From 164c4af404b59f9144f68fcefeeac34326a34372 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 29 Jun 2015 08:40:19 +0200
Subject: Quiet fitting in examples and more links for static docs.

---
 man/Extract.mmkin.Rd      | 5 +++--
 man/mccall81_245T.Rd      | 2 +-
 man/mkinfit.Rd            | 7 +++++++
 man/mkinresplot.Rd        | 2 +-
 man/mmkin.Rd              | 7 +++++--
 man/plot.mkinfit.Rd       | 2 +-
 man/plot.mmkin.Rd         | 2 +-
 man/summary.mkinfit.Rd    | 4 ++--
 man/transform_odeparms.Rd | 2 +-
 9 files changed, 22 insertions(+), 11 deletions(-)

(limited to 'man')

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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