From b60e5b27d3dde18fb93b486bc2fd45baf56e2ed1 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 26 Jun 2015 12:11:39 +0200
Subject: More plotting in help files, fix Make- and .*ignore files

---
 man/DFOP.solution.Rd |  2 +-
 man/FOMC.solution.Rd |  2 +-
 man/HS.solution.Rd   |  2 +-
 man/mkinresplot.Rd   | 13 +++----------
 man/plot.mkinfit.Rd  | 10 ++++------
 man/plot.mmkin.Rd    |  3 ++-
 6 files changed, 12 insertions(+), 20 deletions(-)

(limited to 'man')

diff --git a/man/DFOP.solution.Rd b/man/DFOP.solution.Rd
index 2d8b1735..2bf2a26c 100644
--- a/man/DFOP.solution.Rd
+++ b/man/DFOP.solution.Rd
@@ -31,6 +31,6 @@ DFOP.solution(t, parent.0, k1, k2, g)
   \url{http://focus.jrc.ec.europa.eu/dk} 
 }
 \examples{
-  \dontrun{plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim=c(0,100))}
+  plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim=c(0,100))
 }
 \keyword{ manip }
diff --git a/man/FOMC.solution.Rd b/man/FOMC.solution.Rd
index f4a26e41..d9c4ccae 100644
--- a/man/FOMC.solution.Rd
+++ b/man/FOMC.solution.Rd
@@ -44,6 +44,6 @@ FOMC.solution(t, parent.0, alpha, beta)
   Technology} \bold{24}, 1032-1038
 }
 \examples{
-  \dontrun{plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100))}
+  plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100))
 }
 \keyword{ manip }
diff --git a/man/HS.solution.Rd b/man/HS.solution.Rd
index 71f68a1e..5666bb43 100644
--- a/man/HS.solution.Rd
+++ b/man/HS.solution.Rd
@@ -29,6 +29,6 @@ HS.solution(t, parent.0, k1, k2, tb)
   \url{http://focus.jrc.ec.europa.eu/dk} 
 }
 \examples{
-  \dontrun{plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))}
+  plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))
 }
 \keyword{ manip }
diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd
index 59d19274..eaa861f4 100644
--- a/man/mkinresplot.Rd
+++ b/man/mkinresplot.Rd
@@ -53,19 +53,12 @@
 \author{
   Johannes Ranke
 }
-
 \seealso{
  \code{\link{mkinplot}}, for a way to plot the data and the fitted lines of the
  mkinfit object.  }
 \examples{
-data <- mkin_wide_to_long(schaefer07_complex_case, time = "time")
-model <- mkinmod(
-  parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),
-  A1 = list(type = "SFO", to = "A2"),
-  B1 = list(type = "SFO"),
-  C1 = list(type = "SFO"),
-  A2 = list(type = "SFO"))
-\dontrun{fit <- mkinfit(model, data, plot=TRUE)}
-\dontrun{mkinresplot(fit, "A1")}
+model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
+fit <- mkinfit(model, FOCUS_2006_D)
+mkinresplot(fit, "m1")
 }
 \keyword{ hplot }
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index 7009e7d7..816d7e1c 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -80,13 +80,11 @@
   The function is called for its side effect.
 }
 \examples{
-# One parent compound, one metabolite, both single first order.
-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
+# 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)
-\dontrun{plot(fit)}
+plot(fit)
 }
 \author{
   Johannes Ranke
diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd
index 4f78de2c..a715fdea 100644
--- a/man/plot.mmkin.Rd
+++ b/man/plot.mmkin.Rd
@@ -45,6 +45,7 @@
   Johannes Ranke
 }
 \examples{
-  fits <- mmkin(c("SFO", "FOMC"), list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C))
+  fits <- mmkin(c("SFO", "FOMC", "HS"), list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C))
   plot(fits[, "FOCUS C"])
+  plot(fits["FOMC", ])
 }
-- 
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