/FOMC.solution.R b/R/FOMC.solution.R deleted file mode 100644 index f5e6a7ea..00000000 --- a/R/FOMC.solution.R +++ /dev/null @@ -1,36 +0,0 @@ -#' First-Order Multi-Compartment kinetics -#' -#' Function describing exponential decline from a defined starting value, with -#' a decreasing rate constant. -#' -#' The form given here differs slightly from the original reference by -#' Gustafson and Holden (1990). The parameter \code{beta} corresponds to 1/beta -#' in the original equation. -#' -#' @param t Time. -#' @param parent.0 Starting value for the response variable at time zero. -#' @param alpha Shape parameter determined by coefficient of variation of rate -#' constant values. -#' @param beta Location parameter. -#' @return The value of the response variable at time \code{t}. -#' @note The solution of the FOMC kinetic model reduces to the -#' \code{\link{SFO.solution}} for large values of \code{alpha} and -#' \code{beta} with \eqn{k = \frac{\beta}{\alpha}}{k = beta/alpha}. -#' @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} -#' -#' Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: -#' A new model based on spatial variability. \emph{Environmental Science and -#' Technology} \bold{24}, 1032-1038 -#' @examples -#' -#' plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100)) -#' -#' @export -FOMC.solution <- function(t, parent.0, alpha, beta) -{ - parent = parent.0 / (t/beta + 1)^alpha -} diff --git a/R/HS.solution.R b/R/HS.solution.R deleted file mode 100644 index 890ad8ff..00000000 --- a/R/HS.solution.R +++ /dev/null @@ -1,29 +0,0 @@ -#' Hockey-Stick kinetics -#' -#' Function describing two exponential decline functions with a break point -#' between them. -#' -#' @param t Time. -#' @param parent.0 Starting value for the response variable at time zero. -#' @param k1 First kinetic constant. -#' @param k2 Second kinetic constant. -#' @param tb Break point. Before this time, exponential decline according to -#' \code{k1} is calculated, after this time, exponential decline proceeds -#' according to \code{k2}. -#' @return The value of the response variable at time \code{t}. -#' @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} -#' @examples -#' -#' plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100)) -#' -#' @export -HS.solution <- function(t, parent.0, k1, k2, tb) -{ - parent = ifelse(t <= tb, - parent.0 * exp(-k1 * t), - parent.0 * exp(-k1 * tb) * exp(-k2 * (t - tb))) -} diff --git a/R/IORE.solution.R b/R/IORE.solution.R deleted file mode 100644 index 58807108..00000000 --- a/R/IORE.solution.R +++ /dev/null @@ -1,37 +0,0 @@ -#' Indeterminate order rate equation kinetics -#' -#' Function describing exponential decline from a defined starting value, with -#' a concentration dependent rate constant. -#' -#' @param t Time. -#' @param parent.0 Starting value for the response variable at time zero. -#' @param k__iore Rate constant. Note that this depends on the concentration -#' units used. -#' @param N Exponent describing the nonlinearity of the rate equation -#' @return The value of the response variable at time \code{t}. -#' @note The solution of the IORE kinetic model reduces to the -#' \code{\link{SFO.solution}} if N = 1. The parameters of the IORE model can -#' be transformed to equivalent parameters of the FOMC mode - see the NAFTA -#' guidance for details. -#' @references NAFTA Technical Working Group on Pesticides (not dated) Guidance -#' for Evaluating and Calculating Degradation Kinetics in Environmental Media -#' @keywords manip -#' @examples -#' -#' plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2, ylim = c(0, 100)) -#' \dontrun{ -#' fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) -#' fit.iore <- mkinfit("IORE", FOCUS_2006_C, quiet = TRUE) -#' fit.iore.deS <- mkinfit("IORE", FOCUS_2006_C, solution_type = "deSolve", quiet = TRUE) -#' -#' print(data.frame(fit.fomc$par, fit.iore$par, fit.iore.deS$par, -#' row.names = paste("model par", 1:4))) -#' print(rbind(fomc = endpoints(fit.fomc)$distimes, iore = endpoints(fit.iore)$distimes, -#' iore.deS = endpoints(fit.iore)$distimes)) -#' } -#' -#' @export -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/SFO.solution.R b/R/SFO.solution.R deleted file mode 100644 index 17c16a4d..00000000 --- a/R/SFO.solution.R +++ /dev/null @@ -1,22 +0,0 @@ -#' Single First-Order kinetics -#' -#' Function describing exponential