\name{writeReport}
\alias{writeReport}
\title{
Write a report of a CellNOptR analysis
}
\description{
This function writes a short report of a CellNOptR analysis in an html page, that is linked to the various graphs produced
}
\usage{
writeReport(ModelOriginal, ModelOpt, optimResT1, optimResT2, CNOlist, directory, namesFiles = list(dataPlot = NA, evolFit1 = NA, evolFit2 = NA, SimResults2 = NA, SimResults1 = NA, Scaffold = NA, tscaffold = NA, wscaffold = NA, PKN = NA, wPKN = NA, nPKN = NA), namesData = list(CNOlist=NA, Model=NA),resE)
}
\arguments{
  \item{ModelOriginal}{
the original previous knowledge network (i.e. model that you loaded) in a model list format
}
  \item{ModelOpt}{
the model that was actually used for optimisation (i.e. the scaffold network, after compression and expansion) in a model list format
}
  \item{optimResT1}{
the results of the optimisation at t1, as output by gabinaryT1
}
  \item{optimResT2}{
the results of the optimisation at t2, as output by gabinaryT2. Set this to NA if you have performed a one time point optimisation.
}
  \item{CNOlist}{
a CNOlist
}
  \item{directory}{
the name of a new directory that will be created, where your results will be moved
}
  \item{namesFiles}{
 a list of the names of the files that should have been created. Depending on whether a t2 optimisation was performed or not, all or some of the following fields are expected: dataPlot,evolFit1,evolFit2,SimResults2,SimResults1,Scaffold,tscaffold,wscaffold,PKN,wPKN,nPKN
}
  \item{namesData}{
a list with fields \code{$CNOlist} and \code{$Model} that contain strings that are meaningful identifiers of your data and previous knowledge network (for your own record)
}
  \item{resE}{
a vector with named entries t1, t2 t1andt2, as produced by the function \code{ResidualError}, that contains the residual error associated with the discretisation of the data
}
}
\details{
Future versions of this function might directly write and compile a tex file.
}
\value{
This function produces a directory and moves all the files of namesFiles to it, then it creates an html report that contains infos about the optimisation process.
}
\author{
C.Terfve
}
\seealso{
writeNetwork, writeScaffold
}
\examples{
tmpdir<-tempdir()
setwd(tmpdir)

#load data

data(CNOlistToy,package="CellNOptR")
data(ToyModel,package="CellNOptR")

#pre-process model (partial)

indicesToy<-indexFinder(CNOlistToy,ToyModel,verbose=TRUE)
ToyNCNOcutComp<-compressModel(ToyModel,indicesToy)
indicesToyNCNOcutComp<-indexFinder(CNOlistToy,ToyNCNOcutComp)
ToyNCNOcutCompExp<-expandGates(ToyNCNOcutComp)

#optimise

ToyFields4Sim<-prep4Sim(ToyNCNOcutCompExp)
initBstring<-rep(1,length(ToyNCNOcutCompExp$reacID))
ToyT1opt<-gaBinaryT1(
	CNOlist=CNOlistToy,
	Model=ToyNCNOcutCompExp,
	SimList=ToyFields4Sim,
	indexList=indicesToyNCNOcutComp,
	initBstring=initBstring, 
	maxGens=2,
	PopSize=5,
	verbose=TRUE)

#write report

namesFilesToy<-list(
	dataPlot=NA,
	evolFit1=NA,
	evolFit2=NA,
	SimResults1=NA,
	SimResults2=NA,
	Scaffold=NA,
	ScaffoldDot=NA,
	tscaffold=NA,
	wscaffold=NA,
	PKN=NA,
	PKNdot=NA,
	wPKN=NA,
	nPKN=NA)
writeReport(
	ModelOriginal=ToyModel,
	ModelOpt=ToyNCNOcutCompExp,
	optimResT1=ToyT1opt,
	optimResT2=NA,
	CNOlist=CNOlistToy,
	directory="testToy",
	namesFiles=namesFilesToy,
	namesData=list(CNOlist="Toy",Model="ToyModel"),
	resE=NA)
}