More plotting in help files, fix Make- and .*ignore files

9 files changed, 18 insertions, 25 deletions

diff --git a/.Rbuildignore b/.Rbuildignore
index 19668a0c..d9977a5f 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -2,6 +2,7 @@ GNUmakefile
 README.Rmd
 gmkin_screenshot.png
 ^inst/web$
+^vignettes/.build.timestamp$
 ^vignettes/*.out$
 ^vignettes/*.toc$
 ^vignettes/*.bbl$
diff --git a/.gitignore b/.gitignore
index 755e8142..dd37d0d3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,4 @@
 README.html
-inst/web*
 vignettes/.build.timestamp
 vignettes/*.aux
 vignettes/*.bbl
diff --git a/GNUmakefile b/GNUmakefile
index 1daff86e..19658a85 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -72,7 +72,7 @@ clean:
 	$(RM) -r vignettes/*.syntex.gz
 	$(RM) Rplots.pdf
 
-test: install-no-vignettes
+test: quickinstall
 	cd tests;\
 		"$(RBIN)/Rscript" testthat.R 2>&1 | tee ../test.log
 
@@ -82,12 +82,13 @@ vignettes/%.pdf: vignettes/header.tex vignettes/references.bib vignettes/%.Rnw
 vignettes/%.html: vignettes/mkin_vignettes.css vignettes/%.Rmd
 	"$(RBIN)/Rscript" -e "tools::buildVignette(file = 'vignettes/$*.Rmd', dir = 'vignettes')"
 
-vignettes: install-no-vignettes vignettes/mkin.pdf vignettes/FOCUS_D.html vignettes/FOCUS_L.html vignettes/FOCUS_Z.pdf vignettes/compiled_models.html
+vignettes: quickinstall vignettes/mkin.pdf vignettes/FOCUS_D.html vignettes/FOCUS_L.html vignettes/FOCUS_Z.pdf vignettes/compiled_models.html
 
 sd:
 	rm -rf $(SDDIR)/*
-	"$(RBIN)/Rscript" -e "library(staticdocs); build_site(site_path = '$(SDDIR)')"
-	$(RM) $(SDDIR)/Rplots.pdf
+	@echo Now execute
+	@echo "\nlibrary(staticdocs); build_site(site_path = '$(SDDIR)')\n"
+	$(RBIN)/R
 	cp -r figure $(SDDIR)
 
 r-forge: sd
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", ])
 }