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04.Simulation.R
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2091 lines (1880 loc) · 161 KB
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####################################
##Simulate evolution over networks##
####################################
####################################
##1. Packages, data, and functions##
####################################
####Working directory
setwd("/Users/Chimera/Documents/ThorntonLab/Epistasis/2020")
####Packages
library(data.table)
library(Matrix)
library(ordinalNet)
library(Hmisc)
library(ggplot2)
library(boot)
library(gtools)
library(gplots)
library(glmnetcr)
library(dotCall64)
library(gridExtra)
library(grid)
library(seqinr)
library(stringr)
library(vioplot)
library(rgexf)
library(igraph)
library(nloptr)
library(pROC)
library(MatrixModels)
library(moments)
library(ppcor)
####Custom functions
source("Functions.R")
####Data
load("TG.ACT.NET.rda")
load("DT.JOINT.APPEND.rda")
##Amino acid states
AAs <- c("A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y")
##Split S into two groups (S and Z) for analyses that take account of the genetic code
AAs.extend <- c("A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y","Z")
##Neighbor and distance matrices
AA.NEIGHBORS.S <- read.table(file="AA.neighbors.S.txt",header=T,row.names=1,quote="")
AA.DISTANCES.S <- read.table(file="AA.distance.S.txt", header=T,row.names=1,quote="")
AA.NEIGHBORS.Z <- read.table(file="AA.neighbors.Z.txt",header=T,row.names=1,quote="")
AA.DISTANCES.Z <- read.table(file="AA.distance.Z.txt", header=T,row.names=1,quote="")
AA.NEIGHBORS.N <- read.table(file="AA.neighbors.N.txt",header=T,row.names=1,quote="")
AA.DISTANCES.N <- read.table(file="AA.distance.N.txt", header=T,row.names=1,quote="")
##Lists of genotypes in different models and networks
TG.ERE.LIST <- unique(substr(DT.JOINT[TE.JOINT.CLASS == 'ERE-specific',]$AAseq,2,5))
TG.SRE.LIST <- unique(substr(DT.JOINT[TE.JOINT.CLASS == 'SRE-specific',]$AAseq,2,5))
TH.ERE.LIST <- TG.ERE.LIST[-grep("Z",TG.ERE.LIST)]
TH.SRE.LIST <- TG.SRE.LIST[-grep("Z",TG.SRE.LIST)]
PG.ERE.LIST <- unique(substr(DT.JOINT[PE.JOINT.CLASS == 'ERE-specific',]$AAseq,2,5))
PG.SRE.LIST <- unique(substr(DT.JOINT[PE.JOINT.CLASS == 'SRE-specific',]$AAseq,2,5))
PH.ERE.LIST <- PG.ERE.LIST[-grep("Z",PG.ERE.LIST)]
PH.SRE.LIST <- PG.SRE.LIST[-grep("Z",PG.SRE.LIST)]
MG.ERE.LIST <- unique(substr(DT.JOINT[ME.JOINT.CLASS == 'ERE-specific',]$AAseq,2,5))
MG.SRE.LIST <- unique(substr(DT.JOINT[ME.JOINT.CLASS == 'SRE-specific',]$AAseq,2,5))
MH.ERE.LIST <- MG.ERE.LIST[-grep("Z",MG.ERE.LIST)]
MH.SRE.LIST <- MG.SRE.LIST[-grep("Z",MG.SRE.LIST)]
#Overlap of ERE genotypes in multiple models
TG.ERE.INTERSECT <- which(TG.ERE.LIST %in% PG.ERE.LIST & TG.ERE.LIST %in% MG.ERE.LIST)
PG.ERE.INTERSECT <- which(PG.ERE.LIST %in% TG.ERE.LIST & PG.ERE.LIST %in% MG.ERE.LIST)
MG.ERE.INTERSECT <- which(MG.ERE.LIST %in% PG.ERE.LIST & MG.ERE.LIST %in% TG.ERE.LIST)
TH.ERE.INTERSECT <- which(TH.ERE.LIST %in% PH.ERE.LIST & TH.ERE.LIST %in% MH.ERE.LIST)
PH.ERE.INTERSECT <- which(PH.ERE.LIST %in% TH.ERE.LIST & PH.ERE.LIST %in% MH.ERE.LIST)
MH.ERE.INTERSECT <- which(MH.ERE.LIST %in% PH.ERE.LIST & MH.ERE.LIST %in% TH.ERE.LIST)
#Networks
load("TG.ACT.NET.rda")
load("PG.ACT.NET.rda")
load("MG.ACT.NET.rda")
load("TH.ACT.NET.rda")
load("PH.ACT.NET.rda")
load("MH.ACT.NET.rda")
#################
###2. Simulate###
#################
##Simulation uses a Maynard Smith word game like model
##A genotype is in a network if it is functional, i.e. an activator on ERE, SRE, or both for a given model
##Functional genotypes are connected either via genetic code (G) or via hamming distance (H)
##Any step to a connected genotype is allowed with equal probability
##Paths are started from an ERE-specific genotype
##Paths end when the first SRE-specific genotype is encountered
###Simulations for all ERE-specific starting genotypes
#TG.ALL_ERE.ALL_GENO.SIMULATE <- ms.simulate(TG.ERE.LIST,TG.ACT.NET,"T",100); save(TG.ALL_ERE.ALL_GENO.SIMULATE, file="TG.ALL_ERE.ALL_GENO.SIMULATE.rda")
#PG.ALL_ERE.ALL_GENO.SIMULATE <- ms.simulate(PG.ERE.LIST,PG.ACT.NET,"P",100); save(PG.ALL_ERE.ALL_GENO.SIMULATE, file="PG.ALL_ERE.ALL_GENO.SIMULATE.rda")
#MG.ALL_ERE.ALL_GENO.SIMULATE <- ms.simulate(MG.ERE.LIST,MG.ACT.NET,"M",100); save(MG.ALL_ERE.ALL_GENO.SIMULATE, file="MG.ALL_ERE.ALL_GENO.SIMULATE.rda")
#TH.ALL_ERE.ALL_GENO.SIMULATE <- ms.simulate(TH.ERE.LIST,TH.ACT.NET,"T",100); save(TH.ALL_ERE.ALL_GENO.SIMULATE, file="TH.ALL_ERE.ALL_GENO.SIMULATE.rda")
#PH.ALL_ERE.ALL_GENO.SIMULATE <- ms.simulate(PH.ERE.LIST,PH.ACT.NET,"P",100); save(PH.ALL_ERE.ALL_GENO.SIMULATE, file="PH.ALL_ERE.ALL_GENO.SIMULATE.rda")
#MH.ALL_ERE.ALL_GENO.SIMULATE <- ms.simulate(MH.ERE.LIST,MH.ACT.NET,"M",100); save(MH.ALL_ERE.ALL_GENO.SIMULATE, file="MH.ALL_ERE.ALL_GENO.SIMULATE.rda")
load("TG.ALL_ERE.ALL_GENO.SIMULATE.rda")
load("PG.ALL_ERE.ALL_GENO.SIMULATE.rda")
