Static documentation rebuilt by pkgdown

7 files changed, 143 insertions, 48 deletions

diff --git a/man/DFOP.solution.Rd b/man/DFOP.solution.Rd
index b145984a..8ada60c5 100644
--- a/man/DFOP.solution.Rd
+++ b/man/DFOP.solution.Rd
@@ -1,15 +1,15 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DFOP.solution.R
+% Please edit documentation in R/parent_solutions.R
 \name{DFOP.solution}
 \alias{DFOP.solution}
 \title{Double First-Order in Parallel kinetics}
 \usage{
-DFOP.solution(t, parent.0, k1, k2, g)
+DFOP.solution(t, parent_0, k1, k2, g)
 }
 \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{k1}{First kinetic constant.}
 
@@ -36,4 +36,19 @@ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence
   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{FOMC.solution}()},
+\code{\link{HS.solution}()},
+\code{\link{IORE.solution}()},
+\code{\link{SFO.solution}()},
+\code{\link{SFORB.solution}()},
+\code{\link{logistic.solution}()}
 }
+\concept{parent solutions}
diff --git a/man/FOMC.solution.Rd b/man/FOMC.solution.Rd
index 54430dd1..d326f13a 100644
--- a/man/FOMC.solution.Rd
+++ b/man/FOMC.solution.Rd
@@ -1,15 +1,15 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/FOMC.solution.R
+% Please edit documentation in R/parent_solutions.R
 \name{FOMC.solution}
 \alias{FOMC.solution}
 \title{First-Order Multi-Compartment kinetics}
 \usage{
-FOMC.solution(t, parent.0, alpha, beta)
+FOMC.solution(t, parent_0, alpha, beta)
 }
 \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{alpha}{Shape parameter determined by coefficient of variation of rate
 constant values.}
@@ -49,3 +49,13 @@ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence
   A new model based on spatial variability. \emph{Environmental Science and
   Technology} \bold{24}, 1032-1038
 }
+\seealso{
+Other parent solutions: 
+\code{\link{DFOP.solution}()},
+\code{\link{HS.solution}()},
+\code{\link{IORE.solution}()},
+\code{\link{SFO.solution}()},
+\code{\link{SFORB.solution}()},
+\code{\link{logistic.solution}()}
+}
+\concept{parent solutions}
diff --git a/man/HS.solution.Rd b/man/HS.solution.Rd
index ba96b139..343f83f0 100644
--- a/man/HS.solution.Rd
+++ b/man/HS.solution.Rd
@@ -1,27 +1,16 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/HS.solution.R
+% Please edit documentation in R/parent_solutions.R
 \name{HS.solution}
 \alias{HS.solution}
 \title{Hockey-Stick kinetics}
 \usage{
-HS.solution(t, parent.0, k1, k2, tb)
+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.
@@ -31,10 +20,13 @@ 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}
+\seealso{
+Other parent solutions: 
+\code{\link{DFOP.solution}()},
+\code{\link{FOMC.solution}()},
+\code{\link{IORE.solution}()},
+\code{\link{SFO.solution}()},
+\code{\link{SFORB.solution}()},
+\code{\link{logistic.solution}()}
 }
+\concept{parent solutions}
diff --git a/man/IORE.solution.Rd b/man/IORE.solution.Rd
index ad2df3df..e1f1be1a 100644
--- a/man/IORE.solution.Rd
+++ b/man/IORE.solution.Rd
@@ -1,15 +1,15 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/IORE.solution.R
+% Please edit documentation in R/parent_solutions.R
 \name{IORE.solution}
 \alias{IORE.solution}
 \title{Indeterminate order rate equation kinetics}
 \usage{
-IORE.solution(t, parent.0, k__iore, N)
+IORE.solution(t, parent_0, k__iore, N)
 }
 \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{k__iore}{Rate constant. Note that this depends on the concentration
 units used.}
@@ -48,4 +48,13 @@ The solution of the IORE kinetic model reduces to the
 NAFTA Technical Working Group on Pesticides (not dated) Guidance
   for Evaluating and Calculating Degradation Kinetics in Environmental Media
 }
-\keyword{manip}
+\seealso{
+Other parent solutions: 
+\code{\link{DFOP.solution}()},
+\code{\link{FOMC.solution}()},
+\code{\link{HS.solution}()},
+\code{\link{SFO.solution}()},
+\code{\link{SFORB.solution}()},
+\code{\link{logistic.solution}()}
+}
+\concept{parent solutions}
diff --git a/man/SFO.solution.Rd b/man/SFO.solution.Rd
index 03c0dce8..6892cccc 100644
--- a/man/SFO.solution.Rd
+++ b/man/SFO.solution.Rd
@@ -1,17 +1,17 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/SFO.solution.R
+% Please edit documentation in R/parent_solutions.R
 \name{SFO.solution}
 \alias{SFO.solution}
 \title{Single First-Order kinetics}
 \usage{
-SFO.solution(t, parent.0, k)
+SFO.solution(t, parent_0, k)
 }
 \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{k}{Kinetic constant.}
+\item{k}{Kinetic rate constant.}
 }
 \value{
 The value of the response variable at time \code{t}.
@@ -30,4 +30,19 @@ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence
   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}()},
+\code{\link{FOMC.solution}()},
+\code{\link{HS.solution}()},
+\code{\link{IORE.solution}()},
+\code{\link{SFORB.solution}()},
+\code{\link{logistic.solution}()}
 }
+\concept{parent solutions}
diff --git a/man/SFORB.solution.Rd b/man/SFORB.solution.Rd
index ce9dce73..c70ce13b 100644
--- a/man/SFORB.solution.Rd
+++ b/man/SFORB.solution.Rd
@@ -1,16 +1,12 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/SFORB.solution.R
+% Please edit documentation in R/parent_solutions.R
 \name{SFORB.solution}
 \alias{SFORB.solution}
 \title{Single First-Order Reversible Binding kinetics}
 \usage{
-SFORB.solution(t, parent.0, k_12, k_21, k_1output)
+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.}
@@ -34,10 +30,13 @@ 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}
+\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{logistic.solution}()}
 }
+\concept{parent solutions}
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
@@ -1,21 +1,25 @@
 % 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}.
@@ -23,10 +27,16 @@ 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{
 
@@ -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}