diff --git a/sumulation.vba b/sumulation.vba
new file mode 100644
index 0000000000000000000000000000000000000000..4ede8ca90cc41652f2f7111ec7728053dd55008c
--- /dev/null
+++ b/sumulation.vba
@@ -0,0 +1,3104 @@
+'Simulation module for genetic maps and populations
+
+Function gauss()
+'simulated normally-distributed data
+'use: myvalue = gauss * sd + mean
+
+Dim fac As Double, r As Double, V1 As Double, V2 As Double
+
+10 V1 = 2 * Rnd - 1
+ V2 = 2 * Rnd - 1
+ r = V1 ^ 2 + V2 ^ 2
+ If (r >= 1) Then GoTo 10
+ fac = Sqr(-2 * Log(r) / r)
+ gauss = V2 * fac
+
+End Function
+
+Sub testgauss()
+ Dim mean As Variant
+ Dim sd As Variant
+
+ mean = 0
+ sd = 1
+ myvalue = gauss * sd + mean
+ MsgBox myvalue
+End Sub
+
+Public Sub Simulate_Map()
+'For i = 1 To 1000
+Application.StatusBar = "Simulating map..."
+Application.ScreenUpdating = True: DoEvents: Application.ScreenUpdating = False
+ThisWorkbook.Sheets("SimulMap").Activate
+
+Dim SimulatedChromosome As Integer
+Dim NumberOfSimulatedChromosomes As Integer
+Dim SimulatedMarker As Long
+Dim NumberOfSimulatedMarkers As Long
+Dim NumberOfMarkersInThisChromosome As Long
+Dim SimulRow As Long
+Dim SimulatedMapSize As Double
+Dim ChromosomeSize As Double
+Dim MaxVariationPositionRate As Double
+Dim VariationPosition As Double
+Dim SimulatedMarkerPosition As Double
+Dim AverageChromosomeSize As Double
+Dim SimulatedMarkerDensity As Double
+Dim SimulatedChromosomeSizeVariation As Double
+Dim TotalMapSize As Double
+Dim StartChrSize As Double
+Dim GenomeSize As LongLong 'long is max 2,147,483,647
+Dim nbOfMb As LongLong
+Dim bp_cM_ratio As Double
+
+'Map parameters
+NumberOfSimulatedChromosomes = [N9].Value
+SimulatedMapSize = [N10].Value
+SimulatedMarkerDensity = [N11].Value
+SimulatedChromosomeSizeVariation = [N12].Value / 100
+nbOfMb = [j22].Value
+GenomeSize = nbOfMb * 1000000
+bp_cM_ratio = GenomeSize / SimulatedMapSize
+
+If SimulatedMarkerDensity < 0 Then EquallyDispersed = 1
+If [j11] = "yes" Then EquallyDispersed = 2
+
+If EquallyDispersed = 1 Then
+ SimulatedMarkerDensity = 0 - SimulatedMarkerDensity
+ElseIf EquallyDispersed = 0 Then
+ SimulatedMarkerDensity = SimulatedMarkerDensity + SimulatedMarkerDensity * (NumberOfSimulatedChromosomes / 1000)
+ 'gives better results than SimulatedMarkerDensity alone
+ElseIf EquallyDispersed = 2 Then
+ If SimulatedMarkerDensity < 0 Then SimulatedMarkerDensity = (0 - SimulatedMarkerDensity)
+End If
+
+MaxVariationPositionRate = [J12]
+
+'Map Simulation
+'Define Chromosome sizes
+AverageChromosomeSize = SimulatedMapSize / NumberOfSimulatedChromosomes
+'ExpectedMarkerNumber = Int(SimulatedMapSize / SimulatedMarkerDensity) + 1
+'ExpectedMarkerNumberPerChromosome = Int(ExpectedMarkerNumber / NumberOfSimulatedChromosomes) + 1
+
+Dim SimulatedMap() As Variant
+ReDim SimulatedMap(1000000, 4)
+
+If [b6] <> "" Then
+ msg = "Are you sure you want to clear this simulated map?"
+ Style = vbYesNo + vbCritical + vbDefaultButton1
+ Title = "Clear results"
+ Ctxt = 1000
+ response = MsgBox(msg, Style, Title)
+ If response = vbYes Then
+ ThisWorkbook.Sheets("SimulMap").Range("B6", "F100005").ClearContents
+ ThisWorkbook.Sheets("SimulMap").Range("N22:N24").ClearContents
+ ThisWorkbook.Sheets("SimulMap").Range("J27:O1000").ClearContents
+ ThisWorkbook.Sheets("SimulMap").Range("R22:R25").ClearContents
+ Else
+ GoTo 1000
+ End If
+End If
+
+SimulRow = 0
+NumberOfSimulatedMarkers = 0
+TotalMapSize = 0
+
+[K6] = "Simulating chromosomes... "
+Application.ScreenUpdating = True: DoEvents: Application.ScreenUpdating = False
+
+For SimulatedChromosome = 1 To NumberOfSimulatedChromosomes
+
+ StartChrSize = 0
+ Randomize (Rnd)
+ If Rnd > 0.5 Then SimulatedChromosomeSizeVariation = 0 - SimulatedChromosomeSizeVariation
+' Randomize (Rnd)
+ ChromosomeSize = AverageChromosomeSize + AverageChromosomeSize * (Rnd * SimulatedChromosomeSizeVariation)
+ NumberOfMarkersInThisChromosome = Int(ChromosomeSize / SimulatedMarkerDensity) + 1
+ For SimulatedMarker = 1 To NumberOfMarkersInThisChromosome
+ NumberOfSimulatedMarkers = NumberOfSimulatedMarkers + 1
+ If EquallyDispersed = 1 Then 'fixed positions
+ SimulatedMarkerPosition = (ChromosomeSize / (NumberOfMarkersInThisChromosome - 1)) * (SimulatedMarker - 1)
+ ElseIf EquallyDispersed = 0 Then ' random positions
+ Randomize (Rnd)
+ SimulatedMarkerPosition = Rnd * ChromosomeSize
+ ElseIf EquallyDispersed = 2 Then ' semi-random positions
+ Randomize (Rnd)
+ SimulatedMarkerPosition = (ChromosomeSize / (NumberOfMarkersInThisChromosome - 1)) * (SimulatedMarker - 1)
+ If MaxVariationPositionRate > 0 Then
+ If Rnd > 0.5 Then
+ VariationPosition = (ChromosomeSize / (NumberOfMarkersInThisChromosome - 1)) * Rnd * MaxVariationPositionRate
+ Else
+ VariationPosition = 0 - ((ChromosomeSize / (NumberOfMarkersInThisChromosome - 1)) * Rnd * MaxVariationPositionRate)
+ End If
+ Else
+ VariationPosition = 0
+ End If
+ SimulatedMarkerPosition = SimulatedMarkerPosition + VariationPosition
+ End If
+ ''Debug.Print SimulatedChromosome
+ SimulatedMap(SimulRow, 0) = SimulatedChromosome
+ SimulatedMap(SimulRow, 1) = NumberOfSimulatedMarkers
+ fakeMkphysicalPosition = Int(SimulatedMarkerPosition * bp_cM_ratio)
+' SimulatedMap(SimulRow, 2) = "Chr" & SimulatedChromosome & "_M" & SimulatedMarker
+ SimulatedMap(SimulRow, 2) = "Chr" & SimulatedChromosome & "_" & fakeMkphysicalPosition
+
+ If SimulatedMarker = 1 Then
+ SimulatedMap(SimulRow, 3) = 0
+ ElseIf SimulatedMarker = NumberOfMarkersInThisChromosome Then
+ SimulatedMap(SimulRow, 3) = ChromosomeSize
+' SimulatedMap(SimulRow, 3) = Format(ChromosomeSize, "####.00")
+ Else
+ SimulatedMap(SimulRow, 3) = SimulatedMarkerPosition
+' SimulatedMap(SimulRow, 3) = Format(SimulatedMarkerPosition, "####.00") 'very slow
+ End If
+' 'If SimulatedMarkerPosition > StartChrSize Then StartChrSize = SimulatedMarkerPosition
+ SimulRow = SimulRow + 1
+ Next SimulatedMarker
+ 'FinalChromosomeSize = StartChrSize
+ TotalMapSize = TotalMapSize + ChromosomeSize
+ Cells(26 + SimulatedChromosome, 10) = SimulatedChromosome
+ Cells(26 + SimulatedChromosome, 11) = Format(ChromosomeSize, "####.00")
+ Cells(26 + SimulatedChromosome, 12) = NumberOfMarkersInThisChromosome
+ Cells(26 + SimulatedChromosome, 14) = Format(ChromosomeSize / NumberOfMarkersInThisChromosome, "####.000")
+' chrcM_Mbp = ChromosomeSize / (fakeMkphysicalPosition / 1000000)
+' Cells(26 + SimulatedChromosome, 15) = Format(chrcM_Mbp, "####.00")
+Next SimulatedChromosome
+
+[K6] = ""
+
+[N22] = TotalMapSize
+[N23] = NumberOfSimulatedMarkers
+[N24] = Format(TotalMapSize / NumberOfSimulatedMarkers, "####.000")
+
+[R22] = [N9]
+[r23] = [N10]
+[R24] = [N11]
+[R25] = [N12]
+
+ Cells(26, 10) = "Chr"
+ Cells(26, 11) = "cM"
+ Cells(26, 12) = "Mk"
+ Cells(26, 14) = "density"
+
+'Application.StatusBar = "Writing map..."
+'Application.ScreenUpdating = True: DoEvents: Application.ScreenUpdating = False
+'ThisWorkbook.Sheets("SimulMap").Activate
+'Range("B6:E100005").Select
+'Selection.ClearContents
+
+ThisWorkbook.Sheets("SimulMap").Range("B6").Resize(NumberOfSimulatedMarkers, 4) = SimulatedMap
+Erase SimulatedMap
+
+'Application.StatusBar = "Sorting map by position..."
+'Application.ScreenUpdating = True: DoEvents: Application.ScreenUpdating = False
+
+Range("B6:E100005").Select
+Selection.Sort Key1:=Range("B6"), Order1:=xlAscending, Key2:=Range("E6") _
+, Order2:=xlAscending, Header:=xlGuess, OrderCustom:=1, MatchCase:= _
+False, Orientation:=xlTopToBottom
+
+[b6].Select
+
+'Application.StatusBar = "Sorting map by locus number..."
+'Application.ScreenUpdating = True: DoEvents: Application.ScreenUpdating = False
+
+Range("C6:D100000").Select
+Selection.Sort Key1:=Range("C6"), Order1:=xlAscending, Header:=xlGuess, _
+ OrderCustom:=1, MatchCase:=False, Orientation:=xlTopToBottom
+
+Range("N22").Select
+Application.ScreenUpdating = True
+'Next i
+1000
+Application.StatusBar = False
+End Sub
+
+
+Public Sub Chr_Start_at_0()
+Application.ScreenUpdating = False
+
+If [b6] <> "" Then
+ msg = "Are you sure you want to do this? All marker positions will be recalculated in order to let chromosomes start at position 0"
+ Style = vbYesNo + vbCritical + vbDefaultButton1
+ Title = "Start at 0"
+ Ctxt = 1000
+ response = MsgBox(msg, Style, Title)
+ If response = vbNo Then
+ GoTo 1000
+ End If
+End If
+
+ThisWorkbook.Sheets("SimulMap").Activate
+
+'first, counts the chr parameters (same than Read_Chr_Simulated)
+Range("B6", Range("B1048576").End(xlUp)).Select
+NbOfRows = Selection.Rows.Count
+
+NumbOfMarkInChrTotal = 0
+TotalMapSize = 0
+NumberOfChr = 0
+For i = 6 To NbOfRows + 6
+ If Cells(i + 1, 2) <> Cells(i, 2) Then 'new chr is detected
+ NumberOfChr = NumberOfChr + 1
+ Cells(26 + Cells(i, 2), 10) = Cells(i, 2) 'chr number
+ ChrSize = Cells(i, 5)
+ Cells(26 + Cells(i, 2), 11) = ChrSize 'chr size
+ TotalMapSize = TotalMapSize + Cells(i, 5)
+ NumbOfMarkInChr = i - 5 - NumbOfMarkInChrTotal
+ Cells(26 + Cells(i, 2), 12) = NumbOfMarkInChr
+ MarkerDensity = ChrSize / NumbOfMarkInChr
+ Cells(26 + Cells(i, 2), 14) = MarkerDensity
+ NumbOfMarkInChrTotal = NumbOfMarkInChrTotal + NumbOfMarkInChr
+ End If
+Next
+[N22] = TotalMapSize
+[N23] = NumbOfMarkInChrTotal
+[N24] = TotalMapSize / NumbOfMarkInChrTotal
+[R22] = NumberOfChr
+
+'second, reformats the marker positions to start at 0
+firstRow = 6
+NbOfProcessedRows = 0
+For chromosome = 1 To NumberOfChr
+ NumbOfMarkInChr = Cells(26 + chromosome, 12)
+ FirstPosition = Cells(NbOfProcessedRows + 6, 5)
+ For mark = 1 To NumbOfMarkInChr
+ Cells(NbOfProcessedRows + mark + 5, 5) = Cells(NbOfProcessedRows + mark + 5, 5) - FirstPosition
+ Next
+ NbOfProcessedRows = NbOfProcessedRows + NumbOfMarkInChr
+Next chromosome
+
+'third, re-reads and writes the chr parameters
+NumbOfMarkInChrTotal = 0
+TotalMapSize = 0
+NumberOfChr = 0
+For i = 6 To NbOfRows + 6
+ If Cells(i + 1, 2) <> Cells(i, 2) Then 'new chr is detected
+ NumberOfChr = NumberOfChr + 1
+ Cells(26 + Cells(i, 2), 10) = Cells(i, 2) 'chr number
+ ChrSize = Cells(i, 5)
+ Cells(26 + Cells(i, 2), 11) = ChrSize 'chr size
+ TotalMapSize = TotalMapSize + Cells(i, 5)
+ NumbOfMarkInChr = i - 5 - NumbOfMarkInChrTotal
+ Cells(26 + Cells(i, 2), 12) = NumbOfMarkInChr
+ MarkerDensity = ChrSize / NumbOfMarkInChr
+ Cells(26 + Cells(i, 2), 14) = MarkerDensity
+ NumbOfMarkInChrTotal = NumbOfMarkInChrTotal + NumbOfMarkInChr
+ End If
+Next
+[N22] = TotalMapSize
+[N23] = NumbOfMarkInChrTotal
+[N24] = TotalMapSize / NumbOfMarkInChrTotal
+[R22] = NumberOfChr
+
+1000 [N22].Select
+Application.CutCopyMode = False
+Application.ScreenUpdating = True
+End Sub
+
+
+Sub Add_Trait_To_Population_In_Data()
+
+Application.ScreenUpdating = False
+Init
+
+popType = Sheets("Data").[D4]
+popsize = Sheets("Data").[D5]
+nbloci = Sheets("Data").[D6]
+NbTraits = Sheets("Data").[D7]
+
+nbHeaders = 15
+
+outcellrow = nbloci + NbTraits + nbHeaders + 1
+
+mkQTL1 = ThisWorkbook.Sheets("SimulMap").[R39]
+NbOfTraitsToAdd = ThisWorkbook.Sheets("SimulMap").[R40]
+
+Dim SimulatedTrait() As Variant
+ReDim SimulatedTrait(1 To NbOfTraitsToAdd, 1 To popsize + 2)
+
+MeanAA_QTL1 = ThisWorkbook.Sheets("SimulMap").[R31]
+MeanAB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R32]
+MeanBB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R33]
+VarCoeffAA_QTL1 = ThisWorkbook.Sheets("SimulMap").[R34]
+VarCoeffAB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R35]
+VarCoeffBB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R36]
+SD_AA_QTL1 = MeanAA_QTL1 * VarCoeffAA_QTL1
+SD_AB_QTL1 = MeanAB_QTL1 * VarCoeffAB_QTL1
+SD_BB_QTL1 = MeanBB_QTL1 * VarCoeffBB_QTL1
+
+Randomize (Rnd)
+
+If popType = "SSD" Or popType = "DH" Then
+ For j = 1 To NbOfTraitsToAdd
+ SimulatedTrait(j, 1) = NbTraits + j
+ SimulatedTrait(j, 2) = "SimulatedTrait_" & NbTraits + j
+ For i = 1 To popsize
+ Genotype = Data(i - 1, mkQTL1 - 1)
+ If Genotype = "A" Then
+ myAAvalue = gauss * SD_AA_QTL1 + MeanAA_QTL1
+ SimulatedTrait(j, i + 2) = Format(myAAvalue, "###.00")
+ ElseIf Genotype = "B" Then
+ myBBvalue = gauss * SD_BB_QTL1 + MeanBB_QTL1
+ SimulatedTrait(j, i + 2) = Format(myBBvalue, "###.00")
+ Else
+ SimulatedTrait(j, i + 2) = "-"
+ End If
+ Next
+ Next
+ElseIf popType = "BC1" Then
+ For j = 1 To NbOfTraitsToAdd
+ SimulatedTrait(j, 1) = NbTraits + j
+ SimulatedTrait(j, 2) = "SimulatedTrait_" & NbTraits + j
+ For i = 1 To popsize
+ Genotype = Data(i - 1, mkQTL1 - 1)
+ If Genotype = "A" Then
+ myAAvalue = gauss * SD_AA_QTL1 + MeanAA_QTL1
+ SimulatedTrait(j, i + 2) = Format(myAAvalue, "###.00")
+ ElseIf Genotype = "H" Then
+ myABvalue = gauss * SD_AB_QTL1 + MeanAB_QTL1
+ SimulatedTrait(j, i + 2) = Format(myABvalue, "###.00")
+ Else
+ SimulatedTrait(j, i + 2) = "-"
+ End If
+ Next
+ Next
+ElseIf popType = "F2" Then
+ For j = 1 To NbOfTraitsToAdd
+ SimulatedTrait(j, 1) = NbTraits + j
+ SimulatedTrait(j, 2) = "SimulatedTrait_" & NbTraits + j
+ For i = 1 To popsize
+ Genotype = Data(i - 1, mkQTL1 - 1)
+ If Genotype = "H" Then
+ myABvalue = gauss * SD_AB_QTL1 + MeanAB_QTL1
+ SimulatedTrait(j, i + 2) = Format(myABvalue, "###.00")
+ ElseIf Genotype = "A" Then
+ myAAvalue = gauss * SD_AA_QTL1 + MeanAA_QTL1
+ SimulatedTrait(j, i + 2) = Format(myAAvalue, "###.00")