load("MG.ALL_ERE.ALL_GENO.SIMULATE.rda")
load("TH.ALL_ERE.ALL_GENO.SIMULATE.rda")
load("PH.ALL_ERE.ALL_GENO.SIMULATE.rda")
load("MH.ALL_ERE.ALL_GENO.SIMULATE.rda")
###Additional simulations for subset of ERE-specific genotypes found in all three models
#TG.INT_ERE.ALL_GENO.SIMULATE <- ms.simulate(TG.ERE.LIST[TG.ERE.INTERSECT],TG.ACT.NET,"T",1000); save(TG.INT_ERE.ALL_GENO.SIMULATE, file="TG.INT_ERE.ALL_GENO.SIMULATE.rda")
#PG.INT_ERE.ALL_GENO.SIMULATE <- ms.simulate(PG.ERE.LIST[PG.ERE.INTERSECT],PG.ACT.NET,"P",1000); save(PG.INT_ERE.ALL_GENO.SIMULATE, file="PG.INT_ERE.ALL_GENO.SIMULATE.rda")
#MG.INT_ERE.ALL_GENO.SIMULATE <- ms.simulate(MG.ERE.LIST[MG.ERE.INTERSECT],MG.ACT.NET,"M",1000); save(MG.INT_ERE.ALL_GENO.SIMULATE, file="MG.INT_ERE.ALL_GENO.SIMULATE.rda")
#TH.INT_ERE.ALL_GENO.SIMULATE <- ms.simulate(TH.ERE.LIST[TH.ERE.INTERSECT],TH.ACT.NET,"T",1000); save(TH.INT_ERE.ALL_GENO.SIMULATE, file="TH.INT_ERE.ALL_GENO.SIMULATE.rda")
#PH.INT_ERE.ALL_GENO.SIMULATE <- ms.simulate(PH.ERE.LIST[PH.ERE.INTERSECT],PH.ACT.NET,"P",1000); save(PH.INT_ERE.ALL_GENO.SIMULATE, file="PH.INT_ERE.ALL_GENO.SIMULATE.rda")
#MH.INT_ERE.ALL_GENO.SIMULATE <- ms.simulate(MH.ERE.LIST[MH.ERE.INTERSECT],MH.ACT.NET,"M",1000); save(MH.INT_ERE.ALL_GENO.SIMULATE, file="MH.INT_ERE.ALL_GENO.SIMULATE.rda")
load("TG.INT_ERE.ALL_GENO.SIMULATE.rda")
load("PG.INT_ERE.ALL_GENO.SIMULATE.rda")
load("MG.INT_ERE.ALL_GENO.SIMULATE.rda")
load("TH.INT_ERE.ALL_GENO.SIMULATE.rda")
load("PH.INT_ERE.ALL_GENO.SIMULATE.rda")
load("MH.INT_ERE.ALL_GENO.SIMULATE.rda")
###Simulations for all ERE-specific starting genotypes under selection for increased SRE specificity
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=1,CUTOFF=200); save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1 , file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1.rda")
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=3,CUTOFF=200); save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3 , file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3.rda")
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=5,CUTOFF=200); save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5 , file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5.rda")
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=10,CUTOFF=200); save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10 , file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10.rda")
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=17,CUTOFF=200); save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17 , file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17.rda")
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=31,CUTOFF=200); save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31 , file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31.rda")
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=56,CUTOFF=200); save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56 , file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56.rda")
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=100,CUTOFF=200); save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100 , file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100.rda")
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=177,CUTOFF=200); save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177 , file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177.rda")
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=316,CUTOFF=200); save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316 , file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316.rda")
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=562,CUTOFF=200); save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562 , file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562.rda")
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=1000,CUTOFF=200); save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000 , file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000.rda")
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=1778,CUTOFF=200); save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778 , file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778.rda")
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=3162,CUTOFF=200); save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162 , file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162.rda")
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=5263,CUTOFF=200); save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263 , file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263.rda")
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000 <- sel.simulate(MG.ERE.LIST,MG.ACT.NET,"P",REPS=100,POP.SIZE=10000,CUTOFF=200);save(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000, file="MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263.rda")
