From 8bdb4cd437a9d4663e542f95869e8692aa38dadb Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 7 May 2020 08:59:29 +0200
Subject: Static documentation rebuilt by pkgdown

---
 man/logistic.solution.Rd | 61 +++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 58 insertions(+), 3 deletions(-)

(limited to 'man/logistic.solution.Rd')

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}
-- 
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