+ ElseIf Genotype = "B" Then
+ myBBvalue = gauss * SD_BB_QTL1 + MeanBB_QTL1
+ SimulatedTrait(j, i + 2) = Format(myBBvalue, "###.00")
+ Else
+ SimulatedTrait(j, i + 2) = "-"
+ End If
+ Next
+ Next
+End If
+
+
+Sheets("Data").Activate
+Cells(outcellrow, 1).Resize(NbOfTraitsToAdd, popsize + 2) = SimulatedTrait
+
+Sheets("Data").[D7] = NbTraits + NbOfTraitsToAdd
+End Sub
+
+Sub Add_Random_Trait_To_Population_In_Data()
+
+Application.ScreenUpdating = False
+Init
+
+popType = Sheets("Data").[D4]
+popsize = Sheets("Data").[D5]
+nbloci = Sheets("Data").[D6]
+NbTraits = Sheets("Data").[D7]
+
+nbHeaders = 15
+
+outcellrow = nbloci + NbTraits + nbHeaders + 1
+
+NbOfTraitsToAdd = ThisWorkbook.Sheets("SimulMap").[R43]
+
+Dim SimulatedTrait() As Variant
+ReDim SimulatedTrait(1 To NbOfTraitsToAdd, 1 To popsize + 2)
+
+MeanAA_QTL1 = ThisWorkbook.Sheets("SimulMap").[R31]
+MeanAB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R32]
+MeanBB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R33]
+VarCoeffAA_QTL1 = ThisWorkbook.Sheets("SimulMap").[R34]
+VarCoeffAB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R35]
+VarCoeffBB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R36]
+SD_AA_QTL1 = MeanAA_QTL1 * VarCoeffAA_QTL1
+SD_AB_QTL1 = MeanAB_QTL1 * VarCoeffAB_QTL1
+SD_BB_QTL1 = MeanBB_QTL1 * VarCoeffBB_QTL1
+
+Randomize (Rnd)
+
+For j = 1 To NbOfTraitsToAdd
+ SimulatedTrait(j, 1) = NbTraits + j
+ SimulatedTrait(j, 2) = "RandomTrait_" & NbTraits + j
+ For i = 1 To popsize
+ myvalue = gauss * SD_AA_QTL1 + MeanAA_QTL1
+ SimulatedTrait(j, i + 2) = Format(myvalue, "###.00")
+ Next
+Next
+
+Sheets("Data").Activate
+Cells(outcellrow, 1).Resize(NbOfTraitsToAdd, popsize + 2) = SimulatedTrait
+
+Sheets("Data").[D7] = NbTraits + NbOfTraitsToAdd
+End Sub
+
+Public Sub Read_Simulation_Parameters()
+'only for autobatchmap
+SimulatedPopulationType = VirtualMap(16, 14) 'ONLY BC1 & F2 pops at this stage
+
+SimulatedPopulationSize = VirtualMap(17, 14)
+
+MapFunctionSimul = VirtualMap(18, 14)
+
+ChromosomeSDL1 = VirtualMap(9, 18)
+If ChromosomeSDL1 > 0 Then
+ PositionSDL1 = VirtualMap(10, 18)
+ ViabU = VirtualMap(15, 18) 'differential viability fA/fB for SDL1
+ SDL1AbsoluteNumber = 0
+ For i = 1 To ChromosomeSDL1 - 1
+ SDL1AbsoluteNumber = SDL1AbsoluteNumber + VirtualMap(26 + i, 12)
+ Next
+ SDL1AbsoluteNumber = SDL1AbsoluteNumber + PositionSDL1
+End If
+
+ChromosomeSDL2 = VirtualMap(11, 18)
+If ChromosomeSDL2 > 0 Then
+ PositionSDL2 = VirtualMap(12, 18)
+ ViabV = VirtualMap(17, 18) 'differential viability fA/fB for SDL2
+ SDL2AbsoluteNumber = 0
+ For i = 1 To ChromosomeSDL2 - 1
+ SDL2AbsoluteNumber = SDL2AbsoluteNumber + VirtualMap(26 + i, 12)
+ Next
+ SDL2AbsoluteNumber = SDL2AbsoluteNumber + PositionSDL2
+End If
+
+NumberOfSimulatedTraits = VirtualMap(19, 14)
+NumberOfSimulatedMarkers = VirtualMap(23, 14)
+NumberOfSimulatedChromosomes = VirtualMap(22, 18)
+RandomErrorRate = VirtualMap(18, 10)
+RandomMissingDataRate = VirtualMap(19, 10)
+
+End Sub
+
+Public Sub Simulate_Population_From_Map()
+
+'version for excel 2007+ ONLY
+'On Error GoTo 900
+Dim SegDistortersAreIndependant As Boolean, SDL2ConditionalToSDL1 As Boolean
+Dim genotypeNames() As Variant
+
+Application.ScreenUpdating = False
+
+Read_Parameters
+
+SegDistortersAreIndependant = True
+SDL2ConditionalToSDL1 = False
+
+'QTL1 parameters
+ChrQTL1 = ThisWorkbook.Sheets("SimulMap").[R29]
+MarkerNumberQTL1 = ThisWorkbook.Sheets("SimulMap").[R30]
+MeanAA_QTL1 = ThisWorkbook.Sheets("SimulMap").[R31]
+MeanAB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R32]
+MeanBB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R33]
+VarCoeffAA_QTL1 = ThisWorkbook.Sheets("SimulMap").[R34]
+VarCoeffAB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R35]
+VarCoeffBB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R36]
+SD_AA_QTL1 = MeanAA_QTL1 * VarCoeffAA_QTL1
+SD_AB_QTL1 = MeanAB_QTL1 * VarCoeffAB_QTL1
+SD_BB_QTL1 = MeanBB_QTL1 * VarCoeffBB_QTL1
+Mean_QTL1_for_Random_Backcross = 0.5 * (MeanAA_QTL1 + MeanAB_QTL1)
+SD_AA_QTL1_for_Random_Backcross = Mean_QTL1_for_Random_Backcross * 0.5 * (VarCoeffAA_QTL1 + VarCoeffAB_QTL1)
+Mean_QTL1_for_Random_DH = 0.5 * (MeanAA_QTL1 + MeanBB_QTL1)
+Mean_QTL1_for_Random_F2 = 0.5 * (MeanAA_QTL1 + MeanBB_QTL1)
+
+If AutoBatchMapOn = 0 Then Application.StatusBar = "Starting..."
+
+'Population Parameters
+Sheets("SimulMap").[K6] = "Simulating population... ": Application.ScreenUpdating = True: DoEvents: Application.ScreenUpdating = False
+
+If AutoBatchMapOn = 1 Then
+ NumberOfSimulatedPopulations = 1
+ Read_Simulation_Parameters
+Else
+ ThisWorkbook.Sheets("SimulMap").Activate
+ NumberOfSimulatedPopulations = ThisWorkbook.Sheets("SimulMap").[N15]
+ saveInFiles = ThisWorkbook.Sheets("SimulMap").[O15]
+ VirtualMap = ThisWorkbook.Sheets("SimulMap").UsedRange.Value
+
+ SimulatedPopulationType = ThisWorkbook.Sheets("SimulMap").[N16] 'ONLY BC1 & F2 pops at this stage
+ If SimulatedPopulationType <> "BC1" And SimulatedPopulationType <> "F2" _
+ And SimulatedPopulationType <> "BC2F1" And SimulatedPopulationType <> "SSD" _
+ Then MsgBox "BC1 or F2 or SSD populations only, sorry.": GoTo 1000
+ SimulatedPopulationSize = ThisWorkbook.Sheets("SimulMap").[N17] 'NOT more than 508 individuals at this stage
+' If MaxNumberOfColumns = 256 Then
+ If SimulatedPopulationSize > 16382 And NumberOfSimulatedPopulations = 1 Then
+ SimulatedPopulationSize = 1
+ MsgBox "I can't simulate more than 16382 individuals. If you need more individuals, please simulate 2 or more populations; this will generate Mapmaker/EXP compatible files that you can analyze using the BatchMap command."
+ End If
+' End If
+
+ ChromosomeSDL1 = ThisWorkbook.Sheets("SimulMap").[R9]
+ If ChromosomeSDL1 > 0 Then
+ PositionSDL1 = ThisWorkbook.Sheets("SimulMap").[R10]
+ ViabU = ThisWorkbook.Sheets("SimulMap").[R15] 'differential viability fA/fB for SDL1 (BC1 or F2) - gametic selection
+ ViabU1 = ThisWorkbook.Sheets("SimulMap").[R16] 'differential viability fAA/fBB for SDL1 (F2) - zygotic selection
+ ViabU2 = ThisWorkbook.Sheets("SimulMap").[R17] 'differential viability fAB/fBB for SDL1 (F2) - zygotic selection
+ ViabU3 = ViabU2 / ViabU1 'differential viability fAB/fAA for SDL1 (F2) - zygotic selection
+ SDL1AbsoluteNumber = 0
+ For i = 1 To ChromosomeSDL1 - 1
+ SDL1AbsoluteNumber = SDL1AbsoluteNumber + ThisWorkbook.Sheets("SimulMap").Cells(26 + i, 12)
+ Next
+ SDL1AbsoluteNumber = SDL1AbsoluteNumber + PositionSDL1
+ End If
+
+ ChromosomeSDL2 = ThisWorkbook.Sheets("SimulMap").[R11]
+ If ChromosomeSDL2 > 0 Then
+ PositionSDL2 = ThisWorkbook.Sheets("SimulMap").[R12]
+ ViabV = ThisWorkbook.Sheets("SimulMap").[R18]
+ ViabV1 = ThisWorkbook.Sheets("SimulMap").[R19]
+ ViabV2 = ThisWorkbook.Sheets("SimulMap").[R20]
+ ViabV3 = ViabV2 / ViabV1 'differential viability fAB/fAA for SDL2 (F2) - zygotic selection
+ SDL2AbsoluteNumber = 0
+ For i = 1 To ChromosomeSDL2 - 1
+ SDL2AbsoluteNumber = SDL2AbsoluteNumber + Cells(26 + i, 12)
+ Next
+ SDL2AbsoluteNumber = SDL2AbsoluteNumber + PositionSDL2
+ End If
+
+ 'F2 options for segregation distortion
+ SelTypeGameticMaleSDL1 = ThisWorkbook.Sheets("SimulMap").[X15]
+ SelTypeGameticFemaleSDL1 = ThisWorkbook.Sheets("SimulMap").[X16]
+ SelTypeZygoticSDL1 = ThisWorkbook.Sheets("SimulMap").[X17]
+ SelTypeGameticMaleSDL2 = ThisWorkbook.Sheets("SimulMap").[X18]
+ SelTypeGameticFemaleSDL2 = ThisWorkbook.Sheets("SimulMap").[X19]
+ SelTypeZygoticSDL2 = ThisWorkbook.Sheets("SimulMap").[X20]
+
+ NumberOfSimulatedTraits = 1
+ NumberOfSimulatedRandomTraits = ThisWorkbook.Sheets("SimulMap").[N19]
+
+ nbOfSupPops = 1
+ If NumberOfSimulatedPopulations > 1 And saveInFiles = True Then
+ OperatingSystem = ThisWorkbook.Sheets("hide").Cells(8, 1)
+ OperatingSystem = UCase(Left(OperatingSystem, 3))
+ If OperatingSystem = "WIN" Then
+ FileSaveName = Application.GetSaveAsFilename(Title:="Locate the folder to export the data (Don't rename the MyPop.txt file please): ", InitialFileName:="MyPop.txt", fileFilter:="Text Files (*.txt), *.txt")
+ ElseIf OperatingSystem = "MAC" Then
+ FileSaveName = Application.GetSaveAsFilename(Title:="Locate the folder to export the data (Don't rename the MyPop.txt file please): ", InitialFileName:="MyPop.txt", fileFilter:="TEXT")
+ End If
+ If FileSaveName = False Then GoTo 1000
+
+ LengthOfPath = Len(FileSaveName)
+ OutputPath = Left(FileSaveName, LengthOfPath - 9)
+ 'MsgBox "The output folder will be " & Chr(13) & OutputPath
+ ElseIf NumberOfSimulatedPopulations > 1 And saveInFiles = False Then
+ nbOfSupPops = NumberOfSimulatedPopulations
+ subPopSize = Int(SimulatedPopulationSize / nbOfSupPops)
+ remainderSubPopSize = SimulatedPopulationSize - nbOfSupPops * subPopSize
+ NumberOfSimulatedPopulations = 1
+
+ ReDim genotypeNames(1 To 1, 1 To SimulatedPopulationSize)
+ outcolsub = 1
+ For subPop = 1 To nbOfSupPops
+ For mygenot = 1 To subPopSize
+ genotypeNames(1, outcolsub) = "pop" & subPop & "_genot" & mygenot
+ outcolsub = outcolsub + 1
+ Next
+ Next
+ If remainderSubPopSize > 0 Then
+ genotnumber = subPopSize + 1
+ For mygenot = nbOfSupPops * subPopSize + 1 To SimulatedPopulationSize
+ genotypeNames(1, mygenot) = "pop" & nbOfSupPops & "_genot" & genotnumber
+ genotnumber = genotnumber + 1
+ Next
+ End If
+ MapFunctionSimul = ThisWorkbook.Sheets("SimulMap").[N18]
+ ElseIf NumberOfSimulatedPopulations = 1 And saveInFiles = False Then
+ ReDim genotypeNames(1 To 1, 1 To SimulatedPopulationSize)
+ For mygenot = 1 To SimulatedPopulationSize
+ genotypeNames(1, mygenot) = "pop1" & "_genot" & mygenot
+ Next
+
+ MapFunctionSimul = ThisWorkbook.Sheets("SimulMap").[N18]
+
+ End If
+
+
+ 'Reading map parameters
+ Application.StatusBar = "Reading map parameters"
+
+ 'TotalMapSize = [N22]
+ NumberOfSimulatedMarkers = ThisWorkbook.Sheets("SimulMap").[N23]
+ NumberOfSimulatedChromosomes = ThisWorkbook.Sheets("SimulMap").[R22]
+ RandomErrorRate = [j18]
+ RandomMissingDataRate = [j19]
+
+End If
+'If NumberOfSimulatedPopulations > 1 And AutoBatchMapOn = 0 Then ' simulate genotypes and write in txt files
+
+Dim SimulatedGenotypes() As Variant
+
+Randomize (Rnd)
+
+For SimulatedPopulation = 1 To NumberOfSimulatedPopulations
+
+ If AutoBatchMapOn = 0 Then Application.StatusBar = "Simulating population " & SimulatedPopulation & " of " & NumberOfSimulatedPopulations
+
+ 'ReDim SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedPopulationSize + 1) As Variant
+ ReDim SimulatedGenotypes(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedRandomTraits + 1, SimulatedPopulationSize + 1)
+
+'BACKCROSS
+ If SimulatedPopulationType = "BC1" Then 'fake, because does not simulate properly the 4 possible gametes. However gives correct RFs (+ or -)
+
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+10
+ If AutoBatchMapOn = 0 Then Application.StatusBar = "Pop " & SimulatedPopulation & " of " & NumberOfSimulatedPopulations & ": Genot " & SimulatedGenotype & " of " & SimulatedPopulationSize
+ StartRow = 1
+
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+
+ ChrSize = VirtualMap(26 + chromosome, 11)
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ MarkerPositionOld = 0
+ If Rnd > 0.5 Then Genotype = "A" Else Genotype = "H"
+ SimulatedGenotypes(StartRow, SimulatedGenotype) = Genotype
+ For Marker = 2 To NbOfMrksInChr
+ 'Application.StatusBar = "Pop " & SimulatedPopulation & " of " & NumberOfSimulatedPopulations & " - Chr " & chromosome & " - Mk " & marker
+
+ MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
+ IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
+ If MapFunctionSimul = 1 Then
+ IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
+ ElseIf MapFunctionSimul = 2 Then
+ temp = 2 * (IntervalWithPreviousMarker / 100)
+ IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
+ End If
+ 'IntervalWithPreviousMarkerInRF = IntervalWithPreviousMarker / 100
+
+ If Rnd <= IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+ If Genotype = "A" Then
+ Genotype = "H"
+ ElseIf Genotype = "H" Then
+ Genotype = "A"
+ End If
+ End If
+
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
+
+ 'simulate non-random trait
+ If ChrQTL1 = chromosome Then
+ If Marker = MarkerNumberQTL1 Then
+ If Genotype = "A" Then
+ myAAvalue = gauss * SD_AA_QTL1 + MeanAA_QTL1
+ SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedGenotype) = Format(myAAvalue, "###.00")
+ ElseIf Genotype = "H" Then
+ myABvalue = gauss * SD_AB_QTL1 + MeanAB_QTL1
+ SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedGenotype) = Format(myABvalue, "###.00")
+ End If
+ End If
+ End If
+ MarkerPositionOld = MarkerPosition
+ Next 'Marker
+ StartRow = StartRow + NbOfMrksInChr
+ Next 'chromosome
+
+ GameteIsDead = 0
+ GameteIsDeadSDL1 = 0
+ GameteIsDeadSDL2 = 0
+
+ If ChromosomeSDL1 > 0 Then ' there is a segregation distorter
+ FreqA = ViabU / (1 + ViabU) 'final frequency, 0 to 0.5
+ 'SurvivalA = FreqA * 2 '0 to 1
+ FreqH = 1 / (1 + ViabU) 'final frequency
+ 'SurvivalH = FreqH * 2
+ myRandkillSDL1 = Rnd
+ If ViabU < 1 Then 'selection against AA genotypes or A gametes
+' If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "A" And myRandkill > FreqA Then 'you're dead, gamete A!