load("MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=1,CUTOFF=200); save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1 , file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=3,CUTOFF=200); save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3 , file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=5,CUTOFF=200); save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5 , file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=10,CUTOFF=200); save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10 , file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=17,CUTOFF=200); save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17 , file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=31,CUTOFF=200); save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31 , file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=56,CUTOFF=200); save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56 , file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=100,CUTOFF=200); save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100 , file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=177,CUTOFF=200); save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177 , file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=316,CUTOFF=200); save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316 , file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=562,CUTOFF=200); save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562 , file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=1000,CUTOFF=200); save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000 , file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=1778,CUTOFF=200); save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778 , file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=3162,CUTOFF=200); save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162 , file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=5263,CUTOFF=200); save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263 , file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263.rda")
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000 <- sel.simulate(PG.ERE.LIST,PG.ACT.NET,"P",REPS=100,POP.SIZE=10000,CUTOFF=200);save(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000, file="PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263.rda")
load("PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=1,CUTOFF=200); save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1 , file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=3,CUTOFF=200); save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3 , file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=5,CUTOFF=200); save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5 , file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=10,CUTOFF=200); save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10 , file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=17,CUTOFF=200); save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17 , file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=31,CUTOFF=200); save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31 , file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=56,CUTOFF=200); save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56 , file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=100,CUTOFF=200); save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100 , file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=177,CUTOFF=200); save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177 , file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=316,CUTOFF=200); save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316 , file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=562,CUTOFF=200); save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562 , file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=1000,CUTOFF=200); save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000 , file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=1778,CUTOFF=200); save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778 , file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=3162,CUTOFF=200); save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162 , file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=5263,CUTOFF=200); save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263 , file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263.rda")
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000 <- sel.simulate(TG.ERE.LIST,TG.ACT.NET,"T",REPS=100,POP.SIZE=10000,CUTOFF=200);save(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000, file="TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263.rda")
load("TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000.rda")
#####################
###3. Path Lengths###
#####################
##Set unconnected nodes to NA