decline from a defined starting value. -#' -#' @param t Time. -#' @param parent.0 Starting value for the response variable at time zero. -#' @param k Kinetic constant. -#' @return The value of the response variable at time \code{t}. -#' @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} -#' @examples -#' -#' \dontrun{plot(function(x) SFO.solution(x, 100, 3), 0, 2)} -#' -#' @export -SFO.solution <- function(t, parent.0, k) -{ - parent = parent.0 * exp(-k * t) -} diff --git a/R/SFORB.solution.R b/R/SFORB.solution.R deleted file mode 100644 index 2abe4577..00000000 --- a/R/SFORB.solution.R +++ /dev/null @@ -1,35 +0,0 @@ -#' Single First-Order Reversible Binding kinetics -#' -#' Function describing the solution of the differential equations describing -#' the kinetic model with first-order terms for a two-way transfer from a free -#' to a bound fraction, and a first-order degradation term for the free -#' fraction. The initial condition is a defined amount in the free fraction -#' and no substance in the bound fraction. -#' -#' @param t Time. -#' @param parent.0 Starting value for the response variable at time zero. -#' @param k_12 Kinetic constant describing transfer from free to bound. -#' @param k_21 Kinetic constant describing transfer from bound to free. -#' @param k_1output Kinetic constant describing degradation of the free -#' fraction. -#' @return The value of the response variable, which is the sum of free and -#' bound fractions at time \code{t}. -#' @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} -#' @examples -#' -#' \dontrun{plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)} -#' -#' @export -SFORB.solution = function(t, parent.0, k_12, k_21, k_1output) { - sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 + k_12 * k_21 - (k_12 + k_1output) * k_21) - b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp - b2 = 0.5 * (k_12 + k_21 + k_1output) - sqrt_exp - - parent = parent.0 * - (((k_12 + k_21 - b1)/(b2 - b1)) * exp(-b1 * t) + - ((k_12 + k_21 - b2)/(b1 - b2)) * exp(-b2 * t)) -} diff --git a/R/parent_solutions.R b/R/parent_solutions.R new file mode 100644 index 00000000..f3d3e963 --- /dev/null +++ b/R/parent_solutions.R @@ -0,0 +1,231 @@ +#' Single First-Order kinetics +#' +#' Function describing exponential decline from a defined starting value. +#' +#' @family parent solutions +#' @param t Time. +#' @param parent_0 Starting value for the response variable at time zero. +#' @param k Kinetic rate constant. +#' @return The value of the response variable at time \code{t}. +#' @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} +#' @examples +#' +#' \dontrun{plot(function(x) SFO.solution(x, 100, 3), 0, 2)} +#' +#' @export +SFO.solution <- function(t, parent_0, k) +{ + parent = parent_0 * exp(-k * t) +} + +#' First-Order Multi-Compartment kinetics +#' +#' Function describing exponential decline from a defined starting value, with +#' a decreasing rate constant. +#' +#' The form given here differs slightly from the original reference by +#' Gustafson and Holden (1990). The parameter \code{beta} corresponds to 1/beta +#' in the original equation. +#' +#' @family parent solutions +#' @inherit SFO.solution +#' @param alpha Shape parameter determined by coefficient of variation of rate +#' constant values. +#' @param beta Location parameter. +#' @note The solution of the FOMC kinetic model reduces to the +#' \code{\link{SFO.solution}} for large values of \code{alpha} and +#' \code{beta} with \eqn{k = \frac{\beta}{\alpha}}{k = beta/alpha}. +#' @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} +#' +#' Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: +#' A new model based on spatial variability. \emph{Environmental Science and +#' Technology} \bold{24}, 1032-1038 +#' @examples +#' +#' plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100)) +#' +#' @export +FOMC.solution <- function(t, parent_0, alpha, beta) +{ + parent = parent_0 / (t/beta + 1)^alpha +} + +#' Indeterminate order rate equation kinetics +#' +#' Function describing exponential decline from a defined starting value, with +#' a concentration dependent rate constant. +#' +#' @family parent solutions +#' @inherit SFO.solution +#' @param k__iore Rate constant. Note that this depends on the concentration +#' units used. +#' @param 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. The