+ If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "A" And myRandkillSDL1 > ViabU Then 'you're dead, gamete A!
+ GameteIsDeadSDL1 = 1
+ End If
+ ElseIf ViabU > 1 Then 'selection against H genotypes or B gametes
+' If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "H" And myRandkill > FreqH Then ' you're dead, gamete B!
+ If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "H" And myRandkillSDL1 > 1 / ViabU Then ' you're dead, gamete B!
+ GameteIsDeadSDL1 = 1
+ End If
+ End If
+ End If
+
+ If ChromosomeSDL2 > 0 Then ' there is another segregation distorter
+ FreqA = ViabV / (1 + ViabV) 'final frequency, 0 to 0.5
+ 'SurvivalA = FreqA * 2 '0 to 1
+ FreqH = 1 / (1 + ViabV) 'final frequency
+ 'SurvivalH = FreqH * 2
+ myRandkillSDL2 = Rnd
+ If ViabV < 1 Then 'selection against AA genotypes or A gametes
+ If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "A" And myRandkillSDL2 > ViabV Then '... you're dead, gamete A!
+ GameteIsDeadSDL2 = 1
+ End If
+ ElseIf ViabV > 1 Then 'selection against H genotypes or B gametes
+ If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "H" And myRandkillSDL2 > 1 / ViabV Then '... you're dead, gamete B!
+ GameteIsDeadSDL2 = 1
+ End If
+ End If
+ End If
+
+ If SegDistortersAreIndependant = True Then 'no epistasis
+ If GameteIsDeadSDL1 = 1 Or GameteIsDeadSDL2 = 1 Then GameteIsDead = 1
+ ElseIf SegDistortersAreIndependant = False Then 'both death required, epistasis
+ If SDL2ConditionalToSDL1 = True Then
+ If GameteIsDeadSDL1 = 0 And GameteIsDeadSDL2 = 1 Then GameteIsDead = 1
+ ElseIf SDL2ConditionalToSDL1 = False Then
+ If GameteIsDeadSDL1 = 1 And GameteIsDeadSDL2 = 1 Then GameteIsDead = 1
+ End If
+ End If
+
+ If GameteIsDead = 1 Then GoTo 10
+
+ 'random traits (normally distributed)
+ For mytrait = 1 To NumberOfSimulatedRandomTraits
+ myvalue = gauss * SD_AA_QTL1_for_Random_Backcross + Mean_QTL1_for_Random_Backcross
+ SimulatedGenotypes(NumberOfSimulatedMarkers + NumberOfSimulatedTraits + mytrait, SimulatedGenotype) = Format(myvalue, "###.00")
+' SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
+ Next 'mytrait
+
+ Next 'SimulatedGenotype
+
+ If RandomErrorRate > 0 And RandomErrorRate <= 1 Then
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+ StartRow = 1
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ For Marker = 1 To NbOfMrksInChr
+ If Rnd >= (1 - RandomErrorRate) Then
+ If SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A" Then
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H"
+ ElseIf SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H" Then
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A"
+ End If
+ End If
+ Next Marker
+ StartRow = StartRow + NbOfMrksInChr
+ Next chromosome
+ Next SimulatedGenotype
+ End If
+
+ If RandomMissingDataRate > 0 And RandomMissingDataRate <= 1 Then
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+ StartRow = 1
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ For Marker = 1 To NbOfMrksInChr
+ If Rnd >= 1 - RandomMissingDataRate Then
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "-"
+ End If
+ Next Marker
+ StartRow = StartRow + NbOfMrksInChr
+ Next chromosome
+ Next SimulatedGenotype
+ End If
+
+ For mytrait = 1 To NumberOfSimulatedRandomTraits
+ SimulatedGenotypes(NumberOfSimulatedMarkers + NumberOfSimulatedTraits + mytrait, 0) = "RandomQTrait_" & mytrait
+ Next 'mytrait
+
+ SimulatedGenotypes(NumberOfSimulatedMarkers + 1, 0) = "SimulatedQTrait_1"
+
+
+'BACKCROSS - RARE
+ ElseIf SimulatedPopulationType = "BC1bizarre" Then 'try to mimic better meiosis behavior
+
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+ StartRow = 1
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ ChrSize = VirtualMap(26 + chromosome, 11)
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ MarkerPositionOld = 0
+ Marker = StartRow
+ If Rnd > 0.5 Then Genotype = "A" Else Genotype = "H"
+ SimulatedGenotypes(Marker, SimulatedGenotype) = Genotype
+ If Rnd > 0.5 Then 'Recombined Gamete
+ For Marker = 2 To NbOfMrksInChr
+ MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
+ IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld 'in cM
+ If MapFunctionSimul = 1 Then
+ IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
+ ElseIf MapFunctionSimul = 2 Then
+ temp = 2 * (IntervalWithPreviousMarker / 100)
+ IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
+ End If
+ 'Randomize (Rnd)
+ If Rnd > 1 - 2 * IntervalWithPreviousMarkerInRF Then 'a recombination occurred - seems to generate too many 2ble recombinations
+ If Genotype = "A" Then
+ Genotype = "H"
+ ElseIf Genotype = "H" Then
+ Genotype = "A"
+ End If
+ End If
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
+ MarkerPositionOld = MarkerPosition
+ Next 'Marker
+ Else 'parental gamete
+ For Marker = 2 To NbOfMrksInChr
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
+ Next 'Marker
+ End If
+ StartRow = StartRow + NbOfMrksInChr
+ Next 'chromosome
+
+ Next 'SimulatedGenotype
+
+
+'BC2F1
+ ElseIf SimulatedPopulationType = "BC2F1" Then
+' A FINIR
+
+ BC2FamilySize = 4 ' a mettre en variable
+
+ BC2PopulationSize = SimulatedPopulationSize * BC2FamilySize
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+50
+ StartRow = 1
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ ChrSize = VirtualMap(26 + chromosome, 11)
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ MarkerPositionOld = 0
+ Marker = StartRow
+ If Rnd > 0.5 Then Genotype = "A" Else Genotype = "H"
+ SimulatedGenotypes(Marker, SimulatedGenotype) = Genotype
+ For Marker = 2 To NbOfMrksInChr
+ MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
+ IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
+ If MapFunctionSimul = 1 Then
+ IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
+ ElseIf MapFunctionSimul = 2 Then
+ temp = 2 * (IntervalWithPreviousMarker / 100)
+ IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
+ End If
+ If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+ If Genotype = "A" Then
+ Genotype = "H"
+ ElseIf Genotype = "H" Then
+ Genotype = "A"
+ End If
+ End If
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
+ MarkerPositionOld = MarkerPosition
+ Next Marker
+ StartRow = StartRow + NbOfMrksInChr
+ Next chromosome
+ ' For mytrait = 1 To NumberOfSimulatedRandomTraits
+ ' SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
+ ' Next mytrait
+ Next SimulatedGenotype
+ ' For mytrait = 1 To NumberOfSimulatedRandomTraits
+ ' SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, 0) = "RandomQTrait_" & mytrait
+ ' Next mytrait
+
+
+
+' F2 POPULATION
+ ElseIf SimulatedPopulationType = "F2" Then
+
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+100
+ StartRow = 1
+ Gamete1_Is_Dead = 0
+ Gamete2_Is_Dead = 0
+ Zygote_Is_Dead = 0
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ ChrSize = VirtualMap(26 + chromosome, 11)
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ MarkerPositionOld = 0
+ 'Randomize (Rnd)
+ If Rnd > 0.5 Then genotype1 = "A" Else genotype1 = "B"
+ 'Randomize (Rnd)
+ If Rnd > 0.5 Then genotype2 = "B" Else genotype2 = "A"
+ Marker = StartRow
+ If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "A"
+ If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "B"
+ If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "H"
+ If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "H"
+
+ For Marker = 2 To NbOfMrksInChr
+ MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
+ IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
+ If MapFunctionSimul = 1 Then
+ IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
+ ElseIf MapFunctionSimul = 2 Then
+ temp = 2 * (IntervalWithPreviousMarker / 100)
+ IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
+ End If
+
+ 'male gamete
+ 'Randomize (Rnd)
+ If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+ If genotype1 = "A" Then
+ genotype1 = "B"
+ ElseIf genotype1 = "B" Then
+ genotype1 = "A"
+ End If
+ End If
+ 'selection on male gamete (SDL 1)
+ If SelTypeGameticMaleSDL1 = "x" Then
+ If chromosome = ChromosomeSDL1 Then
+ If Marker = PositionSDL1 Then
+ ''Debug.Print "SDL1 - gam sel", ViabU
+ myRandkill = Rnd
+ If ViabU < 1 Then 'selection against A gametes
+ If genotype1 = "A" And myRandkill > ViabU Then 'gamete A dies
+ Gamete1_Is_Dead = 1
+ ''Debug.Print "killed"
+ End If
+ ElseIf ViabU > 1 Then 'selection against B gametes
+ If genotype1 = "B" And myRandkill > 1 / ViabU Then 'gamete B dies
+ Gamete1_Is_Dead = 1
+ ''Debug.Print "killed"
+ End If
+ End If
+ End If
+ End If
+ End If
+ If SelTypeGameticMaleSDL2 = "x" Then
+ 'selection on male gamete (SDL 2)
+ If chromosome = ChromosomeSDL2 Then
+ If Marker = PositionSDL2 Then
+ myRandkill = Rnd
+ If ViabV < 1 Then 'selection against A gametes
+ If genotype1 = "A" And myRandkill > ViabV Then 'gamete A dies
+ Gamete1_Is_Dead = 1
+ End If
+ ElseIf ViabU > 1 Then 'selection against B gametes
+ If genotype1 = "B" And myRandkill > 1 / ViabV Then 'gamete B dies
+ Gamete1_Is_Dead = 1
+ End If
+ End If
+ End If
+ End If
+ End If
+ 'female gamete
+ If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+ If genotype2 = "A" Then
+ genotype2 = "B"
+ ElseIf genotype2 = "B" Then
+ genotype2 = "A"
+ End If
+ End If
+' Gamete2_Is_Dead = 0
+ 'selection
+ If SelTypeGameticFemaleSDL1 = "x" Then
+ If chromosome = ChromosomeSDL1 Then
+ If Marker = PositionSDL1 Then
+ myRandkill = Rnd
+ If ViabU < 1 Then 'selection against A gametes
+ If genotype2 = "A" And myRandkill > ViabU Then 'gamete A dies
+ Gamete2_Is_Dead = 1
+ End If
+ ElseIf ViabU > 1 Then 'selection against B gametes
+ If genotype2 = "B" And myRandkill > 1 / ViabU Then 'gamete B dies
+ Gamete2_Is_Dead = 1
+ End If
+ End If
+ End If
+ End If
+ End If
+ If SelTypeGameticFemaleSDL2 = "x" Then
+ If chromosome = ChromosomeSDL2 Then
+ If Marker = PositionSDL2 Then
+ myRandkill = Rnd
+ If ViabV < 1 Then 'selection against A gametes
+ If genotype2 = "A" And myRandkill > ViabV Then 'gamete A dies
+ Gamete2_Is_Dead = 1
+ End If
+ ElseIf ViabU > 1 Then 'selection against B gametes
+ If genotype2 = "B" And myRandkill > 1 / ViabV Then 'gamete B dies
+ Gamete2_Is_Dead = 1
+ End If
+ End If
+ End If
+ End If
+ End If
+ 'mating or selfing
+ If genotype1 = "A" And genotype2 = "A" Then Genotype = "A"
+ If genotype1 = "B" And genotype2 = "B" Then Genotype = "B"
+ If genotype1 = "A" And genotype2 = "B" Then Genotype = "H"
+ If genotype1 = "B" And genotype2 = "A" Then Genotype = "H"
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
+ 'simulate non-random trait
+ If ChrQTL1 = chromosome Then
+ If Marker = MarkerNumberQTL1 Then
+ If Genotype = "H" Then
+ myABvalue = gauss * SD_AB_QTL1 + MeanAB_QTL1
+ SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedGenotype) = Format(myABvalue, "###.00")
+ ElseIf Genotype = "A" Then
+ myAAvalue = gauss * SD_AA_QTL1 + MeanAA_QTL1
+ SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedGenotype) = Format(myAAvalue, "###.00")
+ ElseIf Genotype = "B" Then
+ myBBvalue = gauss * SD_BB_QTL1 + MeanBB_QTL1
+ SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedGenotype) = Format(myBBvalue, "###.00")
+ End If
+ End If
+ End If
+ MarkerPositionOld = MarkerPosition
+
+ Next Marker
+ StartRow = StartRow + NbOfMrksInChr
+
+ Next chromosome
+
+ If Gamete1_Is_Dead = 1 Then GoTo 100
+ If Gamete2_Is_Dead = 1 Then GoTo 100
+
+ 'eliminate zygotes
+
+ If ChromosomeSDL1 > 0 Then ' there is a segregation distorter
+ myRandkill = Rnd
+ If ViabU1 < 1 Then 'selection against AA genotype relative to BB genotype
+ If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "A" And myRandkill > ViabU1 Then 'AA killed
+ Zygote_Is_Dead = 1
+ End If
+ ElseIf ViabU1 > 1 Then 'selection against AA genotype relative to BB genotype
+ If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "B" And myRandkill > 1 / ViabU1 Then 'sorry, bad luck... you're dead, gamete B!
+ Zygote_Is_Dead = 1
+ End If
+ End If
+ If ViabU2 < 1 Then 'selection against AB genotype relative to BB genotype
+ If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "H" And myRandkill > ViabU2 Then 'AA killed
+ Zygote_Is_Dead = 1
+ End If
+ ElseIf ViabU2 > 1 Then 'selection against BB genotype versus AB genotype
+ If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "B" And myRandkill > 1 / ViabU2 Then 'sorry, bad luck... you're dead, gamete B!
+ Zygote_Is_Dead = 1
+ End If
+ End If
+ If ViabU3 < 1 Then 'selection against AB genotype relative to AA genotype
+ If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "H" And myRandkill > ViabU3 Then 'AA killed
+ Zygote_Is_Dead = 1
+ End If
+ ElseIf ViabU3 > 1 Then 'selection against AA genotype versus AB genotype
+ If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "A" And myRandkill > 1 / ViabU3 Then 'sorry, bad luck... you're dead, gamete B!
+ Zygote_Is_Dead = 1
+ End If
+ End If
+ End If
+
+ If ChromosomeSDL2 > 0 Then ' there is a segregation distorter
+ myRandkill = Rnd
+ If ViabV1 < 1 Then 'selection against AA genotype relative to BB genotype
+ If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "A" And myRandkill > ViabV1 Then 'AA killed
+ Zygote_Is_Dead = 1
+ End If
+ ElseIf ViabV1 > 1 Then 'selection against AA genotype relative to BB genotype
+ If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "B" And myRandkill > 1 / ViabV1 Then 'sorry, bad luck... you're dead, gamete B!
+ Zygote_Is_Dead = 1
+ End If
+ End If
+ If ViabV2 < 1 Then 'selection against AB genotype relative to BB genotype
+ If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "H" And myRandkill > ViabV2 Then 'AA killed
+ Zygote_Is_Dead = 1
+ End If
+ ElseIf ViabV2 > 1 Then 'selection against BB genotype versus AB genotype
+ If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "B" And myRandkill > 1 / ViabV2 Then 'sorry, bad luck... you're dead, gamete B!
+ Zygote_Is_Dead = 1
+ End If
+ End If
+ If ViabV3 < 1 Then 'selection against AB genotype relative to AA genotype
+ If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "H" And myRandkill > ViabV3 Then 'AA killed
+ Zygote_Is_Dead = 1
+ End If
+ ElseIf ViabV3 > 1 Then 'selection against AA genotype versus AB genotype
+ If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "A" And myRandkill > 1 / ViabV3 Then 'sorry, bad luck... you're dead, gamete B!