TG.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps==0)] <- NA
TH.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps[which(TH.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps==0)] <- NA
PH.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps[which(PH.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps==0)] <- NA
MH.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps[which(MH.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps==0)] <- NA
TG.INT_ERE.ALL_GENO.SIMULATE$Number.Steps[which(TG.INT_ERE.ALL_GENO.SIMULATE$Number.Steps==0)] <- NA
PG.INT_ERE.ALL_GENO.SIMULATE$Number.Steps[which(PG.INT_ERE.ALL_GENO.SIMULATE$Number.Steps==0)] <- NA
MG.INT_ERE.ALL_GENO.SIMULATE$Number.Steps[which(MG.INT_ERE.ALL_GENO.SIMULATE$Number.Steps==0)] <- NA
TH.INT_ERE.ALL_GENO.SIMULATE$Number.Steps[which(TH.INT_ERE.ALL_GENO.SIMULATE$Number.Steps==0)] <- NA
PH.INT_ERE.ALL_GENO.SIMULATE$Number.Steps[which(PH.INT_ERE.ALL_GENO.SIMULATE$Number.Steps==0)] <- NA
MH.INT_ERE.ALL_GENO.SIMULATE$Number.Steps[which(MH.INT_ERE.ALL_GENO.SIMULATE$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263$Number.Steps==0)] <- NA
MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263$Number.Steps==0)] <- NA
PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263$Number.Steps==0)] <- NA
TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000$Number.Steps==0)] <- NA
##Set steps greater than 20 to NA to remove high local peaks
#TG.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps > 20)] <- NA
#TH.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps[which(TH.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps > 20)] <- NA
#PH.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps[which(PH.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps > 20)] <- NA
#MH.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps[which(MH.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps > 20)] <- NA
#
#TG.INT_ERE.ALL_GENO.SIMULATE$Number.Steps[which(TG.INT_ERE.ALL_GENO.SIMULATE$Number.Steps > 20)] <- NA
#PG.INT_ERE.ALL_GENO.SIMULATE$Number.Steps[which(PG.INT_ERE.ALL_GENO.SIMULATE$Number.Steps > 20)] <- NA
#MG.INT_ERE.ALL_GENO.SIMULATE$Number.Steps[which(MG.INT_ERE.ALL_GENO.SIMULATE$Number.Steps > 20)] <- NA
#TH.INT_ERE.ALL_GENO.SIMULATE$Number.Steps[which(TH.INT_ERE.ALL_GENO.SIMULATE$Number.Steps > 20)] <- NA
#PH.INT_ERE.ALL_GENO.SIMULATE$Number.Steps[which(PH.INT_ERE.ALL_GENO.SIMULATE$Number.Steps > 20)] <- NA
#MH.INT_ERE.ALL_GENO.SIMULATE$Number.Steps[which(MH.INT_ERE.ALL_GENO.SIMULATE$Number.Steps > 20)] <- NA
#
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263$Number.Steps > 20)] <- NA
#MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000$Number.Steps[which(MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000$Number.Steps > 20)] <- NA
#
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263$Number.Steps > 20)] <- NA
#PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000$Number.Steps[which(PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000$Number.Steps > 20)] <- NA
#
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1$Number.Steps > 20)] <- NA
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3$Number.Steps > 20)] <- NA
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5$Number.Steps > 20)] <- NA
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10$Number.Steps > 20)] <- NA
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17$Number.Steps > 20)] <- NA
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31$Number.Steps > 20)] <- NA
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56$Number.Steps > 20)] <- NA
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100$Number.Steps > 20)] <- NA
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177$Number.Steps > 20)] <- NA
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316$Number.Steps > 20)] <- NA
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562$Number.Steps > 20)] <- NA
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000$Number.Steps > 20)] <- NA
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778$Number.Steps > 20)] <- NA
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162$Number.Steps > 20)] <- NA
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263$Number.Steps > 20)] <- NA
#TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000$Number.Steps[which(TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000$Number.Steps > 20)] <- NA
##Extract path lengths
TG.ALL_ERE.ALL_GENO.STEPS.N <- TG.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps
PG.ALL_ERE.ALL_GENO.STEPS.N <- PG.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps
MG.ALL_ERE.ALL_GENO.STEPS.N <- MG.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps
TH.ALL_ERE.ALL_GENO.STEPS.N <- TH.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps
PH.ALL_ERE.ALL_GENO.STEPS.N <- PH.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps
