## Not run:
# #Load all the data included in the CoSeg package.
# data(BRCA1Frequencies.df, package="CoSeg")
# data(BRCA2Frequencies.df, package="CoSeg")
# data(MLH1Frequencies.df, package="CoSeg")
# data(USDemographics.df, package="CoSeg")
# data(ChinaDemographics.df, package="CoSeg")
#
# #summaries of all the data
# str(BRCA1Frequencies.df)
# str(BRCA2Frequencies.df)
# str(MLH1Frequencies.df)
# str(USDemographics.df)
# str(ChinaDemographics.df)
#
# #Make a tree with no affection status, g=4 generations above, gdown=2 generations below,
# #seed.age=50, and demographics.df=NULL which defaults to USDemographics.df.
# tree1=MakeTree()
#
# #Make a tree using Chinese demographics instead.
# tree2=MakeTree(demographics.df=ChinaDemographics.df)
#
# #Add affection statust to tree2 using BRCA1Frequencies.df which gives the BRCA1
# #penetrance function
# tree1a=AddAffectedToTree(tree.f=tree1,frequencies.df=BRCA1Frequencies.df)
#
# #make a tree with affection status (same as running MakeTree() and then AddAffectedToTree())
# tree3=MakeAffectedTrees(n=1,g=2,gdown=2,frequencies.df=MLH1Frequencies.df)
# #tree4=MakeAffectedTrees(n=1,g=2,gdown=2,frequencies.df=BRCA2Frequencies.df)
#
#
# #Depending on the size of the pedigree generated, probands (defined here as members of the
# #pedigree who are carriers of the genotype with the disease) may not always be present in
# #the pedigree. To alleviate this problem in this example we manually generate a pedigree.
# #Note that this is from the Mohammadi paper where the Likelihood method originates from.
# ped=data.frame(degree=c(3,2,2,3,3,1,1,2,2,3), momid=c(3,NA,7,3,3,NA,NA,7,NA,8),
# dadid=c(2,NA,6,2,2,NA,NA,6,NA,9), id=1:10, age=c(45,60,50,31,41,68,65,55,62,43),
# female=c(1,0,1,0,1,0,1,1,0,1), y.born=0, dead=0, geno=2, famid=1, bBRCA1.d=0, oBRCA1.d=0,
# bBRCA1.aoo=NA, oBRCA1.aoo=NA, proband=0)
# ped$y.born=2010-ped$age
# ped$geno[c(1,3)]=1
# ped$bBRCA1.d[c(1,3)]=1
# ped$bBRCA1.aoo[1]=45
# ped$bBRCA1.aoo[3]=50
# ped$proband[1]=1
#
# ped=ped[c(6,7,2,3,8,9,1,4,5,10),]
#
# #Calculate the likelihood ratio
# CalculateLikelihoodRatio(ped=ped, affected.vector={ped$bBRCA1.d|ped$oBRCA1.d}, gene="BRCA1")
#
# #Plot the pedigree
# PlotPedigree(ped, affected.vector={ped$bBRCA1.d|ped$oBRCA1.d})
#
# #Rank and plot the members of the pedigree with unknown genotypes
# RankMembers(ped=ped, affected.vector={ped$bBRCA1.d|ped$oBRCA1.d}, gene="BRCA1")
# ## End(Not run)
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