+ Zygote_Is_Dead = 1
+ End If
+ End If
+ End If
+
+ If Zygote_Is_Dead = 1 Then GoTo 100
+ 'random traits
+ For mytrait = 1 To NumberOfSimulatedRandomTraits
+ SimulatedGenotypes(NumberOfSimulatedMarkers + NumberOfSimulatedTraits + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
+ Next mytrait
+
+ Next SimulatedGenotype
+
+ SimulatedGenotypes(NumberOfSimulatedMarkers + 1, 0) = "SimulatedQTrait_1"
+
+ 'random traits names
+ For mytrait = 1 To NumberOfSimulatedRandomTraits
+ SimulatedGenotypes(NumberOfSimulatedMarkers + NumberOfSimulatedTraits + mytrait, 0) = "RandomQTrait_" & mytrait
+ Next mytrait
+
+ If RandomErrorRate > 0 And RandomErrorRate <= 1 Then
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+ StartRow = 1
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ For Marker = 1 To NbOfMrksInChr
+ If Rnd >= 1 - RandomErrorRate Then
+ If SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A" Then
+ If Rnd >= (1 / 3) Then
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H"
+ Else
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "B"
+ End If
+ ElseIf SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "B" Then
+ If Rnd >= (1 / 3) Then
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H"
+ Else
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A"
+ End If
+ ElseIf SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H" Then
+ If Rnd >= 0.5 Then
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A"
+ Else
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "B"
+ End If
+ End If
+ End If
+ Next Marker
+ StartRow = StartRow + NbOfMrksInChr
+ Next chromosome
+ Next SimulatedGenotype
+ End If
+ If RandomMissingDataRate > 0 And RandomMissingDataRate <= 1 Then
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+ StartRow = 1
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ For Marker = 1 To NbOfMrksInChr
+ If Rnd >= 1 - RandomMissingDataRate Then
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "-"
+ End If
+ Next Marker
+ StartRow = StartRow + NbOfMrksInChr
+ Next chromosome
+ Next SimulatedGenotype
+ End If
+
+
+
+'SSD - RIL
+ ElseIf SimulatedPopulationType = "SSD" Then 'it's fake but should work. however does not allow to test for biased estimates
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+ StartRow = 1
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ ChrSize = VirtualMap(26 + chromosome, 11)
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ MarkerPositionOld = 0
+ Marker = StartRow
+ If Rnd > 0.5 Then Genotype = "A" Else Genotype = "B"
+ SimulatedGenotypes(Marker, SimulatedGenotype) = Genotype
+ For Marker = 2 To NbOfMrksInChr
+ MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
+ IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
+ If MapFunctionSimul = 1 Then
+ myRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
+ myR = 2 * myRF / (1 + 2 * myRF)
+ IntervalWithPreviousMarkerInRF = myR ' fake conversion of recombination rate in SSD (the 'R')
+
+' IntervalWithPreviousMarkerInR_MartinAndHospital = 1 ' fake conversion of recombination rate in SSD (the 'R')
+
+ ElseIf MapFunctionSimul = 2 Then
+ temp = 2 * (IntervalWithPreviousMarker / 100)
+ myRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
+ myR = 2 * myRF / (1 + 2 * myRF)
+ IntervalWithPreviousMarkerInRF = myR ' fake conversion of recombination rate in SSD (the 'R')
+ End If
+ 'Randomize (Rnd)
+ If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+ If Genotype = "A" Then
+ Genotype = "B"
+ ElseIf Genotype = "B" Then
+ Genotype = "A"
+ End If
+ End If
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
+
+ 'simulate non-random trait
+ If ChrQTL1 = chromosome Then
+ If Marker = MarkerNumberQTL1 Then
+ If Genotype = "A" Then
+ myAAvalue = gauss * SD_AA_QTL1 + MeanAA_QTL1
+ SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedGenotype) = Format(myAAvalue, "###.00")
+ ElseIf Genotype = "B" Then
+ myBBvalue = gauss * SD_BB_QTL1 + MeanBB_QTL1
+ SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedGenotype) = Format(myBBvalue, "###.00")
+ End If
+ End If
+ End If
+ MarkerPositionOld = MarkerPosition
+ Next Marker
+ StartRow = StartRow + NbOfMrksInChr
+ Next chromosome
+
+ For mytrait = 1 To NumberOfSimulatedRandomTraits
+ SimulatedGenotypes(NumberOfSimulatedMarkers + NumberOfSimulatedTraits + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
+ Next mytrait
+
+ Next SimulatedGenotype
+
+ If RandomErrorRate > 0 And RandomErrorRate <= 1 Then
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+ StartRow = 1
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ For Marker = 1 To NbOfMrksInChr
+ If Rnd >= 1 - RandomErrorRate Then
+ If SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A" Then
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "B"
+ ElseIf SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "B" Then
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A"
+ End If
+ End If
+ Next Marker
+ StartRow = StartRow + NbOfMrksInChr
+ Next chromosome
+ Next SimulatedGenotype
+ End If
+ If RandomMissingDataRate > 0 And RandomMissingDataRate <= 1 Then
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+ StartRow = 1
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ For Marker = 1 To NbOfMrksInChr
+ If Rnd >= 1 - RandomMissingDataRate Then
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "-"
+ End If
+ Next Marker
+ StartRow = StartRow + NbOfMrksInChr
+ Next chromosome
+ Next SimulatedGenotype
+ End If
+ SimulatedGenotypes(NumberOfSimulatedMarkers + 1, 0) = "SimulatedQTrait_1"
+
+ For mytrait = 1 To NumberOfSimulatedRandomTraits
+ SimulatedGenotypes(NumberOfSimulatedMarkers + NumberOfSimulatedTraits + mytrait, 0) = "RandomQTrait_" & mytrait
+ Next 'mytrait
+' ElseIf SimulatedPopulationType = "SSD" Then
+'
+' 'en cours a finir
+'
+' NumberOfSelfings = 6 ' Additional selfings after the F2 = S1 so 6 gives an F8
+'
+' For SimulatedGenotype = 1 To SimulatedPopulationSize
+' StartRow = 1
+' For Chromosome = 1 To NumberOfSimulatedChromosomes
+' ChrSize = VirtualMap(26 + Chromosome, 11)
+' NbOfMrksInChr = VirtualMap(26 + Chromosome, 12)
+' MarkerPositionOld = 0
+' 'Randomize (Rnd)
+' If Rnd > 0.5 Then genotype1 = "A" Else genotype1 = "B"
+' 'Randomize (Rnd)
+' If Rnd > 0.5 Then genotype2 = "B" Else genotype2 = "A"
+' marker = StartRow
+' If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(marker, SimulatedGenotype) = "A"
+' If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(marker, SimulatedGenotype) = "B"
+' If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(marker, SimulatedGenotype) = "H"
+' If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(marker, SimulatedGenotype) = "H"
+'
+' For marker = 2 To NbOfMrksInChr
+' MarkerPosition = VirtualMap(StartRow + marker + 4, 5)
+' IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
+' If MapFunctionSimul = 1 Then
+' IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
+' ElseIf MapFunctionSimul = 2 Then
+' temp = 2 * (IntervalWithPreviousMarker / 100)
+' IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
+' End If
+' 'gamete 1
+' 'Randomize (Rnd)
+' If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+' If genotype1 = "A" Then
+' genotype1 = "B"
+' ElseIf genotype1 = "B" Then
+' genotype1 = "A"
+' End If
+' End If
+' 'gamete 2
+' 'Randomize (Rnd)
+' If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+' If genotype2 = "A" Then
+' genotype2 = "B"
+' ElseIf genotype2 = "B" Then
+' genotype2 = "A"
+' End If
+' End If
+' If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "AA"
+' If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "BB"
+' If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "AB"
+' If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "BA"
+' MarkerPositionOld = MarkerPosition
+' Next marker
+'
+' StartRow = StartRow + NbOfMrksInChr
+' Next Chromosome
+'
+' For mytrait = 1 To NumberOfSimulatedRandomTraits
+' SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
+' Next mytrait
+'
+' For SelfingGeneration = 1 To NumberOfSelfings
+' StartRow = 1
+'
+' For Chromosome = 1 To NumberOfSimulatedChromosomes
+' ChrSize = VirtualMap(26 + Chromosome, 11)
+' NbOfMrksInChr = VirtualMap(26 + Chromosome, 12)
+' MarkerPositionOld = 0
+'
+' If Rnd > 0.5 Then genotype1 = "A" Else genotype1 = "B"
+'
+' If Rnd > 0.5 Then genotype2 = "B" Else genotype2 = "A"
+' marker = StartRow
+' If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(marker, SimulatedGenotype) = "A"
+' If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(marker, SimulatedGenotype) = "B"
+' If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(marker, SimulatedGenotype) = "H"
+' If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(marker, SimulatedGenotype) = "H"
+'
+' For marker = 2 To NbOfMrksInChr
+' MarkerPosition = VirtualMap(StartRow + marker + 4, 5)
+' IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
+' If MapFunctionSimul = 1 Then
+' IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
+' ElseIf MapFunctionSimul = 2 Then
+' temp = 2 * (IntervalWithPreviousMarker / 100)
+' IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
+' End If
+' 'gamete 1
+' 'Randomize (Rnd)
+' If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+' If genotype1 = "A" Then
+' genotype1 = "B"
+' ElseIf genotype1 = "B" Then
+' genotype1 = "A"
+' End If
+' End If
+' 'gamete 2
+' 'Randomize (Rnd)
+' If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+' If genotype2 = "A" Then
+' genotype2 = "B"
+' ElseIf genotype2 = "B" Then
+' genotype2 = "A"
+' End If
+' End If
+' If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "AA"
+' If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "BB"
+' If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "AB"
+' If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "BA"
+' MarkerPositionOld = MarkerPosition
+' Next marker
+'
+' StartRow = StartRow + NbOfMrksInChr
+' Next Chromosome
+'
+' Next SelfingGeneration
+'
+' Next SimulatedGenotype
+'
+' For mytrait = 1 To NumberOfSimulatedRandomTraits
+' SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, 0) = "RandomQTrait_" & mytrait
+' Next mytrait
+
+
+ End If
+
+ Application.ScreenUpdating = True: DoEvents: Application.ScreenUpdating = False
+
+ 'Writing results
+ If NumberOfSimulatedPopulations > 1 And AutoBatchMapOn = 0 Then ' write pop in a .txt file
+
+ FileSaveName = "SimulPop_" & SimulatedPopulation & ".txt"
+ Open FileSaveName For Output As #1
+ If SimulatedPopulationType = "BC1" Then Print #1, "data type f2 backcross"
+ If SimulatedPopulationType = "F2" Then Print #1, "data type f2 intercross"
+ Print #1, Format(SimulatedPopulationSize, "###"); Spc(1); Format(NumberOfSimulatedMarkers, "###"); Spc(1); "0"
+ For Ligne = 1 To NumberOfSimulatedMarkers
+ NomLocus = VirtualMap(Ligne + 5, 4)
+ TexteLocus = ""
+ For Colonne = 1 To SimulatedPopulationSize
+ TexteLocus = TexteLocus & SimulatedGenotypes(Ligne, Colonne)
+ Next
+ Print #1, ; "*" & NomLocus; Spc(1); TexteLocus
+ Next
+ Close #1
+
+ ElseIf AutoBatchMapOn = 1 Then ' write pop in a array
+ For i = 1 To NumberOfSimulatedMarkers
+ For j = 1 To SimulatedPopulationSize
+ Data(j - 1, i - 1) = SimulatedGenotypes(i, j) 'stay in memory
+ Next
+ Next
+
+ ElseIf NumberOfSimulatedPopulations = 1 And AutoBatchMapOn = 0 Then ' write pop in a sheet
+ Application.StatusBar = "Writing results"
+ ClearSimulatedPopulation
+ OutPutSheetName = "SimulPop"
+ 'MsgBox SimulatedPopulationSize
+' If MaxNumberOfColumns = 256 Then
+' If SimulatedPopulationSize <= 254 And SimulatedPopulationSize <= 508 Then
+' ThisWorkbook.Sheets(OutPutSheetName).Range("B15").Resize(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedRandomTraits, SimulatedPopulationSize + 1) = SimulatedGenotypes
+' ElseIf SimulatedPopulationSize > 254 And SimulatedPopulationSize <= 508 Then
+' ThisWorkbook.Sheets(OutPutSheetName).Range("B15").Resize(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedRandomTraits, 255) = SimulatedGenotypes
+' ReDim SimulatedGenotypesPlus(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedRandomTraits, SimulatedPopulationSize - 254 + 1) As Variant
+' For i = 1 To NumberOfSimulatedMarkers
+' For j = 255 To SimulatedPopulationSize
+' SimulatedGenotypesPlus(i, j - 254) = SimulatedGenotypes(i, j)
+' Next
+' Next i
+' ThisWorkbook.Sheets("SimulPop+").Range("B15").Resize(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedRandomTraits, SimulatedPopulationSize - 253) = SimulatedGenotypesPlus
+' End If
+' ElseIf MaxNumberOfColumns = 16384 Then
+ ThisWorkbook.Sheets(OutPutSheetName).Range("B15").Resize(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedRandomTraits + 1, SimulatedPopulationSize + 1) = SimulatedGenotypes
+' End If
+ Application.ScreenUpdating = False
+ ThisWorkbook.Sheets("SimulMap").Activate
+ Range("D6").Select
+ Range(Selection, Selection.End(xlDown)).Select
+ Selection.Copy
+ [N22].Select
+ ThisWorkbook.Sheets(OutPutSheetName).Activate
+ Range("B16").Select
+ Selection.PasteSpecial Paste:=xlPasteValues, Operation:=xlNone, SkipBlanks _
+ :=False, Transpose:=False
+ [c15].Resize(1, SimulatedPopulationSize) = genotypeNames
+ Range("D4") = SimulatedPopulationType
+ Range("D5") = SimulatedPopulationSize
+ Range("D6") = NumberOfSimulatedMarkers
+ Range("D7") = NumberOfSimulatedRandomTraits + 1
+ Range("D8") = nbOfSupPops
+ Range("H4") = "A"
+ Range("H5") = "B"
+ Range("H6") = "C"
+ Range("H7") = "D"
+ Range("H8") = "H"
+ Range("H9") = "-"
+ Range("K4") = "2"
+ [b10] = "Simulated " & SimulatedPopulationType & " data " & Date & " - " & Time
+ Application.CutCopyMode = False
+ [K6] = ""
+ [B15].Select
+ End If
+Next SimulatedPopulation
+
+GoTo 1000
+900
+''Debug.Print Chromosome
+''Debug.Print StartRow
+''Debug.Print marker
+''Debug.Print SimulatedGenotype
+''Debug.Print genotype
+''Debug.Print StartRow + marker - 1
+1000
+'Application.ScreenUpdating = True
+'Next i
+
+If AutoBatchMapOn = 0 Then
+ Sheets("SimulMap").[K6] = ""
+ Application.StatusBar = False
+End If
+
+End Sub
+
+
+
+Public Sub Simulate_Population_From_Map_Save()
+Read_Parameters
+
+'On Error GoTo 900
+Application.ScreenUpdating = False
+If AutoBatchMapOn = 0 Then If AutoBatchMapOn = 0 Then Application.StatusBar = "Starting..."
+
+ThisWorkbook.Sheets("SimulMap").Activate
+
+'Population Parameters
+NumberOfSimulatedPopulations = [N15]
+SimulatedPopulationType = [N16] 'ONLY BC1 & F2 pops at this stage
+If SimulatedPopulationType <> "BC1" And SimulatedPopulationType <> "F2" And SimulatedPopulationType <> "BC2F1" Then MsgBox "BC1 or F2 populations only, sorry.": GoTo 1000
+SimulatedPopulationSize = [N17] 'NOT more than 508 individuals at this stage
+If AutoBatchMapOn = 0 And SimulatedPopulationSize > 508 And NumberOfSimulatedPopulations = 1 Then
+ SimulatedPopulationSize = 508
+ MsgBox "I can't simulate more than 508 individuals. If you need more indivuduals, please simulate 2 or more populations; this will generate Mapmaker/EXP compatible files that you can analyze using the BatchMap command."