MH.ALL_ERE.ALL_GENO.STEPS.N <- MH.ALL_ERE.ALL_GENO.SIMULATE$Number.Steps
TG.INT_ERE.ALL_GENO.STEPS.N <- TG.INT_ERE.ALL_GENO.SIMULATE$Number.Steps
PG.INT_ERE.ALL_GENO.STEPS.N <- PG.INT_ERE.ALL_GENO.SIMULATE$Number.Steps
MG.INT_ERE.ALL_GENO.STEPS.N <- MG.INT_ERE.ALL_GENO.SIMULATE$Number.Steps
TH.INT_ERE.ALL_GENO.STEPS.N <- TH.INT_ERE.ALL_GENO.SIMULATE$Number.Steps
PH.INT_ERE.ALL_GENO.STEPS.N <- PH.INT_ERE.ALL_GENO.SIMULATE$Number.Steps
MH.INT_ERE.ALL_GENO.STEPS.N <- MH.INT_ERE.ALL_GENO.SIMULATE$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263$Number.Steps
MG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.N <- MG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263$Number.Steps
PG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.N <- PG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N17$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N31$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N56$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N100$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N177$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N316$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N562$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1000$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N1778$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N3162$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N5263$Number.Steps
TG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.N <- TG.ALL_ERE.ALL_GENO.SEL.SIMULATE.N10000$Number.Steps
##Path length for each model/network combination averaged across starting genotypes
#Mean for all starting genotypes
TG.ALL_ERE.ALL_GENO.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
TH.ALL_ERE.ALL_GENO.STEPS.AVG <- mean(TH.ALL_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
PH.ALL_ERE.ALL_GENO.STEPS.AVG <- mean(PH.ALL_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
MH.ALL_ERE.ALL_GENO.STEPS.AVG <- mean(MH.ALL_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.N,na.rm=TRUE)
#SD for all starting genotypes
TG.ALL_ERE.ALL_GENO.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
TH.ALL_ERE.ALL_GENO.STEPS.SD <- sd(TH.ALL_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
PH.ALL_ERE.ALL_GENO.STEPS.SD <- sd(PH.ALL_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
MH.ALL_ERE.ALL_GENO.STEPS.SD <- sd(MH.ALL_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.N,na.rm=TRUE)
MG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.N,na.rm=TRUE)
PG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.N,na.rm=TRUE)
TG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.N,na.rm=TRUE)
#Mean for common starting genotypes
TG.INT_ERE.ALL_GENO.STEPS.AVG <- mean(TG.INT_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
PG.INT_ERE.ALL_GENO.STEPS.AVG <- mean(PG.INT_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
MG.INT_ERE.ALL_GENO.STEPS.AVG <- mean(MG.INT_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
TH.INT_ERE.ALL_GENO.STEPS.AVG <- mean(TH.INT_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
PH.INT_ERE.ALL_GENO.STEPS.AVG <- mean(PH.INT_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
MH.INT_ERE.ALL_GENO.STEPS.AVG <- mean(MH.INT_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N1.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N3.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N5.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N10.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N17.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N31.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N56.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N100.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N177.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N316.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N562.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N1000.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N1778.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N3162.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N5263.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N10000.STEPS.AVG <- mean(MG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N1.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N3.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N5.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N10.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N17.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N31.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N56.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N100.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N177.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N316.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N562.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N1000.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N1778.