#this example not run because it takes longer than 5 secs
#note - type example(FunctionName, run.dontrun=TRUE) to run the example where FunctionName is
#the name of the function
##Data generation
SampleSites=10
NumberLoci=4
MaxAlleles=4
if(MaxAlleles==2){
NumberAllelesAtEachLocus=rep(2,NumberLoci)
}else{
NumberAllelesAtEachLocus=sample(2:MaxAlleles,NumberLoci,replace=TRUE)
}
TestData=array(0,dim=c(MaxAlleles,SampleSites,NumberLoci))
for(i in 1:NumberLoci){
for(j in 1:NumberAllelesAtEachLocus[i]){
TestData[j,,i]=sample(1:10,SampleSites,replace=TRUE)
}
}
##This data is simulated in Europe which is around Longitude -9 to 38 and Latitude 34 to 60
TestCoordinates=array(0,dim=c(SampleSites,2))
TestCoordinates[,1]=runif(SampleSites,-9,38)
TestCoordinates[,2]=runif(SampleSites,34,60)
##This simulates the unknown data
NumberUnknowns=2
UnknownData=array(0,dim=c(NumberUnknowns,2,NumberLoci))
for(i in 1:NumberUnknowns){
for(j in 1:NumberLoci){
UnknownData[i,,j]=sample(1:NumberAllelesAtEachLocus[j],2)
}
}
##MaxGridLength is the maximum number of boxes allowed
##to span the region in either direction
##Note that this number was reduced to allow the example to run in less than 5 secs
##RhoParameter is a tuning constant
print("MaxGridLength is intentionally set really low for fast examples.
Meaningful results will most likely require a higher value.")
##Fits the allele frequency surfaces only
#SurfaceTrials=FitMultinomialModel(TestData,TestCoordinates,
#MaxGridLength=20,RhoParameter=10)
#str(SurfaceTrials)
##Plotting the model
#PlotAlleleFrequencySurface(SurfaceTrials,LocusNumber=1,AlleleNumber=1,
# MaskWater=TRUE,Scale=FALSE)
##You can generate heatmaps of unknown individual's placements from with the allele
##surfaces using GenerateHeatMaps or use FitMultinomialModelFindUnknowns
#HeatMapTrials=GenerateHeatMaps(SurfaceTrials,UnknownData,NumberLoci=NumberLoci)
##Plotting the unknown heat map
#PlotUnknownHeatMap(HeatMapTrials,UnknownNumber=1,MaskWater=TRUE)
##Fitting the model and finding the unknown locations
UnknownTrials=FitMultinomialModelFindUnknowns(TestData,TestCoordinates,
UnknownData,MaxGridLength=20,RhoParameter=10)
str(UnknownTrials)
##Plotting the unknown heat map
PlotUnknownHeatMap(UnknownTrials,UnknownNumber=1,MaskWater=TRUE)
##Fitting the admixed model
#AdmixedTrials=FitMultinomialAdmixedModelFindUnknowns(TestData,TestCoordinates,
# UnknownData,MaxGridLength=10,RhoParameter=10)
##Plots the admixed surface disregarding fractions less than 0.01
#PlotAdmixedSurface(AdmixedTrials,UnknownNumber=1)
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