+End If
+
+MapFunctionSimul = [N18]
+
+ChromosomeSDL1 = [R9]
+PositionSDL1 = [R10]
+ViabU = [R15] 'differential viability fA/fB for SDL1
+SDL1AbsoluteNumber = 0
+For i = 1 To ChromosomeSDL1 - 1
+ SDL1AbsoluteNumber = SDL1AbsoluteNumber + Cells(26 + i, 12)
+Next
+SDL1AbsoluteNumber = SDL1AbsoluteNumber + PositionSDL1
+
+ChromosomeSDL2 = [R11]
+PositionSDL2 = [R12]
+ViabV = [R17] 'differential viability fA/fB for SDL2
+SDL2AbsoluteNumber = 0
+For i = 1 To ChromosomeSDL2 - 1
+ SDL2AbsoluteNumber = SDL2AbsoluteNumber + Cells(26 + i, 12)
+Next
+SDL2AbsoluteNumber = SDL2AbsoluteNumber + PositionSDL2
+
+NumberOfSimulatedTraits = [N19]
+
+If NumberOfSimulatedPopulations > 1 Then
+ If AutoBatchMapOn = 0 Then
+ OperatingSystem = ThisWorkbook.Sheets("hide").Cells(8, 1)
+ OperatingSystem = UCase(Left(OperatingSystem, 3))
+ If OperatingSystem = "WIN" Then
+ FileSaveName = Application.GetSaveAsFilename(Title:="Locate the folder to export the data (Don't rename the MyPop.txt file please): ", InitialFileName:="MyPop.txt", fileFilter:="Text Files (*.txt), *.txt")
+ ElseIf OperatingSystem = "MAC" Then
+ FileSaveName = Application.GetSaveAsFilename(Title:="Locate the folder to export the data (Don't rename the MyPop.txt file please): ", InitialFileName:="MyPop.txt", fileFilter:="TEXT")
+ End If
+ If FileSaveName = False Then GoTo 1000
+
+ LengthOfPath = Len(FileSaveName)
+ OutputPath = Left(FileSaveName, LengthOfPath - 9)
+ 'MsgBox "The output folder will be " & Chr(13) & OutputPath
+ End If
+End If
+
+'Reading map parameters
+If AutoBatchMapOn = 0 Then Application.StatusBar = "Reading map parameters"
+
+VirtualMap = ThisWorkbook.Sheets("SimulMap").UsedRange.Value
+'TotalMapSize = [N22]
+NumberOfSimulatedMarkers = [N23]
+NumberOfSimulatedChromosomes = [R22]
+
+If NumberOfSimulatedPopulations > 1 And AutoBatchMapOn = 0 Then ' simulate genotypes and write in txt files
+ For SimulatedPopulation = 1 To NumberOfSimulatedPopulations
+ If AutoBatchMapOn = 0 Then Application.StatusBar = "Simulating population " & SimulatedPopulation & " of " & NumberOfSimulatedPopulations
+
+ ReDim SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedPopulationSize + 1) As Variant
+
+ StartRow = 1
+
+ If SimulatedPopulationType = "BC1" Then
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ ChrSize = VirtualMap(26 + chromosome, 11)
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+ MarkerPositionOld = 0
+ 'Randomize (Rnd)
+ If Rnd > 0.5 Then Genotype = "A" Else Genotype = "H"
+ Marker = StartRow
+ SimulatedGenotypes(Marker, SimulatedGenotype) = Genotype
+ For Marker = 2 To NbOfMrksInChr
+ MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
+ IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
+ If MapFunctionSimul = 1 Then
+ IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
+ ElseIf MapFunctionSimul = 2 Then
+ temp = 2 * (IntervalWithPreviousMarker / 100)
+ IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
+ End If
+ 'Randomize (Rnd)
+ If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+ If Genotype = "A" Then
+ Genotype = "H"
+ ElseIf Genotype = "H" Then
+ Genotype = "A"
+ End If
+ End If
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
+ MarkerPositionOld = MarkerPosition
+ Next Marker
+ Next SimulatedGenotype
+ StartRow = StartRow + NbOfMrksInChr
+ Next chromosome
+
+ ElseIf SimulatedPopulationType = "F2" Then
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ ChrSize = VirtualMap(26 + chromosome, 11)
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+ MarkerPositionOld = 0
+ 'Randomize (Rnd)
+ If Rnd > 0.5 Then genotype1 = "A" Else genotype1 = "B"
+ 'Randomize (Rnd)
+ If Rnd > 0.5 Then genotype2 = "B" Else genotype2 = "A"
+ Marker = StartRow
+ If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "A"
+ If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "B"
+ If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "H"
+ If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "H"
+
+ For Marker = 2 To NbOfMrksInChr
+ MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
+ IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
+ If MapFunctionSimul = 1 Then
+ IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
+ ElseIf MapFunctionSimul = 2 Then
+ temp = 2 * (IntervalWithPreviousMarker / 100)
+ IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
+ End If
+ 'gamete 1
+ 'Randomize (Rnd)
+ If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+ If genotype1 = "A" Then
+ genotype1 = "B"
+ ElseIf genotype1 = "B" Then
+ genotype1 = "A"
+ End If
+ End If
+ 'gamete 2
+ 'Randomize (Rnd)
+ If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+ If genotype2 = "A" Then
+ genotype2 = "B"
+ ElseIf genotype2 = "B" Then
+ genotype2 = "A"
+ End If
+ End If
+ If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A"
+ If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "B"
+ If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H"
+ If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H"
+ MarkerPositionOld = MarkerPosition
+ Next Marker
+ Next SimulatedGenotype
+ StartRow = StartRow + NbOfMrksInChr
+ Next chromosome
+ End If
+
+ 'Writing in .txt file
+
+ FileSaveName = "SimulPop_" & SimulatedPopulation & ".txt"
+ Open FileSaveName For Output As #1
+ If SimulatedPopulationType = "BC1" Then Print #1, "data type f2 backcross"
+ If SimulatedPopulationType = "F2" Then Print #1, "data type f2 intercross"
+ Print #1, Format(SimulatedPopulationSize, "###"); Spc(1); Format(NumberOfSimulatedMarkers, "###"); Spc(1); "0"
+ For Ligne = 1 To NumberOfSimulatedMarkers
+ NomLocus = VirtualMap(Ligne + 5, 4)
+ TexteLocus = ""
+ For Colonne = 1 To SimulatedPopulationSize
+ TexteLocus = TexteLocus & SimulatedGenotypes(Ligne, Colonne)
+ Next
+ Print #1, ; "*" & NomLocus; Spc(1); TexteLocus
+ Next
+ Close #1
+
+ Next SimulatedPopulation
+
+ElseIf NumberOfSimulatedPopulations = 1 Or AutoBatchMapOn = 1 Then 'if only one population, write in the SimulPop sheet
+ If AutoBatchMapOn = 0 Then Application.StatusBar = "Simulating population"
+ ReDim SimulatedGenotypes(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedTraits, SimulatedPopulationSize + 1) As Variant
+ StartRow = 1
+
+ If SimulatedPopulationType = "BC1" And ChromosomeSDL1 = 0 Then 'there is no SDL (Segregation Distortion Locus) in the genome
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ ChrSize = VirtualMap(26 + chromosome, 11)
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+ MarkerPositionOld = 0
+ Marker = StartRow
+ If Rnd > 0.5 Then Genotype = "A" Else Genotype = "H"
+ SimulatedGenotypes(Marker, SimulatedGenotype) = Genotype
+ For Marker = 2 To NbOfMrksInChr
+ MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
+ IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
+ If MapFunctionSimul = 1 Then
+ IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
+ ElseIf MapFunctionSimul = 2 Then
+ temp = 2 * (IntervalWithPreviousMarker / 100)
+ IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
+ End If
+ If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+ If Genotype = "A" Then
+ Genotype = "H"
+ ElseIf Genotype = "H" Then
+ Genotype = "A"
+ End If
+ End If
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
+ MarkerPositionOld = MarkerPosition
+ Next Marker
+ For mytrait = 1 To NumberOfSimulatedTraits
+ SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
+ Next mytrait
+ Next SimulatedGenotype
+ StartRow = StartRow + NbOfMrksInChr
+ Next chromosome
+ For mytrait = 1 To NumberOfSimulatedTraits
+ SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, 0) = "RandomQTrait_" & mytrait
+ Next mytrait
+
+ ElseIf SimulatedPopulationType = "BC2F1" And ChromosomeSDL1 = 0 Then 'there is no SDL (Segregation Distortion Locus) in the genome
+ BC2FamilySize = 4
+ BC2PopulationSize = SimulatedPopulationSize * BC2FamilySize
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+50
+ StartRow = 1
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ ChrSize = VirtualMap(26 + chromosome, 11)
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ MarkerPositionOld = 0
+ Marker = StartRow
+ If Rnd > 0.5 Then Genotype = "A" Else Genotype = "H"
+ SimulatedGenotypes(Marker, SimulatedGenotype) = Genotype
+ For Marker = 2 To NbOfMrksInChr
+ MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
+ IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
+ If MapFunctionSimul = 1 Then
+ IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
+ ElseIf MapFunctionSimul = 2 Then
+ temp = 2 * (IntervalWithPreviousMarker / 100)
+ IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
+ End If
+ If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+ If Genotype = "A" Then
+ Genotype = "H"
+ ElseIf Genotype = "H" Then
+ Genotype = "A"
+ End If
+ End If
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
+ MarkerPositionOld = MarkerPosition
+ Next Marker
+ StartRow = StartRow + NbOfMrksInChr
+ Next chromosome
+' For mytrait = 1 To NumberOfSimulatedTraits
+' SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
+' Next mytrait
+ Next SimulatedGenotype
+' For mytrait = 1 To NumberOfSimulatedTraits
+' SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, 0) = "RandomQTrait_" & mytrait
+' Next mytrait
+
+ ElseIf SimulatedPopulationType = "BC1" And ChromosomeSDL1 > 0 Then 'there is a SDL (Segregation Distortion Locus) in the genome
+ ''Debug.Print "zzz"
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+100
+ StartRow = 1
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ ChrSize = VirtualMap(26 + chromosome, 11)
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ MarkerPositionOld = 0
+ Marker = StartRow
+ If Rnd > 0.5 Then Genotype = "A" Else Genotype = "H"
+ SimulatedGenotypes(Marker, SimulatedGenotype) = Genotype
+ For Marker = 2 To NbOfMrksInChr
+ MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
+ IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
+ If MapFunctionSimul = 1 Then
+ IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
+ ElseIf MapFunctionSimul = 2 Then
+ temp = 2 * (IntervalWithPreviousMarker / 100)
+ IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
+ End If
+ If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+ If Genotype = "A" Then
+ Genotype = "H"
+ ElseIf Genotype = "H" Then
+ Genotype = "A"
+ End If
+ End If
+ SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
+ MarkerPositionOld = MarkerPosition
+ Next Marker
+ StartRow = StartRow + NbOfMrksInChr
+ Next chromosome
+
+ 'fA/fH = u
+ 'frequency of A = fA = u /(1+u)
+ 'frequency of B = fB = 1 /(1+u)
+ myRandkill = Rnd
+ If ViabU < 1 Then 'selection against AA genotypes or A gametes
+ If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "A" And myRandkill > (ViabU / (1 + ViabU)) Then 'sorry, bad luck... you're dead, gamete A!
+ 'kill individual/gamete and simulate again
+ GoTo 100
+ End If
+ ElseIf ViabU > 1 Then 'selection against H genotypes or B gametes
+ If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "H" And myRandkill < (1 / (1 + ViabU)) Then 'sorry, bad luck... you're dead, gamete B!
+ 'kill individual/gamete and simulate again
+ GoTo 100
+ End If
+ End If
+ If ChromosomeSDL2 > 0 Then
+ If ViabV < 1 Then 'selection against AA genotypes or A gametes
+ If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "A" And myRandkill > (ViabV / (1 + ViabV)) Then 'sorry, bad luck... you're dead, gamete A!
+ 'kill individual/gamete and simulate again
+ GoTo 100
+ End If
+ ElseIf ViabV > 1 Then 'selection against H genotypes or B gametes
+ If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "H" And myRandkill < (1 / (1 + ViabV)) Then 'sorry, bad luck... you're dead, gamete B!
+ 'kill individual/gamete and simulate again
+ GoTo 100
+ End If
+ End If
+ End If
+ For mytrait = 1 To NumberOfSimulatedTraits
+ SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
+ Next mytrait
+ Next SimulatedGenotype
+ For mytrait = 1 To NumberOfSimulatedTraits
+ SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, 0) = "RandomQTrait_" & mytrait
+ Next mytrait
+
+ ElseIf SimulatedPopulationType = "F2" Then
+ For chromosome = 1 To NumberOfSimulatedChromosomes
+ ChrSize = VirtualMap(26 + chromosome, 11)
+ NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
+ For SimulatedGenotype = 1 To SimulatedPopulationSize
+ MarkerPositionOld = 0
+ 'Randomize (Rnd)
+ If Rnd > 0.5 Then genotype1 = "A" Else genotype1 = "B"
+ 'Randomize (Rnd)
+ If Rnd > 0.5 Then genotype2 = "B" Else genotype2 = "A"
+ Marker = StartRow
+ If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "A"
+ If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "B"
+ If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "H"
+ If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "H"
+
+ For Marker = 2 To NbOfMrksInChr
+ MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
+ IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
+ If MapFunctionSimul = 1 Then
+ IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
+ ElseIf MapFunctionSimul = 2 Then
+ temp = 2 * (IntervalWithPreviousMarker / 100)
+ IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
+ End If
+ 'gamete 1
+ 'Randomize (Rnd)
+ If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+ If genotype1 = "A" Then
+ genotype1 = "B"
+ ElseIf genotype1 = "B" Then
+ genotype1 = "A"
+ End If
+ End If
+ 'gamete 2
+ 'Randomize (Rnd)
+ If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
+ If genotype2 = "A" Then
+ genotype2 = "B"
+ ElseIf genotype2 = "B" Then
+ genotype2 = "A"
+ End If
+ End If
+ If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A"
+ If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "B"
+ If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H"
+ If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H"
+ MarkerPositionOld = MarkerPosition
+ Next Marker
+ Next SimulatedGenotype
+ For mytrait = 1 To NumberOfSimulatedTraits
+ SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
+ Next mytrait
+ StartRow = StartRow + NbOfMrksInChr
+ Next chromosome
+ For mytrait = 1 To NumberOfSimulatedTraits
+ SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, 0) = "RandomQTrait_" & mytrait
+ Next mytrait
+ End If
+
+ If AutoBatchMapOn = 0 Then
+ Application.StatusBar = "Writing results"
+ ClearSimulatedPopulation
+ OutPutSheetName = "SimulPop"
+ 'MsgBox SimulatedPopulationSize
+ If SimulatedPopulationSize <= 254 And SimulatedPopulationSize <= 508 Then
+ ThisWorkbook.Sheets(OutPutSheetName).Range("B15").Resize(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedTraits, SimulatedPopulationSize + 1) = SimulatedGenotypes
+ ElseIf SimulatedPopulationSize > 254 And SimulatedPopulationSize <= 508 Then
+ ThisWorkbook.Sheets(OutPutSheetName).Range("B15").Resize(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedTraits, 255) = SimulatedGenotypes
+ ReDim SimulatedGenotypesPlus(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedTraits, SimulatedPopulationSize - 254 + 1) As Variant
+ For i = 1 To NumberOfSimulatedMarkers
+ For j = 255 To SimulatedPopulationSize
+ SimulatedGenotypesPlus(i, j - 254) = SimulatedGenotypes(i, j)
+ Next
+ Next i
+ ThisWorkbook.Sheets("SimulPop+").Range("B15").Resize(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedTraits, SimulatedPopulationSize - 253) = SimulatedGenotypesPlus
+ End If
+ Application.ScreenUpdating = False
+ ThisWorkbook.Sheets("SimulMap").Activate
+ Range("D6").Select
+ Range(Selection, Selection.End(xlDown)).Select
+ Selection.Copy
+ [N22].Select
+ ThisWorkbook.Sheets(OutPutSheetName).Activate
+ Range("B16").Select
+ Selection.PasteSpecial Paste:=xlPasteValues, Operation:=xlNone, SkipBlanks _
+ :=False, Transpose:=False
+
+ Range("D4") = SimulatedPopulationType
+ Range("D5") = SimulatedPopulationSize
+ Range("D6") = NumberOfSimulatedMarkers
+ Range("D7") = NumberOfSimulatedTraits
+ Range("H4") = "A"
+ Range("H5") = "B"
+ Range("H6") = "C"
+ Range("H7") = "D"
+ Range("H8") = "H"
+ Range("H9") = "-"
+ Range("K4") = "2"
+ If SimulatedPopulationType = "BC1" Then
+ [b10] = "Simulated BC1 data " & Date & " - " & Time
+ ElseIf SimulatedPopulationType = "F2" Then
+ [b10] = "Simulated F2 data " & Date & " - " & Time
+ End If
+ Application.CutCopyMode = False
+ [B15].Select
+ ElseIf AutoBatchMapOn = 1 Then
+' MsgBox SimulatedPopulationSize
+ For i = 1 To NumberOfSimulatedMarkers
+ For j = 1 To SimulatedPopulationSize
+ Data(j - 1, i - 1) = SimulatedGenotypes(i, j) 'stay in memory
+ Next
+ Next
+ OutPutSheetName = "Data"
+
+ ThisWorkbook.Sheets(OutPutSheetName).Range("D4") = SimulatedPopulationType
+ ThisWorkbook.Sheets(OutPutSheetName).Range("D5") = SimulatedPopulationSize
+ ThisWorkbook.Sheets(OutPutSheetName).Range("D6") = NumberOfSimulatedMarkers
+ ThisWorkbook.Sheets(OutPutSheetName).Range("D7") = "0"
+ ThisWorkbook.Sheets(OutPutSheetName).Range("H4") = "A"
+ ThisWorkbook.Sheets(OutPutSheetName).Range("H5") = "B"
+ ThisWorkbook.Sheets(OutPutSheetName).Range("H6") = "C"
+ ThisWorkbook.Sheets(OutPutSheetName).Range("H7") = "D"
+ ThisWorkbook.Sheets(OutPutSheetName).Range("H8") = "H"
+ ThisWorkbook.Sheets(OutPutSheetName).Range("H9") = "-"
+ ThisWorkbook.Sheets(OutPutSheetName).Range("K4") = "2"
+ End If
+
+End If
+
+GoTo 1000
+900
+''Debug.Print Chromosome
+''Debug.Print StartRow
+''Debug.Print marker
+''Debug.Print SimulatedGenotype
+''Debug.Print genotype
+''Debug.Print StartRow + marker - 1
+1000
+'Application.ScreenUpdating = True
+'Next i
+If AutoBatchMapOn = 0 Then Application.StatusBar = False
+End Sub
+
+Public Sub ClearSimulatedPopulation()
+ Application.ScreenUpdating = False
+ ThisWorkbook.Sheets("SimulPop").Activate
+ Range("B15:xfd1048576").ClearContents
+ Range("D4").ClearContents
+ Range("D5").ClearContents
+ Range("D6").ClearContents
+ Range("D7").ClearContents
+ Range("H4").ClearContents
+ Range("H5").ClearContents
+ Range("H6").ClearContents
+ Range("H7").ClearContents
+ Range("H8").ClearContents
+ Range("H9").ClearContents
+ Range("K4").ClearContents
+ [b10].ClearContents
+' ThisWorkbook.Sheets("SimulPop+").Activate
+' Range("B15:IV60000").ClearContents
+' Range("D4").ClearContents
+' Range("D5").ClearContents
+' Range("D6").ClearContents
+' Range("D7").ClearContents
+' Range("H4").ClearContents
+' Range("H5").ClearContents
+' Range("H6").ClearContents
+' Range("H7").ClearContents
+' Range("H8").ClearContents
+' Range("H9").ClearContents
+' Range("K4").ClearContents
+' [B13].ClearContents
+ ThisWorkbook.Sheets("SimulPop").Activate
+If AutoBatchMapOn = 0 And ClearAllResultsMode = 0 Then Application.ScreenUpdating = True
+End Sub
+
+
+Public Sub Clear_BatchMap_Results()
+Application.ScreenUpdating = False
+If ThisWorkbook.Sheets("BatchMap").[h8] <> "" Then
+ If ClearAllResultsMode = 0 Then
+ msg = "Are you sure you want to clear the batch results?"
