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authorJohannes Ranke <jranke@uni-bremen.de>2015-06-29 08:40:19 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-06-29 09:40:46 +0200
commit164c4af404b59f9144f68fcefeeac34326a34372 (patch)
tree24001a99d1f505e5f299a541e6a233b25c3ad6db /man
parent79c7da1992b1013a8809eaf6ad60103c2fc45611 (diff)
Quiet fitting in examples and more links for static docs.
Diffstat (limited to 'man')
-rw-r--r--man/Extract.mmkin.Rd5
-rw-r--r--man/mccall81_245T.Rd2
-rw-r--r--man/mkinfit.Rd7
-rw-r--r--man/mkinresplot.Rd2
-rw-r--r--man/mmkin.Rd7
-rw-r--r--man/plot.mkinfit.Rd2
-rw-r--r--man/plot.mmkin.Rd2
-rw-r--r--man/summary.mkinfit.Rd4
-rw-r--r--man/transform_odeparms.Rd2
9 files changed, 22 insertions, 11 deletions
diff --git a/man/Extract.mmkin.Rd b/man/Extract.mmkin.Rd
index 361da3e4..cd40e247 100644
--- a/man/Extract.mmkin.Rd
+++ b/man/Extract.mmkin.Rd
@@ -26,8 +26,9 @@
Johannes Ranke
}
\examples{
- # Only use one core so we pass R CMD check
- fits <- mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C), cores = 1)
+ # Only use one core, to pass R CMD check --as-cran
+ fits <- mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C),
+ cores = 1, quiet = TRUE)
fits["FOMC", ]
fits[, "B"]
fits[, "B", drop = TRUE]$FOMC
diff --git a/man/mccall81_245T.Rd b/man/mccall81_245T.Rd
index a2618d51..7cc5c363 100644
--- a/man/mccall81_245T.Rd
+++ b/man/mccall81_245T.Rd
@@ -38,7 +38,7 @@
# 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")
+ fixed_parms = "k_phenol_sink", quiet = TRUE)
summary(fit.2, data = FALSE)
}
\keyword{datasets}
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index c6b6d601..8f65717a 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -216,6 +216,13 @@ mkinfit(mkinmod, observed,
A list with "mkinfit" and "modFit" in the class attribute.
A summary can be obtained by \code{\link{summary.mkinfit}}.
}
+\seealso{
+ Plotting methods \code{\link{plot.mkinfit}} and
+ \code{\link{mkinparplot}}.
+
+ Fitting of several models to several datasets in a single call to
+ \code{\link{mmkin}}.
+}
\note{
The implementation of iteratively reweighted least squares is inspired by the
work of the KinGUII team at Bayer Crop Science (Walter Schmitt and Zhenglei
diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd
index eaa861f4..cdcfbd37 100644
--- a/man/mkinresplot.Rd
+++ b/man/mkinresplot.Rd
@@ -58,7 +58,7 @@
mkinfit object. }
\examples{
model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
-fit <- mkinfit(model, FOCUS_2006_D)
+fit <- mkinfit(model, FOCUS_2006_D, quiet = TRUE)
mkinresplot(fit, "m1")
}
\keyword{ hplot }
diff --git a/man/mmkin.Rd b/man/mmkin.Rd
index 4859d658..f701890a 100644
--- a/man/mmkin.Rd
+++ b/man/mmkin.Rd
@@ -34,8 +34,11 @@ mmkin(models, datasets,
}
}
\value{
- A matrix of "mkinfit" objects that can be indexed using the
- model and dataset names as row and column indices.
+ A matrix of \code{\link{mkinfit}} objects that can be indexed using the model
+ and dataset names as row and column indices.
+}
+\seealso{
+ \code{\link{[.mmkin}} for subsetting, \code{\link{plot.mmkin}} for plotting.
}
\author{
Johannes Ranke
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index 816d7e1c..be3de9fd 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -83,7 +83,7 @@
# One parent compound, one metabolite, both single first order, path from
# parent to sink included
SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D)
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
plot(fit)
}
\author{
diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd
index 696b3d06..a3367234 100644
--- a/man/plot.mmkin.Rd
+++ b/man/plot.mmkin.Rd
@@ -47,7 +47,7 @@
\examples{
# Only use one core not to offend CRAN checks
fits <- mmkin(c("FOMC", "HS"), list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C),
- cores = 1)
+ cores = 1, quiet = TRUE)
plot(fits[, "FOCUS C"])
plot(fits["FOMC", ])
}
diff --git a/man/summary.mkinfit.Rd b/man/summary.mkinfit.Rd
index 472b5dec..746d9886 100644
--- a/man/summary.mkinfit.Rd
+++ b/man/summary.mkinfit.Rd
@@ -67,9 +67,9 @@
\url{http://focus.jrc.ec.europa.eu/dk}
}
\author{
- Johannes Ranke <jranke@{harlan.com,uni-bremen.de}>
+ Johannes Ranke
}
\examples{
- summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A))
+ summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
}
\keyword{ utilities }
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
index cc1d1611..c6034424 100644
--- a/man/transform_odeparms.Rd
+++ b/man/transform_odeparms.Rd
@@ -65,7 +65,7 @@ SFO_SFO <- mkinmod(
parent = list(type = "SFO", to = "m1", sink = TRUE),
m1 = list(type = "SFO"))
# Fit the model to the FOCUS example dataset D using defaults
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D)
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
summary(fit, data=FALSE) # See transformed and backtransformed parameters
\dontrun{

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