parameters of the IORE model can +#' be transformed to equivalent parameters of the FOMC mode - see the NAFTA +#' guidance for details. +#' @references NAFTA Technical Working Group on Pesticides (not dated) Guidance +#' for Evaluating and Calculating Degradation Kinetics in Environmental Media +#' @examples +#' +#' plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2, ylim = c(0, 100)) +#' \dontrun{ +#' fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) +#' fit.iore <- mkinfit("IORE", FOCUS_2006_C, quiet = TRUE) +#' fit.iore.deS <- mkinfit("IORE", FOCUS_2006_C, solution_type = "deSolve", quiet = TRUE) +#' +#' print(data.frame(fit.fomc$par, fit.iore$par, fit.iore.deS$par, +#' row.names = paste("model par", 1:4))) +#' print(rbind(fomc = endpoints(fit.fomc)$distimes, iore = endpoints(fit.iore)$distimes, +#' iore.deS = endpoints(fit.iore)$distimes)) +#' } +#' +#' @export +IORE.solution <- function(t, parent_0, k__iore, N) +{ + parent = (parent_0^(1 - N) - (1 - N) * k__iore * t)^(1/(1 - N)) +} + +#' Double First-Order in Parallel kinetics +#' +#' Function describing decline from a defined starting value using the sum of +#' two exponential decline functions. +#' +#' @family parent solutions +#' @inherit SFO.solution +#' @param t Time. +#' @param k1 First kinetic constant. +#' @param k2 Second kinetic constant. +#' @param g Fraction of the starting value declining according to the first +#' kinetic constant. +#' @examples +#' +#' plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim = c(0,100)) +#' +#' @export +DFOP.solution <- function(t, parent_0, k1, k2, g) +{ + parent = g * parent_0 * exp(-k1 * t) + + (1 - g) * parent_0 * exp(-k2 * t) +} + +#' Hockey-Stick kinetics +#' +#' Function describing two exponential decline functions with a break point +#' between them. +#' +#' @family parent solutions +#' @inherit HS.solution +#' @param tb Break point. Before this time, exponential decline according to +#' \code{k1} is calculated, after this time, exponential decline proceeds +#' according to \code{k2}. +#' @examples +#' +#' plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100)) +#' +#' @export +HS.solution <- function(t, parent_0, k1, k2, tb) +{ + parent = ifelse(t <= tb, + parent_0 * exp(-k1 * t), + parent_0 * exp(-k1 * tb) * exp(-k2 * (t - tb))) +} + +#' Single First-Order Reversible Binding kinetics +#' +#' Function describing the solution of the differential equations describing +#' the kinetic model with first-order terms for a two-way transfer from a free +#' to a bound fraction, and a first-order degradation term for the free +#' fraction. The initial condition is a defined amount in the free fraction +#' and no substance in the bound fraction. +#' +#' @family parent solutions +#' @inherit HS.solution +#' @param k_12 Kinetic constant describing transfer from free to bound. +#' @param k_21 Kinetic constant describing transfer from bound to free. +#' @param k_1output Kinetic constant describing degradation of the free +#' fraction. +#' @return The value of the response variable, which is the sum of free and +#' bound fractions at time \code{t}. +#' @examples +#' +#' \dontrun{plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)} +#' +#' @export +SFORB.solution = function(t, parent_0, k_12, k_21, k_1output) { + sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 + k_12 * k_21 - (k_12 + k_1output) * k_21) + b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp + b2 = 0.5 * (k_12 + k_21 + k_1output) - sqrt_exp + + parent = parent_0 * + (((k_12 + k_21 - b1)/(b2 - b1)) * exp(-b1 * t) + + ((k_12 + k_21 - b2)/(b1 - b2)) * exp(-b2 * t)) +} + +#' Logistic kinetics +#' +#' Function describing exponential decline from a defined starting value, with +#' an increasing rate constant, supposedly caused by microbial growth +#' +#' @family parent solutions +#' @inherit SFO.solution +#' @param kmax Maximum rate constant. +#' @param k0 Minumum rate constant effective at time zero. +#' @param r Growth rate of the increase in the rate constant. +#' @note The solution of the logistic model reduces to the +#' \code{\link{SFO.solution}} if \code{k0} is equal to \code{kmax}. +#' @examples +#' +#' # 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 +#' +#' @export +logistic.solution <- function(t, parent_0, kmax, k0, r) +{ + parent = parent_0 * (kmax / (kmax - k0 + k0 * exp (r * t))) ^(kmax/r) +} |