new package

DESCRIPTION

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+Package: disentangle
+Type: Package
+Title: What the package does (short line)
+Version: 1.0
+Date: 2012-11-30
+Author: Who wrote it
+Maintainer: Who to complain to <yourfault@somewhere.net>
+Description: More about what it does (maybe more than one line)
+License: What license is it under?

NAMESPACE

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+exportPattern("^[[:alpha:]]+")

R/newnode.r

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+newnode<-function(name, inputs=NA, outputs=NA, graph = 'nodes', newgraph=F, notes=F, code=NA, ttype=NA, plot = T){
+  # USAGE
+  # nodes <- newnode(  # adds to a graph called nodes
+  # name = 'aquire the raw data'  # the name of the node being added 
+  # inputs = REQUIRED c('external sources','collected by researcher') # single or multiple inputs to it
+  # outputs = OPTIONAL c('file server','metadata','cleaning') # single or multiple outputs from it
+  # append=F # append to existing graph?  if False remove old graph of that name and start new
+  # TODO 
+  # nodes <- addEdge(from='analyse using stats package',
+  # to='new data in database server',graph=nodes,weights=1)
+  # INIT
+  # source('http://bioconductor.org/biocLite.R')
+  # biocLite("Rgraphviz")
+  # or may be needed for eg under ubuntu
+  # biocLite("Rgraphviz", configure.args=c("--with-graphviz=/usr"))
+  require(Rgraphviz)
+  # FURTHER INFO
+  # see the Rgraphviz examples
+  # example(layoutGraph)
+  # require(biocGraph) # for imageMap
+  # TODO change names in following
+  dsc <- name
+  i <- inputs
+  o <- outputs
+  #   if(!exists('nodes')) {
+  if(newgraph==T) {    
+    nodes <- new("graphNEL", nodes=c(dsc),
+               edgemode="directed")
+    # nodes <- addEdge(from=i, to=dsc, graph=nodes, 1)    
+  } else {
+    if(length(grep(dsc,nodes@nodes)) == 0) nodes <- addNode(node=dsc,object=nodes)
+  }  
+  if(sum(i %in% nodes@nodes) != length(i)) {
+    inew <- i[!i %in% nodes@nodes]
+    nodes <- addNode(node=inew,object=nodes)   
+  }
+  nodes <- addEdge(i, dsc, nodes, 1)
+  #}
+  if(!is.na(o[1])){
+  if(sum(o %in% nodes@nodes) != length(o)) {
+    onew <- o[!o %in% nodes@nodes]
+    nodes <- addNode(node=onew,object=nodes)   
+  }
+  nodes <- addEdge(from=dsc, to=o, graph=nodes, 1)  
+  }
+  if(plot == T){
+    try(silent=T,dev.off())
+    plot(nodes,attrs=list(node=list(label="foo", fillcolor="grey",shape="ellipse", fixedsize=FALSE), edge=list(color="black")))
+  }
+  return(nodes)
+}

man/disentangle-package.Rd

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+\name{disentangle-package}
+\alias{disentangle-package}
+\alias{disentangle}
+\docType{package}
+\title{disentangle things
+What the package does (short line)
+~~ package title ~~
+}
+\description{
+More about what it does (maybe more than one line)
+~~ A concise (1-5 lines) description of the package ~~
+}
+\details{
+\tabular{ll}{
+Package: \tab disentangle\cr
+Type: \tab Package\cr
+Version: \tab 1.0\cr
+Date: \tab 2012-11-30\cr
+License: \tab What license is it under?\cr
+}
+~~ An overview of how to use the package, including the most important functions ~~
+}
+\author{
+Who wrote it
+
+Maintainer: Who to complain to <yourfault@somewhere.net>
+~~ The author and/or maintainer of the package ~~
+}
+\references{
+~~ Literature or other references for background information ~~
+}
+
+\keyword{ package }
+\seealso{
+~~ Optional links to other man pages, e.g. ~~
+~~ \code{\link[<pkg>:<pkg>-package]{<pkg>}} ~~
+}
+\examples{
+~~ simple examples of the most important functions ~~
+}

man/newnode.Rd

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+\name{newnode}
+\alias{newnode}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{new node
+%%  ~~function to do ... ~~
+}
+\description{adds to a graphviz graph
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+}
+\usage{
+newnode(name, inputs = NA, outputs = NA, graph = "nodes", newgraph = F, notes = F, code = NA, ttype = NA, plot = T)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{name}{
+%%     ~~Describe \code{name} here~~
+}
+  \item{inputs}{
+%%     ~~Describe \code{inputs} here~~
+}
+  \item{outputs}{
+%%     ~~Describe \code{outputs} here~~
+}
+  \item{graph}{
+%%     ~~Describe \code{graph} here~~
+}
+  \item{newgraph}{
+%%     ~~Describe \code{newgraph} here~~
+}
+  \item{notes}{
+%%     ~~Describe \code{notes} here~~
+}
+  \item{code}{
+%%     ~~Describe \code{code} here~~
+}
+  \item{ttype}{
+%%     ~~Describe \code{ttype} here~~
+}
+  \item{plot}{
+%%     ~~Describe \code{plot} here~~
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+%%  ~~who you are~~
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+require(disentangle)
+nodes <- newnode(name = 'aquire the raw data',
+                 inputs = c('plan', 'external sources',
+                   'collected by researcher'),
+                 outputs = 'cleaning',
+                 newgraph=T)
+
+nodes <- newnode(name = 'file server',
+                 inputs = 'cleaning'
+                 )
+
+nodes <- newnode(name = 'database server',
+                 inputs = 'file server',
+                 outputs = c('metadata database')
+                 )
+
+nodes <- newnode(name = 'search engine web server',
+                 inputs ='metadata database',
+                 outputs = NA
+                 )
+
+nodes <- newnode(name = 'calculate new data',
+                 inputs = 'database server',
+                 outputs =
+                 c('analyse using stats package','database server',
+                   'metadata database', 'technical documentation')
+                 )
+
+nodes <- newnode(name = 'analyse using stats package',
+                 inputs = c('database server','simulation',
+                   'file server', 'cleaning'),
+                 outputs = c('results', 'metadata database',
+                   'cleaning', 'technical documentation')
+                 )
+
+nodes <- newnode(name = 'communicate the results',
+                 inputs ='results',
+                 outputs = c('journal publication')
+                 )
+
+nodes <- newnode(name='technical documentation',
+                 inputs = c('aquire the raw data',
+                   'communicate the results'),
+                 outputs = 'cleaning'
+                 )
+
+nodes <- newnode(name = 'archive at end of project',
+                 inputs ='journal publication',
+                 outputs = c('repurposed data','file server',
+                   'destroy')
+                 )
+
+#dev.copy2pdf(file='transformations_overview.pdf')
+#dev.off();                 
+
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ ~kwd1 }
+\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line