+ Style = vbYesNo + vbCritical + vbDefaultButton1
+ Title = "Clear results"
+ Ctxt = 1000
+ response = MsgBox(msg, Style, Title)
+ End If
+
+ If response = vbYes Or ClearAllResultsMode = 1 Then
+ If MaxNumberOfColumns = 256 Then
+ ThisWorkbook.Sheets("BatchMap").Range("A5:IV60000").ClearContents
+ ThisWorkbook.Sheets("BatchMap").Range("H5:IV6").Interior.ColorIndex = xlNone
+ Else
+ ThisWorkbook.Sheets("BatchMap").Range("A5:XFD60000").ClearContents
+ ThisWorkbook.Sheets("BatchMap").Range("H5:XFD6").Interior.ColorIndex = xlNone
+ End If
+ ThisWorkbook.Sheets("BatchMap").[D4].ClearContents
+ ThisWorkbook.Sheets("BatchMap").[f4].ClearContents
+ ThisWorkbook.Sheets("BatchMap").Range("C8:G60000").Interior.ColorIndex = xlNone
+
+ Else
+ GoTo 1000
+ End If
+End If
+'[H8].Select
+1000
+'If AutoBatchMapOn = 0 And ClearAllResultsMode = 0 Then Application.ScreenUpdating = True
+End Sub
+
+Public Sub Clear_BigBatchMap_Results()
+Application.ScreenUpdating = False
+If [c6] <> "" Then
+ If ClearAllResultsMode = 0 Then
+ msg = "Are you sure you want to clear the batch results?"
+ Style = vbYesNo + vbCritical + vbDefaultButton1
+ Title = "Clear results"
+ Ctxt = 1000
+ response = MsgBox(msg, Style, Title)
+ End If
+ If response = vbYes Or ClearAllResultsMode = 1 Then
+ If MaxNumberOfColumns = 256 Then
+ ThisWorkbook.Sheets("BigBatch").Range("A4:IV60000").ClearContents
+ Else
+ ThisWorkbook.Sheets("BigBatch").Range("A4:XFD60000").ClearContents
+ End If
+ Else
+ GoTo 1000
+ End If
+End If
+[c6].Select
+1000
+If AutoBatchMapOn = 0 And ClearAllResultsMode = 0 Then Application.ScreenUpdating = True
+End Sub
+
+Public Sub Compute_Stats_Batch()
+'On Error GoTo 900
+Application.ScreenUpdating = False
+Application.StatusBar = "Computing statistics..."
+
+ThisWorkbook.Sheets("BatchMap").Activate
+'Expected cM values from simulated map
+NumberOfMarkers = ThisWorkbook.Sheets("SimulMap").[N23]
+For i = 2 To NumberOfMarkers
+ ExpectedRelativeDistance = ThisWorkbook.Sheets("SimulMap").Cells(i + 5, 5) - ThisWorkbook.Sheets("SimulMap").Cells(i + 4, 5)
+ ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 6) = ExpectedRelativeDistance
+ If ThisWorkbook.Sheets("SimulMap").Cells(i + 4, 2) <> ThisWorkbook.Sheets("SimulMap").Cells(i + 5, 2) Then 'new chr is detected
+ ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 6).ClearContents
+ End If
+Next i
+
+NumberOfProcessedFiles = [D4]
+'Average etc on batch results
+For i = 1 To NumberOfMarkers
+ mkchr = ThisWorkbook.Sheets("SimulMap").Cells(i + 5, 2)
+ ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 1) = mkchr
+ SumOfDistances = 0
+ MinDist = 1000000
+ MaxDist = 0
+ ExpectedRelativeDistance = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6)
+ If ExpectedRelativeDistance <> "" Then
+ For SimPop = 1 To NumberOfProcessedFiles
+ BatchDist = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, SimPop + 7)
+ SumOfDistances = SumOfDistances + BatchDist
+ If BatchDist < MinDist Then MinDist = BatchDist
+ If BatchDist > MaxDist Then MaxDist = BatchDist
+ Next
+ AverageDistance = SumOfDistances / NumberOfProcessedFiles
+ ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 3) = MinDist
+ ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 4) = MaxDist
+ ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 5) = AverageDistance
+ ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 7) = AverageDistance - ExpectedRelativeDistance
+ End If
+Next i
+
+For SimPop = 1 To NumberOfProcessedFiles
+ TotalMapSize = 0
+ For i = 1 To NumberOfMarkers
+ BatchDist = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, SimPop + 7)
+ If BatchDist <> "" Then
+ TotalMapSize = TotalMapSize + BatchDist
+ End If
+ Next
+ ThisWorkbook.Sheets("BatchMap").Cells(5, SimPop + 7) = TotalMapSize
+ ThisWorkbook.Sheets("BatchMap").Cells(6, SimPop + 7) = TotalMapSize / NumberOfMarkers 'mk density
+Next
+
+SumAverageSize = 0
+SumAverageDensity = 0
+MinSize = 1000000
+MaxSize = 0
+MinDensity = 1000000
+MaxDensity = 0
+
+For SimPop = 1 To NumberOfProcessedFiles
+ Mapsize = ThisWorkbook.Sheets("BatchMap").Cells(5, SimPop + 7)
+ mapdensity = ThisWorkbook.Sheets("BatchMap").Cells(6, SimPop + 7)
+ If Mapsize > MaxSize Then MaxSize = Mapsize
+ If Mapsize < MinSize Then MinSize = Mapsize
+ If mapdensity > MaxDensity Then MaxDensity = mapdensity
+ If mapdensity < MinDensity Then MinDensity = mapdensity
+ SumAverageSize = SumAverageSize + Mapsize
+ SumAverageDensity = SumAverageDensity + mapdensity
+Next
+AverageSize = SumAverageSize / NumberOfProcessedFiles
+AverageDensity = SumAverageDensity / NumberOfProcessedFiles
+
+[C5] = MinSize
+[D5] = MaxSize
+[c6] = MinDensity
+[D6] = MaxDensity
+[E5] = AverageSize
+[E6] = AverageDensity
+
+[G5] = "Total map size"
+[G6] = "Marker density"
+[A7] = "Chr"
+[b7] = "Marker"
+[C7] = "Min"
+[D7] = "Max"
+[E7] = "Average"
+[F7] = "Expected"
+[G7] = "Diff."
+
+Range(Cells(8, 3), Cells(7 + NumberOfMarkers, 7)).Select
+Selection.Interior.ColorIndex = 15
+Range(Cells(5, 8), Cells(6, 256)).Select
+Selection.Interior.ColorIndex = 15
+
+GoTo 1000
+900
+MsgBox "An error occurred."
+1000
+[h8].Select
+Application.StatusBar = False
+'Application.ScreenUpdating = True
+End Sub
+
+Public Sub Compute_Stats_Batch_Chi2()
+'On Error GoTo 900
+Application.ScreenUpdating = False
+Application.StatusBar = "Computing statistics..."
+
+ThisWorkbook.Sheets("BatchMap").Activate
+'Expected cM values from simulated map
+NumberOfMarkers = ThisWorkbook.Sheets("SimulMap").[N23]
+For i = 2 To NumberOfMarkers
+ ExpectedRelativeDistance = ThisWorkbook.Sheets("SimulMap").Cells(i + 5, 5) - ThisWorkbook.Sheets("SimulMap").Cells(i + 4, 5)
+ 'keep it or it won't work
+ 'ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 6) = ExpectedRelativeDistance
+ If ThisWorkbook.Sheets("SimulMap").Cells(i + 4, 2) <> ThisWorkbook.Sheets("SimulMap").Cells(i + 5, 2) Then 'new chr is detected
+ ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 6).ClearContents
+ End If
+Next i
+
+NumberOfProcessedFiles = ThisWorkbook.Sheets("BatchMap").[D4]
+
+MyBatchresults = ThisWorkbook.Sheets("BatchMap").Range(Cells(1, 1), Cells(NumberOfMarkers + 7, NumberOfProcessedFiles + 7)).Value
+
+'Average etc on batch results
+For i = 1 To NumberOfMarkers
+ mkchr = ThisWorkbook.Sheets("SimulMap").Cells(i + 5, 2)
+ ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 1) = mkchr
+ SumOfChi2 = 0
+ MinChi2 = 1000000
+ MaxChi2 = 0
+ 'ExpectedRelativeDistance = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6)
+ If ExpectedRelativeDistance <> "" Then
+ For SimPop = 1 To NumberOfProcessedFiles
+ BatchChi2 = MyBatchresults(i + 7, SimPop + 7)
+ SumOfChi2 = SumOfChi2 + BatchChi2
+ If BatchChi2 < MinChi2 Then MinChi2 = BatchChi2
+ If BatchChi2 > MaxChi2 Then MaxChi2 = BatchChi2
+ Next
+ AverageChi2 = SumOfChi2 / NumberOfProcessedFiles
+ ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 3) = MinChi2
+ ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 4) = MaxChi2
+ ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 5) = AverageChi2
+ End If
+Next i
+
+'ranks
+SDL1on = ThisWorkbook.Sheets("SimulMap").[R9]
+SDL2on = ThisWorkbook.Sheets("SimulMap").[R11]
+If SDL1on = 1 Then SDL1number = ThisWorkbook.Sheets("SimulMap").[R10]
+If SDL2on = 1 Then SDL2number = ThisWorkbook.Sheets("SimulMap").[R12]
+'For i = 2 To NumberOfMarkers - 1
+' ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6) = 0
+' 'ExpectedRelativeDistance = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6)
+' For SimPop = 1 To NumberOfProcessedFiles
+' BatchChi2 = MyBatchresults(i + 7, SimPop + 7)
+' BatchChi2Before = MyBatchresults(i + 6, SimPop + 7)
+' BatchChi2After = MyBatchresults(i + 8, SimPop + 7)
+' If BatchChi2 < BatchChi2Before Or BatchChi2 < BatchChi2After Then
+' ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6) = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6) + 1
+' If i = SDL1number Or i = SDL2number Then
+' ThisWorkbook.Sheets("BatchMap").Cells(i + 7, SimPop + 7).Select
+' Selection.Interior.ColorIndex = 15
+' End If
+' End If
+'' If BatchChi2 < BatchChi2Before Then
+'' If i = SDL1number Or i = SDL2number Then
+'' ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 7) = ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 7) + 1
+'' ThisWorkbook.Sheets("BatchMap").Cells(i + 6, SimPop + 7).Select
+'' Selection.Interior.ColorIndex = 15
+'' End If
+'' End If
+'' If BatchChi2 < BatchChi2After Then
+'' If i = SDL1number Or i = SDL2number Then
+'' ThisWorkbook.Sheets("BatchMap").Cells(i + 8, 7) = ThisWorkbook.Sheets("BatchMap").Cells(i + 8, 7) + 1
+'' ThisWorkbook.Sheets("BatchMap").Cells(i + 8, SimPop + 7).Select
+'' Selection.Interior.ColorIndex = 15
+'' End If
+'' End If
+' Next
+' ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6) = 100 * (ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6) / NumberOfProcessedFiles)
+' ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 7) = 100 - ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6)
+'' If i = SDL1number Or i = SDL2number Then
+''' ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 7) = 100 * (ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 7) / NumberOfProcessedFiles)
+''' ThisWorkbook.Sheets("BatchMap").Cells(i + 8, 7) = 100 * (ThisWorkbook.Sheets("BatchMap").Cells(i + 8, 7) / NumberOfProcessedFiles)
+'' End If
+'Next i
+
+
+For SimPop = 1 To NumberOfProcessedFiles
+ SDL1isNotaPeak = 0
+ mychi2SDL1 = ThisWorkbook.Sheets("BatchMap").Cells(SDL1number + 7, SimPop + 7)
+ For i = 1 To NumberOfMarkers
+ myChi2 = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, SimPop + 7)
+ If myChi2 > mychi2SDL1 Then
+ 'it's a peak, not on SDL1
+ ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 7) = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 7) + 1
+ ThisWorkbook.Sheets("BatchMap").Cells(i + 7, SimPop + 7).Select
+ Selection.Interior.ColorIndex = 15
+ SDL1isNotaPeak = 1
+ End If
+ Next
+ If SDL1isNotaPeak = 1 Then 'in this pop
+ 'SDL1 is not a peak
+ ThisWorkbook.Sheets("BatchMap").Cells(SDL1number + 7, 6) = ThisWorkbook.Sheets("BatchMap").Cells(SDL1number + 7, 6) + 1
+ End If
+Next
+
+For i = 1 To NumberOfMarkers
+ ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 7) = 100 * (ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 7)) / NumberOfProcessedFiles
+Next
+
+ThisWorkbook.Sheets("BatchMap").Cells(SDL1number + 7, 6) = 100 * (ThisWorkbook.Sheets("BatchMap").Cells(SDL1number + 7, 6) / NumberOfProcessedFiles)
+ThisWorkbook.Sheets("BatchMap").Cells(SDL1number + 7, 7) = 100 - ThisWorkbook.Sheets("BatchMap").Cells(SDL1number + 7, 6)
+
+'For SimPop = 1 To NumberOfProcessedFiles
+' TotalMapSize = 0
+' For i = 1 To NumberOfMarkers
+' BatchDist = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, SimPop + 7)
+' If BatchDist <> "" Then
+' TotalMapSize = TotalMapSize + BatchDist
+' End If
+' Next
+' ThisWorkbook.Sheets("BatchMap").Cells(5, SimPop + 7) = TotalMapSize
+' ThisWorkbook.Sheets("BatchMap").Cells(6, SimPop + 7) = TotalMapSize / NumberOfMarkers 'mk density
+'Next
+
+SumAverageChi2 = 0
+SumAverageDensity = 0
+MinChi2 = 1000000
+MaxChi2 = 0
+MinDensity = 1000000
+MaxDensity = 0
+
+For SimPop = 1 To NumberOfProcessedFiles
+ MapChi2 = ThisWorkbook.Sheets("BatchMap").Cells(5, SimPop + 7)
+ mapdensity = ThisWorkbook.Sheets("BatchMap").Cells(6, SimPop + 7)
+ If MapChi2 > MaxChi2 Then MaxChi2 = MapChi2
+ If MapChi2 < MinChi2 Then MinChi2 = MapChi2
+ If mapdensity > MaxDensity Then MaxDensity = mapdensity
+ If mapdensity < MinDensity Then MinDensity = mapdensity
+ SumAverageChi2 = SumAverageChi2 + MapChi2
+ SumAverageDensity = SumAverageDensity + mapdensity
+Next
+AverageChi2 = SumAverageChi2 / NumberOfProcessedFiles
+AverageDensity = SumAverageDensity / NumberOfProcessedFiles
+
+[C5] = MinChi2
+[D5] = MaxChi2
+[c6] = MinDensity
+[D6] = MaxDensity
+[E5] = AverageChi2
+[E6] = AverageDensity
+
+'[G5] = "Total map size"
+'[G6] = "Marker density"
+[A7] = "Chr"
+[b7] = "Marker"
+[C7] = "Min"
+[D7] = "Max"
+[E7] = "Average"
+[F7] = "% no peak"
+[G7] = "% peak"
+
+Range(Cells(8, 3), Cells(7 + NumberOfMarkers, 7)).Select
+Selection.Interior.ColorIndex = 15
+Range(Cells(5, 8), Cells(6, 256)).Select
+Selection.Interior.ColorIndex = 15
+
+GoTo 1000
+900
+MsgBox "An error occurred."
+1000
+[h8].Select
+Application.StatusBar = False
+'Application.ScreenUpdating = True
+End Sub
+
+Public Sub ShowDistribMapSizesFromBigBatch()
+ FromBigBatch = 1
+ ShowDistributionMapSizes
+ FromBigBatch = 0
+End Sub
+
+Public Sub ShowDistributionMapSizes()
+
+Application.ScreenUpdating = False
+Application.StatusBar = "cleaning..."