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N3162.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N5263.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N10000.STEPS.AVG <- mean(PG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N1.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N3.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N5.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N10.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N17.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N31.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N56.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N100.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N177.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N316.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N562.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N1000.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N1778.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N3162.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N5263.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N10000.STEPS.AVG <- mean(TG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
#SD for common starting genotypes
TG.INT_ERE.ALL_GENO.STEPS.SD <- sd(TG.INT_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
PG.INT_ERE.ALL_GENO.STEPS.SD <- sd(PG.INT_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
MG.INT_ERE.ALL_GENO.STEPS.SD <- sd(MG.INT_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
TH.INT_ERE.ALL_GENO.STEPS.SD <- sd(TH.INT_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
PH.INT_ERE.ALL_GENO.STEPS.SD <- sd(PH.INT_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
MH.INT_ERE.ALL_GENO.STEPS.SD <- sd(MH.INT_ERE.ALL_GENO.STEPS.N,na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N1.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N3.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N5.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N10.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N17.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N31.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N56.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N100.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N177.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N316.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N562.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N1000.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N1778.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N3162.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N5263.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
MG.INT_ERE.ALL_GENO.SEL.N10000.STEPS.SD <- sd(MG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.N[,MG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N1.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N3.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N5.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N10.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N17.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N31.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N56.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N100.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N177.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N316.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N562.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N1000.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N1778.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N3162.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N5263.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
PG.INT_ERE.ALL_GENO.SEL.N10000.STEPS.SD <- sd(PG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.N[,PG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N1.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N3.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N5.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N10.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N17.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N31.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N56.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N100.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N177.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N316.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N562.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N1000.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N1778.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N3162.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N5263.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
TG.INT_ERE.ALL_GENO.SEL.N10000.STEPS.SD <- sd(TG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.N[,TG.ERE.INTERSECT],na.rm=TRUE)
#Collect means
