cran check related fixes

DESCRIPTION

@@ -20,15 +20,15 @@ Depends:
     deSolve (>= 1.12),
     Matrix (>= 1.2)
 Imports: 
-    glpkAPI,
+    igraph,
     methods,
     utils,
     stats,
     graphics,
     Rcpp
 Suggests: 
+    glpkAPI,
     sybilSBML,
-    igraph,
     knitr,
     rmarkdown
 LinkingTo: Rcpp,

NAMESPACE

@@ -27,6 +27,7 @@ export(diffuseR)
 export(emptyHood)
 export(evalArena)
 export(extractMed)
+export(findFeeding)
 export(flushSubs)
 export(getArena)
 export(getCorrM)
@@ -77,6 +78,7 @@ exportMethods(diffuseR)
 exportMethods(emptyHood)
 exportMethods(evalArena)
 exportMethods(extractMed)
+exportMethods(findFeeding)
 exportMethods(flushSubs)
 exportMethods(getArena)
 exportMethods(getCorrM)
@@ -112,6 +114,15 @@ importFrom(graphics,par)
 importFrom(graphics,points)
 importFrom(graphics,segments)
 importFrom(graphics,text)
+importFrom(igraph,E)
+importFrom(igraph,V)
+importFrom(igraph,add.edges)
+importFrom(igraph,degree)
+importFrom(igraph,delete.edges)
+importFrom(igraph,delete.vertices)
+importFrom(igraph,graph.empty)
+importFrom(igraph,layout_with_fr)
+importFrom(igraph,vcount)
 importFrom(stats,cor)
 importFrom(stats,dist)
 importFrom(stats,hclust)

NEWS

@@ -1,4 +1,4 @@
-BacArena v1.0.1 (Release date: 2016-01-05)
+BacArena v1.0.1 (Release date: 2016-01-06)
 =============
 
 Changes:

R/Arena.R

@@ -1496,16 +1496,18 @@ setMethod("statPheno", "Eval", function(object, type_nr=1, phenotype_nr, dict=NU
 #' @description The generic function \code{findFeeding} 
 #' @export
 #' @rdname findFeeding
-#' @import igraph
+#' @importFrom igraph graph.empty add.edges delete.edges delete.vertices V E degree vcount layout_with_fr
+#' 
+#' @param object An object of class Eval.
 #' @param tcut Integer giving the minimal mutual occurence ot be considered (dismiss very seldom feedings)
 #' @param scut List of substance names which should be ignored
 #' @param legendpos A character variable declaring the position of the legend
 #' @param dict List defining new substance names. List entries are intepreted as old names and the list names as the new ones.
 #' @return Graph (igraph)
 #' 
+setGeneric("findFeeding", function(object, dict=NULL, tcut=5, scut=list(), legendpos="topleft"){standardGeneric("findFeeding")})
 #' @export
 #' @rdname findFeeding
-setGeneric("findFeeding", function(object, dict=NULL, tcut=5, scut=list(), legendpos="topleft"){standardGeneric("findFeeding")})
 setMethod("findFeeding", "Eval", function(object, dict=NULL, tcut=5, scut=list(), legendpos="topleft"){
 
   # possible problem inactive phenotype is not mentioned in object@phenotypes...
@@ -1554,8 +1556,8 @@ setMethod("findFeeding", "Eval", function(object, dict=NULL, tcut=5, scut=list()
   # graph
   pindex <- rownames(mat_phen)# phenotype index
   cindex <- colnames(res) # substance color index
-  g <-graph.empty(n=length(pindex), directed=TRUE)
-  V(g)$name <- gsub("pheno","",pindex)
+  g <-igraph::graph.empty(n=length(pindex), directed=TRUE)
+  igraph::V(g)$name <- gsub("pheno","",pindex)
 
 
   # 3) Combinatorics: check for all pairs of phenotypes if they 
@@ -1580,7 +1582,7 @@ setMethod("findFeeding", "Eval", function(object, dict=NULL, tcut=5, scut=list()
               new_edge <- c(which(pindex==combi[,i][1]), which(pindex==combi[,i][2]))
             }else new_edge <- c(which(pindex==combi[,i][2]), which(pindex==combi[,i][1]))
             col <- colpal3[which(cindex == colnames(feeding)[x])]
-            g <<- add.edges(g, new_edge, color=col, weight=length(co_occ))
+            g <<- igraph::add.edges(g, new_edge, color=col, weight=length(co_occ))
           })
         }
         #cat("\npossible cross feeding at time steps\n")
@@ -1590,11 +1592,11 @@ setMethod("findFeeding", "Eval", function(object, dict=NULL, tcut=5, scut=list()
     }
   }
 
-  g <- delete.edges(g, which(E(g)$weight<tcut)) # delete seldom feedings
-  g <- delete.vertices(g, which(degree(g, mode="all") == 0)) # delete unconnected
+  g <- igraph::delete.edges(g, which(igraph::E(g)$weight<tcut)) # delete seldom feedings
+  g <- igraph::delete.vertices(g, which(igraph::degree(g, mode="all") == 0)) # delete unconnected
 
-  if(vcount(g) >= 2){
-    plot(g, layout=layout_with_fr, vertex.size=5,
+  if(igraph::vcount(g) >= 2){
+    plot(g, layout=igraph::layout_with_fr, vertex.size=5,
          edge.arrow.size=0.3, edge.width=E(g)$weight/10)
     legend(legendpos,legend=cindex, col=colpal3, pch=19, cex=0.7)
   }

R/Stuff.R

@@ -120,13 +120,15 @@ estimate_lrw <- function(grid_n, grid_m){
 #'
 #' @return Returns an object of class \code{Eval} which can be used for subsequent analysis steps.
 #' @examples
+#' \donttest{ 
 #' sim <- openArena()
 #' evalArena(sim, time=7, phencol = TRUE, 
 #'           plot_items=c("Population", "EX_o2(e)", "EX_for(e)",
 #'           "EX_glc(e)", "EX_for(e)"))
+#'}
 openArena <- function(){
   data(Ec_core, envir = environment())
-  bac = Bac(model=Ec_core, growtype="exponential")
+  bac = Bac(model=Ec_core, type="E. coli")
   arena = Arena(n=50, m=50, stir=F, Lx=0.0125, Ly=0.0125)
   addOrg(arena, bac, amount=50)
   addSubs(arena, smax=0, difspeed=6.7e-6)

README.md

@@ -6,7 +6,7 @@ Existing genome-scale metabolic models can be used to simulate growth and intera
 In BacArena two well established methods are merged: a) Flux balance analysis to predict the activity of
 metabolic reactions and b) Agent based modelling in order to provide an environment.
 
-It has been  efficiently implemented in R language (with some C++ routines) and is freely available [CRAN](https://cran.r-project.org/web/packages/BacArena/index.html).
+It has been  efficiently implemented in R language (with some C++ routines) and is freely available [CRAN](https://cran.r-project.org/package=BacArena).
 
 Features:
 - Each organism is represented individually

examples/pao_sim.R

@@ -7,7 +7,7 @@ library(RcppArmadillo)
 library(sybil)
 library(compiler)
 setwd("/Users/euba/GitRep/BacArena/")
-#setwd("uni/bacarena")
+#setwd("~/uni/bacarena")
 #setwd('P:/GitRep/BacArena')
 #setwd('P:/GitRep/BacArena')