+ThisWorkbook.Sheets("Distrib").Activate
+
+NumberOfIntervals = ThisWorkbook.Sheets("Distrib").[M516]
+ThisWorkbook.Sheets("Distrib").Cells.ClearContents
+ThisWorkbook.Sheets("Distrib").Cells.Interior.ColorIndex = xlNone
+ ThisWorkbook.Sheets("Distrib").Cells.Borders(xlDiagonalDown).LineStyle = xlNone
+ ThisWorkbook.Sheets("Distrib").Cells.Borders(xlDiagonalUp).LineStyle = xlNone
+ ThisWorkbook.Sheets("Distrib").Cells.Borders(xlEdgeLeft).LineStyle = xlNone
+ ThisWorkbook.Sheets("Distrib").Cells.Borders(xlEdgeTop).LineStyle = xlNone
+ ThisWorkbook.Sheets("Distrib").Cells.Borders(xlEdgeBottom).LineStyle = xlNone
+ ThisWorkbook.Sheets("Distrib").Cells.Borders(xlEdgeRight).LineStyle = xlNone
+ ThisWorkbook.Sheets("Distrib").Cells.Borders(xlInsideVertical).LineStyle = xlNone
+ ThisWorkbook.Sheets("Distrib").Cells.Borders(xlInsideHorizontal).LineStyle = xlNone
+
+popType = ThisWorkbook.Sheets("SimulMap").[N16]
+popsize = ThisWorkbook.Sheets("SimulMap").[N17]
+EmapSize = ThisWorkbook.Sheets("SimulMap").[N22]
+
+If FromBigBatch = 0 Then
+ MyBatchMatrix = ThisWorkbook.Sheets("BatchMap").Range("A5:IV6").Value
+ valeurMax = ThisWorkbook.Sheets("BatchMap").[D5]
+ valeurMin = ThisWorkbook.Sheets("BatchMap").[C5]
+ NumberOfValues = ThisWorkbook.Sheets("BatchMap").[D4]
+Else
+ MyBatchMatrix = ThisWorkbook.Sheets("BigBatch").Range("C6:D10010").Value
+
+ ThisWorkbook.Sheets("BigBatch").Activate
+ NumberOfValues = ThisWorkbook.Sheets("SimulMap").[n3]
+ '
+ Range("C6:D10005").Select
+ Range("D6").Activate
+ Selection.Sort Key1:=Range("D6"), Order1:=xlAscending, Header:=xlGuess, _
+ OrderCustom:=1, MatchCase:=False, Orientation:=xlTopToBottom
+
+ [D6].Select
+ valeurMin = [D6]
+ valeurMax = Cells(5 + NumberOfValues, 4)
+End If
+
+Application.StatusBar = "writing intervals"
+If NumberOfIntervals = 0 Or NumberOfIntervals = "" Then NumberOfIntervals = 40
+[M516] = NumberOfIntervals
+IntervalSize = Int(valeurMax - valeurMin) / NumberOfIntervals
+
+ReDim VectorFrequencies(1, NumberOfIntervals + 1) As Long
+ReDim VectorBounds(2, NumberOfIntervals + 16) As Double
+
+mininterval = valeurMin
+For Interval = 1 To NumberOfIntervals + 1
+ ThisWorkbook.Sheets("Distrib").Cells(510, Interval + 15) = mininterval
+ VectorBounds(0, Interval + 15) = mininterval
+ maxinterval = mininterval + IntervalSize
+ ThisWorkbook.Sheets("Distrib").Cells(509, Interval + 15) = maxinterval
+ VectorBounds(1, Interval + 15) = maxinterval
+ mininterval = maxinterval
+ 'ThisWorkbook.Sheets("Distrib").Cells(515, interval + 15) = "0"
+ VectorFrequencies(0, Interval - 1) = 0
+Next
+
+Application.StatusBar = "counting frequencies"
+For Colonne = 8 To NumberOfValues + 7
+ If FromBigBatch = 0 Then Mapsize = MyBatchMatrix(1, Colonne) Else Mapsize = MyBatchMatrix(Colonne - 7, 2)
+ 'ThisWorkbook.Sheets("Distrib").Cells(5, Colonne) = MapSize
+ For Interval = 1 To NumberOfIntervals + 1
+' If MapSize >= ThisWorkbook.Sheets("Distrib").Cells(510, interval + 15) Then
+' If MapSize < ThisWorkbook.Sheets("Distrib").Cells(509, interval + 15) Then
+' VectorFrequencies(0, interval + 15) = VectorFrequencies(0, interval + 15) + 1
+' ThisWorkbook.Sheets("Distrib").Cells(515, interval + 15) = ThisWorkbook.Sheets("Distrib").Cells(515, interval + 15) + 1
+' End If
+' End If
+ If Mapsize >= VectorBounds(0, Interval + 15) Then
+ If Mapsize < VectorBounds(1, Interval + 15) Then
+ VectorFrequencies(0, Interval - 1) = VectorFrequencies(0, Interval - 1) + 1
+ End If
+ End If
+ Next
+Next
+
+[P515].Resize(1, NumberOfIntervals + 1) = VectorFrequencies
+
+Application.StatusBar = "drawing..."
+For Interval = 1 To NumberOfIntervals + 1
+ effectif = VectorFrequencies(0, Interval - 1)
+ For Ligne = 1 To effectif
+ ThisWorkbook.Sheets("Distrib").Cells(500 - Ligne, Interval + 15).Interior.ColorIndex = 25
+ Next Ligne
+Next
+Application.StatusBar = "finishing..."
+
+ThisWorkbook.Sheets("Distrib").Activate
+If FromBigBatch = 0 Then
+ [M517].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.005)": [K517] = "Percent. 0.005"
+ [M518].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.995)": [K518] = "Percent. 0.995"
+ [M519].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.025)": [K519] = "Percent. 0.025"
+ [M520].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.975)": [K520] = "Percent. 0.975"
+ [M521].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.05)": [K521] = "Percent. 0.05"
+ [M522].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.95)": [K522] = "Percent. 0.95"
+ [M523].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.1666)": [K523] = "Percent. 0.167"
+ [M524].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.8333)": [K524] = "Percent. 0.833"
+ [M525].Formula = "=MEDIAN(BatchMap!H5:IV5,0.8333)": [K525] = "Median"
+ [M526].Formula = "=Average(BatchMap!H5:IV5)": [K526] = "Average"
+
+ ActiveSheet.Shapes("cbDrawAgain").Select
+ Selection.OnAction = "ShowDistributionMapSizes"
+
+ ActiveSheet.Shapes("cbBack").Select
+ Selection.OnAction = "ActiverBatchMap"
+Else
+
+ [M517].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.005)": [K517] = "Percent. 0.005"
+ [M518].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.995)": [K518] = "Percent. 0.995"
+ [M519].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.025)": [K519] = "Percent. 0.025"
+ [M520].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.975)": [K520] = "Percent. 0.975"
+ [M521].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.05)": [K521] = "Percent. 0.05"
+ [M522].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.95)": [K522] = "Percent. 0.95"
+ [M523].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.1666)": [K523] = "Percent. 0.167"
+ [M524].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.8333)": [K524] = "Percent. 0.833"
+ [M525].Formula = "=MEDIAN(BigBatch!D6:D60000,0.5)": [K525] = "Median"
+ [M526].Formula = "=Average(BigBatch!D6:D60000)": [K526] = "Average"
+
+ ActiveSheet.Shapes("cbDrawAgain").Select
+ Selection.OnAction = "ShowDistribMapSizesFromBigBatch"
+
+ ActiveSheet.Shapes("cbBack").Select
+ Selection.OnAction = "ActiverBigBatchMap"
+
+End If
+
+[M516] = NumberOfIntervals
+[o516] = "Histogram of map sizes"
+[K516] = "Number of intervals:"
+[o518] = "Based on [P1 x P2] simulated map "
+[o519] = NumberOfValues & " " & popType & " populations of " & popsize & " individuals simulated"
+[o520] = "Expected map size: " & Format(EmapSize, "####.##") & " cM"
+
+1000
+[M516].Select
+Application.StatusBar = False
+
+End Sub
+
+
+Public Sub Draw_Simulated_Map()
+Application.StatusBar = "Starting"
+Application.ScreenUpdating = False
+Dim MyTime
+MyTime = Time
+
+'Init
+'If Probleme = 1 Then GoTo 1000
+
+' Sort_Frameed_Map Macro
+ThisWorkbook.Sheets("SimulMap").Activate
+
+If [b6] = "" Then MsgBox "No simulated map to draw": GoTo 1000
+
+'remise ö z_ro de la feuille de r_sultats ("Draw")
+Application.DisplayAlerts = False
+ ThisWorkbook.Sheets("DrawSimulMap").Delete
+ ThisWorkbook.Sheets("DrawSimulMap0").Select
+ ThisWorkbook.Sheets("DrawSimulMap0").Copy Before:=ThisWorkbook.Sheets(11)
+ ThisWorkbook.Sheets("DrawSimulMap0 (2)").Select
+ ThisWorkbook.Sheets("DrawSimulMap0 (2)").Name = "DrawSimulMap"
+ ThisWorkbook.Sheets("DrawSimulMap0").Activate
+Application.DisplayAlerts = True
+
+ResultSheetName = "DrawSimulMap"
+
+ThisWorkbook.Sheets("SimulMap").Activate
+ThisWorkbook.Sheets("SimulMap").Range("B6", Range("B1048576").End(xlUp)).Select
+NbOfRowsMap = Selection.Rows.Count
+[b6].Select
+
+TotalNumberOfMarkers = NbOfRowsMap
+
+firstRow = 6
+LastRow = firstRow + TotalNumberOfMarkers - 1
+
+Read_Map_Drawing_Parameters
+MyMinLabelsSpacing = MyLabelsSpacing
+
+If EchelleVert = "" Or EchelleVert = 0 Then EchelleVert = Application.InputBox(prompt:="Drawing scale? (Suggestion: choose from 1 to 5)", Title:="Draw Map", Type:=1)
+If EchelleVert = False Then GoTo 1000
+Application.StatusBar = "Resetting window"
+
+Application.StatusBar = "Loading data"
+'VirtualRawData = ThisWorkbook.Sheets("SimulMap").UsedRange.Value
+VirtualRawData = ThisWorkbook.Sheets("SimulMap").Range(Cells(1, 1), Cells(firstRow + TotalNumberOfMarkers, 26)).Value
+ThisWorkbook.Sheets(ResultSheetName).Activate
+
+ChrSpace = MyChromosomeSpacing * 15
+SizeSmallSecondLine = EchelleHorizont
+LargCarte = 7
+
+Xorigin = 0
+Yorigin = 100
+
+MarkerChromosomeOld = 0
+FirstChromosome = ThisWorkbook.Sheets("DrawSimulMap").[b6]
+
+Application.StatusBar = "Drawing map..."
+
+For Row = firstRow To LastRow
+ MarkerChromosome = VirtualRawData(Row, 2)
+ If MarkerChromosome <> MarkerChromosomeOld Then ' new LG
+ Application.StatusBar = "Drawing LG " & MarkerChromosome
+
+ For Row2 = Row To TotalNumberOfMarkers + firstRow 'look for chr size
+ If VirtualRawData(Row2, 2) <> MarkerChromosome Then
+ ChromosomeSize = VirtualRawData(Row2 - 1, 5)
+ NbOfMarkersInChr = Row2 - Row
+ GoTo 100
+ End If
+ Next Row2
+100
+ If LabelPositionsOption = 2 Then
+ MarkerLabelPositionOld = 0 - Yorigin
+ ElseIf LabelPositionsOption = 1 Then 'even mark label positions
+ MyLabelsSpacing = ChromosomeSize * EchelleVert / (NbOfMarkersInChr - 1)
+ If MyMinLabelsSpacing < MyLabelsSpacing Then MyLabelsSpacing = MyMinLabelsSpacing
+ MarkerLabelPositionOld = 0 - MyLabelsSpacing / EchelleVert
+ End If
+
+ With ActiveSheet.Shapes.AddLine(Xorigin + (MarkerChromosome - FirstChromosome) * ChrSpace - 16, _
+ Yorigin + 5, _
+ Xorigin + (MarkerChromosome - FirstChromosome) * ChrSpace - 16, _
+ Yorigin + ChromosomeSize * EchelleVert + 5)
+ .Name = "MarkChr_" & MarkerChromosome
+ End With
+ With ActiveSheet.Shapes.AddShape(msoShapeRectangle, Xorigin + (MarkerChromosome - FirstChromosome) * ChrSpace - 16, Yorigin - 20, 100#, MyFontSize + 10)
+ .TextFrame.Characters.Text = "LG " & MarkerChromosome
+ .Fill.Visible = False
+ .Line.Visible = False
+ .Name = "MarkChrName_" & MarkerChromosome
+ .TextFrame.Characters.Font.Name = MyFontName
+ .TextFrame.Characters.Font.Size = MyFontSize + 5
+ End With
+ MarkerChromosomeOld = MarkerChromosome
+ End If
+
+ MarkerName = VirtualRawData(Row, 4)
+ MarkerPosition = VirtualRawData(Row, 5) ' absolute positions
+
+ If LabelPositionsOption = 2 Then
+ If MarkerPosition - MarkerLabelPositionOld < MyLabelsSpacing / EchelleVert Then 'if < 5 cm
+ MarkerLabelPosition = MarkerLabelPositionOld + MyLabelsSpacing / EchelleVert
+ MarkerLabelPositionOld = MarkerLabelPosition
+ Else
+ MarkerLabelPosition = MarkerPosition
+ MarkerLabelPositionOld = MarkerLabelPosition
+ End If
+ ElseIf LabelPositionsOption = 1 Then
+ If MarkerPosition - MarkerLabelPositionOld > MyLabelsSpacing Then
+ MarkerLabelPositionOld = MarkerLabelPositionOld + (MarkerPosition - MarkerLabelPositionOld) / 1.5
+ End If
+ MarkerLabelPosition = MarkerLabelPositionOld + MyLabelsSpacing / EchelleVert
+ MarkerLabelPositionOld = MarkerLabelPosition
+ End If
+ MarkerNumber = Row
+
+ With ActiveSheet.Shapes.AddLine(Xorigin + (MarkerChromosome - FirstChromosome) * ChrSpace - 16, Yorigin + MarkerPosition * EchelleVert + 5, Xorigin + _
+ (MarkerChromosome - FirstChromosome) * ChrSpace - 9, Yorigin + MarkerPosition * EchelleVert + 5)
+ '.Name = "Markline_" & MarkerNumber
+ End With
+ With ActiveSheet.Shapes.AddLine(Xorigin + (MarkerChromosome - FirstChromosome) * ChrSpace - 9, _
+ Yorigin + MarkerPosition * EchelleVert + 5, _
+ Xorigin + (MarkerChromosome - FirstChromosome) * ChrSpace - 2 + SizeSmallSecondLine, _
+ Yorigin + MarkerLabelPosition * EchelleVert + 5)
+ '.Name = "Markline_" & MarkerNumber
+ End With
+ With ActiveSheet.Shapes.AddShape(msoShapeRectangle, _
+ Xorigin + (MarkerChromosome - FirstChromosome) * ChrSpace + SizeSmallSecondLine, _
+ Yorigin + MarkerLabelPosition * EchelleVert, _
+ 120#, MyFontSize * 2)
+ .TextFrame.Characters.Text = MarkerName & " (" & Format(MarkerPosition, "###0.0") & ")"
+ .Fill.Visible = False
+ .Line.Visible = False
+ '.TextFrame.Characters.Font.Name = MyfontName
+ '.TextFrame.Characters.Font.Size = MyfontSize
+ .Name = "Mark_" & MarkerNumber
+ End With
+Next Row
+
+Dim MyTime2: MyTime2 = Time: TempsEcoule = MyTime2 - MyTime
+ActiveWindow.Zoom = 100
+'Application.CommandBars("Map Zoom").Visible = True
+ThisWorkbook.Sheets("DrawSimulMap").Activate
+ResetFontIndicator
+ResetFontSize
+1000 Application.StatusBar = False
+
+End Sub
+
+
+Public Sub Read_Chr_Simulated()
+Application.ScreenUpdating = False
+ThisWorkbook.Sheets("SimulMap").Activate
+
+Range("B6", Range("B1048576").End(xlUp)).Select
+NbOfRows = Selection.Rows.Count
+
+Range("J27:N1000").ClearContents
+
+NumbOfMarkInChrTotal = 0
+TotalMapSize = 0
+NumberOfChr = 0
+For i = 6 To NbOfRows + 6
+ If Cells(i + 1, 2) <> Cells(i, 2) Then 'new chr is detected
+ NumberOfChr = NumberOfChr + 1
+ Cells(26 + Cells(i, 2), 10) = Cells(i, 2) 'chr number
+ ChrSize = Cells(i, 5)
+ Cells(26 + Cells(i, 2), 11) = ChrSize 'chr size
+ TotalMapSize = TotalMapSize + Cells(i, 5)
+ NumbOfMarkInChr = i - 5 - NumbOfMarkInChrTotal
+ Cells(26 + Cells(i, 2), 12) = NumbOfMarkInChr
+ MarkerDensity = ChrSize / NumbOfMarkInChr
+ Cells(26 + Cells(i, 2), 14) = MarkerDensity
+ NumbOfMarkInChrTotal = NumbOfMarkInChrTotal + NumbOfMarkInChr
+ End If
+Next
+[N22] = TotalMapSize
+[N23] = NumbOfMarkInChrTotal
+[N24] = TotalMapSize / NumbOfMarkInChrTotal
+[R22] = NumberOfChr
+
+[N22].Select
+Application.ScreenUpdating = True
+End Sub
+
+Public Sub Add_Simulated_To_Map_1()
+Application.ScreenUpdating = False
+ Sheets("SimulMap").Activate
+ Range("B6:F6").Select
+ Range(Selection, Selection.End(xlDown)).Select
+ Copy_Values_MD
+ Range("B6").Select
+ Sheets("CompMap").Activate
+ Range("B6:f1048576").Select
+ Selection.ClearContents
+ Range("B6").Select
+' ActiveSheet.Paste
+ Paste_Values_MD
+ Range("B6").Select
+End Sub
+
+Public Sub Add_Simulated_To_Map_2()
+Application.ScreenUpdating = False
+ Sheets("SimulMap").Activate
+ Range("B6:F6").Select
+ Range(Selection, Selection.End(xlDown)).Select
+ Copy_Values_MD
+ Range("B6").Select
+ Sheets("CompMap").Activate
+ Range("H6:L1048576").Select
+ Selection.ClearContents
+ Range("H6").Select
+' ActiveSheet.Paste
+ Paste_Values_MD
+ Range("H6").Select
+End Sub
+
+
+Public Sub BatchMap()
+'Reads a series of mapmaker/EXP compatible data files, computes the map and reports a summary
+'Assumes that the linkage group are already defined and ordered.
