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-rw-r--r--R/parent_solutions.R128
-rw-r--r--log/test.log40
-rw-r--r--man/FOMC.solution.Rd4
-rw-r--r--man/IORE.solution.Rd4
4 files changed, 88 insertions, 88 deletions
diff --git a/R/parent_solutions.R b/R/parent_solutions.R
index 04226b73..f11cbff9 100644
--- a/R/parent_solutions.R
+++ b/R/parent_solutions.R
@@ -7,7 +7,7 @@
#' @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
+#' @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,
@@ -25,33 +25,33 @@
#' @export
SFO.solution <- function(t, parent_0, k)
{
- parent = parent_0 * exp(-k * t)
+ 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
+#' @inherit SFO.solution
#' @param alpha Shape parameter determined by coefficient of variation of rate
-#' constant values.
+#' 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
+#' \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}
-#'
+#'
#' 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,
@@ -62,119 +62,119 @@ SFO.solution <- function(t, parent_0, k)
#' 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
+ 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
+#' @inherit SFO.solution
#' @param k__iore Rate constant. Note that this depends on the concentration
-#' units used.
+#' 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.
+#' \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
+#' 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$par,
+#'
+#' print(data.frame(fit.fomc$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,
+#' 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))
+ 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
+#' @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.
+#' 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)
+ 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 DFOP.solution
+#' @inherit DFOP.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}.
+#' \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)))
+ 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 SFO.solution
+#' @inherit SFO.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.
+#' fraction.
#' @return The value of the response variable, which is the sum of free and
-#' bound fractions at time \code{t}.
+#' 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)
+ sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 - 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
@@ -184,19 +184,19 @@ SFORB.solution = function(t, parent_0, k_12, k_21, k_1output) {
}
#' 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
+#' @inherit SFO.solution
#' @param kmax Maximum rate constant.
#' @param k0 Minimum 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}.
+#' \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),
@@ -213,10 +213,10 @@ SFORB.solution = function(t, parent_0, k_12, k_21, k_1output) {
#' 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,
@@ -225,14 +225,14 @@ SFORB.solution = function(t, parent_0, k_12, k_21, k_1output) {
#' 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)
+ parent = parent_0 * (kmax / (kmax - k0 + k0 * exp (r * t))) ^(kmax/r)
}
diff --git a/log/test.log b/log/test.log
index 95d50017..52b92245 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,53 +1,53 @@
ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
-✔ | 5 | Analytical solutions for coupled models [3.4s]
+✔ | 5 | Analytical solutions for coupled models [3.3s]
✔ | 5 | Calculation of Akaike weights
✔ | 3 | Export dataset for reading into CAKE
✔ | 12 | Confidence intervals and p-values [1.0s]
-✔ | 1 12 | Dimethenamid data from 2018 [33.0s]
+✔ | 1 12 | Dimethenamid data from 2018 [31.5s]
────────────────────────────────────────────────────────────────────────────────
Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data
Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
────────────────────────────────────────────────────────────────────────────────
-✔ | 14 | Error model fitting [5.6s]
+✔ | 14 | Error model fitting [4.9s]
✔ | 5 | Time step normalisation
✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s]
-✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9s]
+✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s]
✔ | 1 | Fitting the logistic model [0.2s]
-✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [26.9s]
+✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [23.7s]
✔ | 1 12 | Nonlinear mixed-effects models [0.3s]
────────────────────────────────────────────────────────────────────────────────
Skip (test_mixed.R:74:3): saemix results are reproducible for biphasic fits
Reason: Fitting with saemix takes around 10 minutes when using deSolve
────────────────────────────────────────────────────────────────────────────────
✔ | 3 | Test dataset classes mkinds and mkindsg
-✔ | 10 | Special cases of mkinfit calls [0.6s]
-✔ | 3 | mkinfit features [0.8s]
-✔ | 8 | mkinmod model generation and printing [0.3s]
-✔ | 3 | Model predictions with mkinpredict [0.4s]
-✔ | 7 | Multistart method for saem.mmkin models [44.7s]
-✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.8s]
-✔ | 9 | Nonlinear mixed-effects models with nlme [9.9s]
-✔ | 16 | Plotting [10.5s]
+✔ | 10 | Special cases of mkinfit calls [0.5s]
+✔ | 3 | mkinfit features [0.7s]
+✔ | 8 | mkinmod model generation and printing [0.2s]
+✔ | 3 | Model predictions with mkinpredict [0.3s]
+✔ | 7 | Multistart method for saem.mmkin models [36.3s]
+✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [8.9s]
+✔ | 16 | Plotting [10.0s]
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 1 37 | saemix parent models [76.1s]
+✔ | 1 37 | saemix parent models [72.0s]
────────────────────────────────────────────────────────────────────────────────
Skip (test_saemix_parent.R:153:3): We can also use mkin solution methods for saem
Reason: This still takes almost 2.5 minutes although we do not solve ODEs
────────────────────────────────────────────────────────────────────────────────
-✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
✔ | 11 | Processing of residue series
-✔ | 7 | Fitting the SFORB model [3.9s]
+✔ | 7 | Fitting the SFORB model [3.7s]
✔ | 1 | Summaries of old mkinfit objects
✔ | 5 | Summary [0.2s]
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s]
-✔ | 9 | Hypothesis tests [8.4s]
-✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
+✔ | 9 | Hypothesis tests [8.1s]
+✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 237.3 s
+Duration: 216.5 s
── Skipped tests ──────────────────────────────────────────────────────────────
• Fitting this ODE model with saemix takes about 15 minutes on my system (1)
diff --git a/man/FOMC.solution.Rd b/man/FOMC.solution.Rd
index eeee85f9..d645113c 100644
--- a/man/FOMC.solution.Rd
+++ b/man/FOMC.solution.Rd
@@ -30,8 +30,8 @@ in the original equation.
}
\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}.
+\code{\link{SFO.solution}} for large values of \code{alpha} and \code{beta}
+with \eqn{k = \frac{\beta}{\alpha}}{k = beta/alpha}.
}
\examples{
diff --git a/man/IORE.solution.Rd b/man/IORE.solution.Rd
index 1150f023..5d0126a7 100644
--- a/man/IORE.solution.Rd
+++ b/man/IORE.solution.Rd
@@ -37,9 +37,9 @@ guidance for details.
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,
+ 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)$distimes,
+ print(rbind(fomc = endpoints(fit.fomc)$distimes, iore = endpoints(fit.iore)$distimes,
iore.deS = endpoints(fit.iore)$distimes))
}

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