Another overhaul of analytical solutions

Still in preparation for analytical solutions of coupled models

1 files changed, 6 insertions, 46 deletions

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,