+'Needs to have the sequences pasted in My sequences
+'Max 254 genotypes
+
+'On Error GoTo 900
+Dim MyTime
+MyTime = Time
+BatchMode = 1
+AutoBatchMapOn = 0
+
+Application.ScreenUpdating = False
+
+msg = "Are you sure you want to continue? This will clear the previous batch results and the current sequences."
+Style = vbYesNo
+Title = "Confirmation"
+Ctxt = 1000
+response = MsgBox(msg, Style, Title)
+If response = vbNo Then GoTo 1100
+
+If ThisWorkbook.Sheets("SimulMap").[b6] = "" Then MsgBox ("Please simulate a map first"): GoTo 1100
+
+ThisWorkbook.Sheets("Menus").Range("N24:IV1023").ClearContents
+ThisWorkbook.Sheets("Menus").Range("J24:J1023").ClearContents
+
+CopySequencesFromSimulatedMap
+
+nbseq = ThisWorkbook.Sheets("Menus").Cells(23, 19)
+If nbseq = 0 Then
+ MsgBox ("Please simulate a map first")
+ ActiverSimulate
+ GoTo 1100
+End If
+
+Application.StatusBar = "reading Menu"
+MenuMatrix = ThisWorkbook.Sheets("Menus").UsedRange.Value
+
+Read_Mapping_Options
+
+If ThisWorkbook.Sheets("Data").[D4] <> "" And ThisWorkbook.Sheets("Data").[c16] <> "" Then
+ msg = "Do you want to store the data that are in the 'Data' window before importation?"
+ Style = vbYesNo + vbCritical + vbDefaultButton1
+ Title = "Import Mapmaker data"
+ Ctxt = 1000
+ response = MsgBox(msg, Style, Title)
+ If response = vbYes Then Store_Data
+End If
+
+Application.StatusBar = "Erasing current data"
+ThisWorkbook.Sheets("Data").Range("B15:IV60000").ClearContents
+'ThisWorkbook.Sheets("Data+").Range("B15:IV60000").ClearContents
+
+NumberOfFilesToProcess = ThisWorkbook.Sheets("SimulMap").[n3]
+If NumberOfFilesToProcess > MaxNumberOfColumns - 7 Then BigBatchMode = 1 Else BigBatchMode = 0
+
+NbLocus = ThisWorkbook.Sheets("SimulMap").[N23]
+Indiv = ThisWorkbook.Sheets("SimulMap").[N17]
+
+myfilename = Application.GetOpenFilename(Title:="Locate the SimulPop_1.txt file")
+If myfilename = False Then GoTo 1100
+Workbooks.OpenText Filename:=myfilename, DataType:=xlDelimited, Tab:=True, Space:=True, ConsecutiveDelimiter:=True
+
+If BigBatchMode = 0 Then
+ ThisWorkbook.Sheets("BatchMap").Range("A5:IV60000").ClearContents
+ ThisWorkbook.Sheets("BatchMap").[D4].ClearContents
+ ThisWorkbook.Sheets("BatchMap").[f4].ClearContents
+ ThisWorkbook.Sheets("BatchMap").Range("C8:G60000").Interior.ColorIndex = xlNone
+ ThisWorkbook.Sheets("BatchMap").Range("H5:IV6").Interior.ColorIndex = xlNone
+ ReDim BatchResults(NbLocus + 1, NumberOfFilesToProcess) As Variant
+Else
+ ThisWorkbook.Sheets("BigBatch").Range("C6:D60000").ClearContents
+ ReDim BigBatchResults(NumberOfFilesToProcess, 2) As Variant
+End If
+
+LengthOfPath = Len(myfilename)
+OutputPath = Left(myfilename, LengthOfPath - 5)
+myfilename = ActiveWorkbook.Name
+Workbooks(myfilename).Close savechanges:=False
+
+For CurrentPopulation = 1 To NumberOfFilesToProcess
+ 'Application.StatusBar = "Population " & CurrentPopulation & ":" ' Importing data file
+ Import_Mapmaker_data_For_Batch
+ Application.StatusBar = "Population " & CurrentPopulation & ": Computing map"
+ ComputeMapForAutoBatch
+ 'If BigBatchMode = 0 Then ThisWorkbook.Sheets("BatchMap").Cells(7, CurrentPopulation + 7) = "Pop" & CurrentPopulation
+ If BigBatchMode = 0 Then BatchResults(0, CurrentPopulation - 1) = "Pop" & CurrentPopulation
+Next
+
+If BigBatchMode = 0 Then
+ ThisWorkbook.Sheets("BatchMap").Activate
+ ThisWorkbook.Sheets("BatchMap").[D4] = NumberOfFilesToProcess
+ NumberOfMarkers = ThisWorkbook.Sheets("SimulMap").[N23]
+ ThisWorkbook.Sheets("BatchMap").[f4] = NumberOfMarkers
+ [h7].Resize(NbLocus + 3, NumberOfFilesToProcess) = BatchResults
+ ThisWorkbook.Sheets("SimulMap").Activate
+ Range("D6").Select
+ Range(Selection, Selection.End(xlDown)).Select
+ Selection.Copy
+ [N22].Select
+ ThisWorkbook.Sheets("BatchMap").Activate
+ Range("B8").Select
+ Selection.PasteSpecial Paste:=xlPasteValues, Operation:=xlNone, SkipBlanks _
+ :=False, Transpose:=False
+
+ Compute_Stats_Batch
+Else
+ ThisWorkbook.Sheets("BigBatch").Activate
+ [c6].Resize(NumberOfFilesToProcess, 2) = BigBatchResults
+End If
+
+Dim MyTime2
+MyTime2 = Time
+TempsEcoule = MyTime2 - MyTime
+Application.StatusBar = "Batchmap total time was " & Format(TempsEcoule, "h:mm:ss")
+
+GoTo 1000
+900 MsgBox "An error occurred during the BatchMap procedure."
+GoTo 1100
+1000
+BatchMode = 0
+'Application.StatusBar = False
+If BigBatchMode = 0 Then
+ ThisWorkbook.Sheets("BatchMap").Activate
+Else
+ ThisWorkbook.Sheets("BigBatch").Activate
+End If
+
+Beep
+[h8].Select
+1100
+End Sub
+
+
+Public Sub Auto_Batch_Map()
+'Same than BatchMap but simulates populations at the same time so saves CPU time
+'Simulates a series of populations, computes the map and reports a summary
+'Assumes that the linkage groups are already defined and ordered.
+'Needs to have the sequences pasted in My sequences
+
+'On Error GoTo 900
+Dim MyTime
+MyTime = Time
+BatchMode = 1
+AutoBatchMapOn = 1
+
+Application.ScreenUpdating = False
+
+msg = "Are you sure you want to continue? This will clear the previous batch results and the current sequences."
+Style = vbYesNo
+Title = "Confirmation"
+Ctxt = 1000
+response = MsgBox(msg, Style, Title)
+If response = vbNo Then GoTo 1100
+
+If ThisWorkbook.Sheets("SimulMap").[b6] = "" Then MsgBox ("Please simulate a map first"): GoTo 1100
+
+ThisWorkbook.Sheets("Menus").Range("N24:IV1023").ClearContents
+ThisWorkbook.Sheets("Menus").Range("J24:J1023").ClearContents
+
+CopySequencesFromSimulatedMap
+
+nbseq = ThisWorkbook.Sheets("Menus").Cells(23, 19)
+If nbseq = 0 Then
+ MsgBox ("Please simulate a map first")
+ ActiverSimulate
+ GoTo 1100
+End If
+
+Application.StatusBar = "reading Menu "
+ MenuMatrix = ThisWorkbook.Sheets("Menus").UsedRange.Value
+Application.StatusBar = "reading simulation parameters"
+ VirtualMap = ThisWorkbook.Sheets("SimulMap").UsedRange.Value
+ Read_Simulation_Parameters
+
+If SimulatedPopulationType <> "BC1" And SimulatedPopulationType <> "F2" And SimulatedPopulationType <> "BC2F1" And SimulatedPopulationType <> "SSD" Then MsgBox "BC1 or F2 populations only, sorry.": GoTo 1000
+
+Application.StatusBar = "reading mapping options"
+ Read_Mapping_Options
+
+NumberOfFilesToProcess = ThisWorkbook.Sheets("SimulMap").[n3]
+
+BigBatchMode = 0
+If MaxNumberOfColumns = 256 Then
+ If NumberOfFilesToProcess > 249 Then BigBatchMode = 1 Else BigBatchMode = 0
+End If
+
+NbLocus = ThisWorkbook.Sheets("SimulMap").[N23]
+Indiv = ThisWorkbook.Sheets("SimulMap").[N17]
+
+ReDim Data(Indiv, NbLocus) As Variant
+Application.StatusBar = "Clearing"
+
+If BigBatchMode = 0 Then
+ ThisWorkbook.Sheets("BatchMap").Range("A5:IV60000").ClearContents
+ ThisWorkbook.Sheets("BatchMap").[D4].ClearContents
+ ThisWorkbook.Sheets("BatchMap").[f4].ClearContents
+ ThisWorkbook.Sheets("BatchMap").Range("C8:G60000").Interior.ColorIndex = xlNone
+ ThisWorkbook.Sheets("BatchMap").Range("H5:XFD60000").Interior.ColorIndex = xlNone
+ ReDim BatchResults(NbLocus + 1, NumberOfFilesToProcess) As Variant
+Else
+ ThisWorkbook.Sheets("BigBatch").Range("C6:D60000").ClearContents
+ ReDim BigBatchResults(NumberOfFilesToProcess, 2) As Variant
+End If
+
+For CurrentPopulation = 1 To NumberOfFilesToProcess
+ Application.StatusBar = "Processing population " & CurrentPopulation
+ Simulate_Population_From_Map
+ ComputeMapForAutoBatch
+ 'If BigBatchMode = 0 Then ThisWorkbook.Sheets("BatchMap").Cells(7, CurrentPopulation + 7) = "Pop" & CurrentPopulation
+ If BigBatchMode = 0 Then BatchResults(0, CurrentPopulation - 1) = "Pop" & CurrentPopulation
+Next
+
+If BigBatchMode = 0 Then
+ ThisWorkbook.Sheets("BatchMap").Activate
+ [D4] = NumberOfFilesToProcess
+ NumberOfMarkers = ThisWorkbook.Sheets("SimulMap").[N23]
+ [f4] = NumberOfMarkers
+ [h7].Resize(NbLocus + 3, NumberOfFilesToProcess) = BatchResults
+ ThisWorkbook.Sheets("SimulMap").Activate
+ Range("D6").Select
+ Range(Selection, Selection.End(xlDown)).Select
+ Selection.Copy
+ [N22].Select
+ ThisWorkbook.Sheets("BatchMap").Activate
+ Range("B8").Select
+ Selection.PasteSpecial Paste:=xlPasteValues, Operation:=xlNone, SkipBlanks _
+ :=False, Transpose:=False
+
+ Compute_Stats_Batch
+Else
+ ThisWorkbook.Sheets("BigBatch").Activate
+ [c6].Resize(NumberOfFilesToProcess, 2) = BigBatchResults
+End If
+
+Dim MyTime2
+MyTime2 = Time
+TempsEcoule = MyTime2 - MyTime
+Application.StatusBar = "Autobatchmap total time was " & Format(TempsEcoule, "h:mm:ss")
+GoTo 1000
+900 MsgBox "An error occurred during the AutoBatchMap procedure."
+GoTo 1100
+1000
+If BigBatchMode = 0 Then
+ ThisWorkbook.Sheets("BatchMap").Activate
+Else
+ ThisWorkbook.Sheets("BigBatch").Activate
+End If
+AutoBatchMapOn = 0
+BigBatchMode = 1
+'Application.StatusBar = False
+Beep
+[h8].Select
+1100
+End Sub
+
+
+Public Sub Auto_Batch_Map_Chi2()
+'Same than BatchMap but simulates populations at the same time so saves CPU time
+'Simulates a series of populations, computes the map and reports a summary
+'Assumes that the linkage groups are already defined and ordered.
+'Needs to have the sequences pasted in My sequences
+
+'On Error GoTo 900
+Dim MyTime
+MyTime = Time
+BatchMode = 1
+AutoBatchMapOn = 1
+
+Application.ScreenUpdating = False
+
+msg = "Are you sure you want to continue? This will clear the previous batch results and the current sequences."
+Style = vbYesNo
+Title = "Confirmation"
+Ctxt = 1000
+response = MsgBox(msg, Style, Title)
+If response = vbNo Then GoTo 1100
+
+If ThisWorkbook.Sheets("SimulMap").[b6] = "" Then MsgBox ("Please simulate a map first"): GoTo 1100
+
+ThisWorkbook.Sheets("Menus").Range("N24:IV1023").ClearContents
+ThisWorkbook.Sheets("Menus").Range("J24:J1023").ClearContents
+
+CopySequencesFromSimulatedMap
+
+nbseq = ThisWorkbook.Sheets("Menus").Cells(23, 19)
+If nbseq = 0 Then
+ MsgBox ("Please simulate a map first")
+ ActiverSimulate
+ GoTo 1100
+End If
+
+Application.StatusBar = "reading Menu "
+ MenuMatrix = ThisWorkbook.Sheets("Menus").UsedRange.Value
+Application.StatusBar = "reading simulation parameters"
+ VirtualMap = ThisWorkbook.Sheets("SimulMap").UsedRange.Value
+ Read_Simulation_Parameters
+
+If SimulatedPopulationType <> "BC1" And SimulatedPopulationType <> "F2" And SimulatedPopulationType <> "BC2F1" And SimulatedPopulationType <> "SSD" Then MsgBox "BC1 or F2 populations only, sorry.": GoTo 1000
+
+Application.StatusBar = "reading mapping options"
+ Read_Mapping_Options
+
+NumberOfFilesToProcess = ThisWorkbook.Sheets("SimulMap").[n3]
+
+BigBatchMode = 0
+If MaxNumberOfColumns = 256 Then
+ If NumberOfFilesToProcess > 249 Then BigBatchMode = 1 Else BigBatchMode = 0
+End If
+
+NbLocus = ThisWorkbook.Sheets("SimulMap").[N23]
+Indiv = ThisWorkbook.Sheets("SimulMap").[N17]
+
+ReDim Data(Indiv, NbLocus) As Variant
+
+Application.StatusBar = "Clearing"
+
+If BigBatchMode = 0 Then
+ ThisWorkbook.Sheets("BatchMap").Range("A5:IV60000").ClearContents
+ ThisWorkbook.Sheets("BatchMap").[D4].ClearContents
+ ThisWorkbook.Sheets("BatchMap").[f4].ClearContents
+ ThisWorkbook.Sheets("BatchMap").Range("C5:XFD60000").Interior.ColorIndex = xlNone
+ 'ThisWorkbook.Sheets("BatchMap").Range("H5:XFD7").Interior.ColorIndex = xlNone
+ ReDim BatchResults(NbLocus + 1, NumberOfFilesToProcess) As Variant
+Else
+ ThisWorkbook.Sheets("BigBatch").Range("C6:D60000").ClearContents
+ ReDim BigBatchResults(NumberOfFilesToProcess, 2) As Variant
+End If
+
+For CurrentPopulation = 1 To NumberOfFilesToProcess
+ Application.StatusBar = "Processing population " & CurrentPopulation
+ Simulate_Population_From_Map
+ 'ComputeMapForAutoBatch
+
+ ComputeChiSquareForAutoBatch
+
+ 'If BigBatchMode = 0 Then ThisWorkbook.Sheets("BatchMap").Cells(7, CurrentPopulation + 7) = "Pop" & CurrentPopulation
+ If BigBatchMode = 0 Then BatchResults(0, CurrentPopulation - 1) = "Pop" & CurrentPopulation
+Next
+
+If BigBatchMode = 0 Then
+ ThisWorkbook.Sheets("BatchMap").Activate
+ [D4] = NumberOfFilesToProcess
+ NumberOfMarkers = ThisWorkbook.Sheets("SimulMap").[N23]
+ [f4] = NumberOfMarkers
+
+ [h7].Resize(NbLocus + 3, NumberOfFilesToProcess) = BatchResults
+
+ ThisWorkbook.Sheets("SimulMap").Activate
+ Range("D6").Select
+ Range(Selection, Selection.End(xlDown)).Select
+ Selection.Copy
+ [N22].Select
+ ThisWorkbook.Sheets("BatchMap").Activate
+ Range("B8").Select
+ Selection.PasteSpecial Paste:=xlPasteValues, Operation:=xlNone, SkipBlanks _
+ :=False, Transpose:=False
+
+ Compute_Stats_Batch_Chi2
+Else
+ ThisWorkbook.Sheets("BigBatch").Activate
+ [c6].Resize(NumberOfFilesToProcess, 2) = BigBatchResults
+End If
+
+Dim MyTime2
+MyTime2 = Time
+TempsEcoule = MyTime2 - MyTime
+Application.StatusBar = "Autobatchmap total time was " & Format(TempsEcoule, "h:mm:ss")
+GoTo 1000
+900 MsgBox "An error occurred during the AutoBatchMap procedure."
+GoTo 1100
+1000
+If BigBatchMode = 0 Then
+ ThisWorkbook.Sheets("BatchMap").Activate
+Else
+ ThisWorkbook.Sheets("BigBatch").Activate
+End If
+AutoBatchMapOn = 0
+BigBatchMode = 1
+'Application.StatusBar = False
+Beep
+[h8].Select
+1100
+End Sub
+