2 files changed, 42 insertions, 35 deletions
diff --git a/man/mccall81_245T.Rd b/man/mccall81_245T.Rd
new file mode 100644
index 0000000..6c1a137
--- /dev/null
+++ b/man/mccall81_245T.Rd
@@ -0,0 +1,42 @@
+\name{mccall81_245T}
+\alias{mccall81_245T}
+\docType{data}
+\title{
+  Datasets on aerobic soil metabolism of 2,4,5-T in six soils
+}
+\description{
+ Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding
+ 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether
+ extracts.
+}
+\usage{mccall81_245T}
+\format{
+  A dataframe containing the following variables.
+  \describe{
+    \item{\code{name}}{the name of the compound observed. Note that T245 is used as 
+                       an acronym for 2,4,5-T. T245 is a legitimate object name
+                       in R, which is necessary for specifying models using
+                       \code{\link{mkinmod}}.} 
+    \item{\code{time}}{a numeric vector containing sampling times in days after
+                       treatment}
+    \item{\code{value}}{a numeric vector containing concentrations in percent of applied radioactivity}
+    \item{\code{soil}}{a factor containing the name of the soil}
+  }
+}
+\source{
+  McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107
+  \url{http://dx.doi.org/10.1021/jf00103a026}
+}
+\examples{
+  SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"),
+                         phenol = list(type = "SFO", to = "anisole"),
+                         anisole = list(type = "SFO"))
+  \dontrun{fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))
+  summary(fit.1, data = FALSE)}
+  # No covariance matrix and k_phenol_sink is really small, therefore fix it to zero
+  fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),
+                 parms.ini = c(k_phenol_sink = 0),
+                 fixed_parms = "k_phenol_sink")
+  summary(fit.2, data = FALSE)
+}
+\keyword{datasets}
diff --git a/man/mccall81_245T_soil_metabolism.Rd b/man/mccall81_245T_soil_metabolism.Rd
deleted file mode 100644
index 2ccc23d..0000000
--- a/man/mccall81_245T_soil_metabolism.Rd
+++ /dev/null
@@ -1,35 +0,0 @@
-\name{mccall81_245T_soil_metabolism}
-\Rdversion{1.1}
-\alias{commerce}
-\alias{catlin}
-\alias{fargo}
-\alias{keith}
-\alias{walla_walla}
-\alias{cecil}
-\docType{data}
-\title{
-  Datasets on aerobic soil metabolism of 2,4,5-T in six soils
-}
-\description{
- Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding 2,4,5-trichlorophenol and 
- 2,4,5-trichloroanisole as recovered in diethylether extracts.
-}
-\usage{mccall81_245T_soil_metabolism}
-\format{
-  6 dataframes containing the following variables.
-  \describe{
-    \item{\code{name}}{the name of the compound observed. Note that T245 is used as an acronym for 2,4,5-T. T245 is 
-                       a legitimate object name in R, which is necessary for
-                       specifying models using \code{\link{mkinmod}}.}
-    \item{\code{time}}{a numeric vector containing sampling times in days after treatment}
-    \item{\code{value}}{a numeric vector containing concentrations in percent of applied radioactivity}
-  }
-}
-\source{
-  McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107
-  \url{http://dx.doi.org/10.1021/jf00103a026}
-}
-\examples{
-  commerce
-}
-\keyword{datasets}