minor minor vignettes

euba · Feb 3, 2015 · 2187796 · 2187796
1 parent dab4b90
commit 2187796
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diff --git a/R/Organism.R b/R/Organism.R
@@ -1,5 +1,3 @@
-
-
 # Organism is the class which contains the metabolic model and other features of the organisms in the arena
 
 ########################################################################################################

diff --git a/doc/documentation.pdf b/doc/documentation.pdf
diff --git a/vignettes/BacArena-Introduction.Rmd b/vignettes/BacArena-Introduction.Rmd
@@ -22,6 +22,7 @@ Some features
 BacArena is avaible as R package:
 ```{r}
 library("BacArena")
+library("sybil")
 ```
 
 ## Getting started
@@ -40,13 +41,14 @@ addSubs(arena, smax=2000)
 And now let the games begin: 
 
 ```{r}
-evalsim <- simulate(arena, time=20)
+evalsim <- simulate(arena, time=5)
 ```
 
 The figure sizes have been customised so that you can easily put two images side-by-side. 
 
 ```{r, fig.show='hold'}
-plotCurves(evalsim, remove=T)
+plotCurves(evalsim, remove=T, retdata=F)
+#evalArena(evalsim, plot_items=c('population'), phencol=T, retdata=F)
 ```
 
 

diff --git a/zombified/chemostat.R b/zombified/chemostat.R
@@ -1,5 +1,7 @@
-source(file="R/Arena.R")
-source(file="R/Eval.R")
+source(file="Arena.R")
+#source(file="R/Arena.R")
+source(file="Eval.R")
+#source(file="R/Eval.R")
 medium <- c(15, 60)
 names(medium) <- c("EX_pi(e)","EX_glc(e)")
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		@@ -1,5 +1,3 @@


		# Organism is the class which contains the metabolic model and other features of the organisms in the arena

		########################################################################################################
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