ALL.ALL_GENO.STEPS.AVG <- c(TG.ALL_ERE.ALL_GENO.STEPS.AVG,TG.INT_ERE.ALL_GENO.STEPS.AVG,
PG.ALL_ERE.ALL_GENO.STEPS.AVG,PG.INT_ERE.ALL_GENO.STEPS.AVG,
MG.ALL_ERE.ALL_GENO.STEPS.AVG,MG.INT_ERE.ALL_GENO.STEPS.AVG,
TH.ALL_ERE.ALL_GENO.STEPS.AVG,TH.INT_ERE.ALL_GENO.STEPS.AVG,
PH.ALL_ERE.ALL_GENO.STEPS.AVG,PH.INT_ERE.ALL_GENO.STEPS.AVG,
MH.ALL_ERE.ALL_GENO.STEPS.AVG,MH.INT_ERE.ALL_GENO.STEPS.AVG)
MG.ALL_ERE.ALL_GENO.AVG <- c(MG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.AVG,MG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.AVG,MG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.AVG,MG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.AVG,MG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.AVG,MG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.AVG,MG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.AVG,MG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.AVG,MG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.AVG,MG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.AVG,MG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.AVG,MG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.AVG,MG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.AVG,MG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.AVG,MG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.AVG,MG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.AVG)
PG.ALL_ERE.ALL_GENO.AVG <- c(PG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.AVG,PG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.AVG,PG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.AVG,PG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.AVG,PG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.AVG,PG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.AVG,PG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.AVG,PG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.AVG,PG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.AVG,PG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.AVG,PG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.AVG,PG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.AVG,PG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.AVG,PG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.AVG,PG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.AVG,PG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.AVG)
TG.ALL_ERE.ALL_GENO.AVG <- c(TG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.AVG,TG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.AVG,TG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.AVG,TG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.AVG,TG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.AVG,TG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.AVG,TG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.AVG,TG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.AVG,TG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.AVG,TG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.AVG,TG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.AVG,TG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.AVG,TG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.AVG,TG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.AVG,TG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.AVG,TG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.AVG)
MG.INT_ERE.ALL_GENO.AVG <- c(MG.INT_ERE.ALL_GENO.SEL.N1.STEPS.AVG,MG.INT_ERE.ALL_GENO.SEL.N3.STEPS.AVG,MG.INT_ERE.ALL_GENO.SEL.N5.STEPS.AVG,MG.INT_ERE.ALL_GENO.SEL.N10.STEPS.AVG,MG.INT_ERE.ALL_GENO.SEL.N17.STEPS.AVG,MG.INT_ERE.ALL_GENO.SEL.N31.STEPS.AVG,MG.INT_ERE.ALL_GENO.SEL.N56.STEPS.AVG,MG.INT_ERE.ALL_GENO.SEL.N100.STEPS.AVG,MG.INT_ERE.ALL_GENO.SEL.N177.STEPS.AVG,MG.INT_ERE.ALL_GENO.SEL.N316.STEPS.AVG,MG.INT_ERE.ALL_GENO.SEL.N562.STEPS.AVG,MG.INT_ERE.ALL_GENO.SEL.N1000.STEPS.AVG,MG.INT_ERE.ALL_GENO.SEL.N1778.STEPS.AVG,MG.INT_ERE.ALL_GENO.SEL.N3162.STEPS.AVG,MG.INT_ERE.ALL_GENO.SEL.N5263.STEPS.AVG,MG.INT_ERE.ALL_GENO.SEL.N10000.STEPS.AVG)
PG.INT_ERE.ALL_GENO.AVG <- c(PG.INT_ERE.ALL_GENO.SEL.N1.STEPS.AVG,PG.INT_ERE.ALL_GENO.SEL.N3.STEPS.AVG,PG.INT_ERE.ALL_GENO.SEL.N5.STEPS.AVG,PG.INT_ERE.ALL_GENO.SEL.N10.STEPS.AVG,PG.INT_ERE.ALL_GENO.SEL.N17.STEPS.AVG,PG.INT_ERE.ALL_GENO.SEL.N31.STEPS.AVG,PG.INT_ERE.ALL_GENO.SEL.N56.STEPS.AVG,PG.INT_ERE.ALL_GENO.SEL.N100.STEPS.AVG,PG.INT_ERE.ALL_GENO.SEL.N177.STEPS.AVG,PG.INT_ERE.ALL_GENO.SEL.N316.STEPS.AVG,PG.INT_ERE.ALL_GENO.SEL.N562.STEPS.AVG,PG.INT_ERE.ALL_GENO.SEL.N1000.STEPS.AVG,PG.INT_ERE.ALL_GENO.SEL.N1778.STEPS.AVG,PG.INT_ERE.ALL_GENO.SEL.N3162.STEPS.AVG,PG.INT_ERE.ALL_GENO.SEL.N5263.STEPS.AVG,PG.INT_ERE.ALL_GENO.SEL.N10000.STEPS.AVG)
TG.INT_ERE.ALL_GENO.AVG <- c(TG.INT_ERE.ALL_GENO.SEL.N1.STEPS.AVG,TG.INT_ERE.ALL_GENO.SEL.N3.STEPS.AVG,TG.INT_ERE.ALL_GENO.SEL.N5.STEPS.AVG,TG.INT_ERE.ALL_GENO.SEL.N10.STEPS.AVG,TG.INT_ERE.ALL_GENO.SEL.N17.STEPS.AVG,TG.INT_ERE.ALL_GENO.SEL.N31.STEPS.AVG,TG.INT_ERE.ALL_GENO.SEL.N56.STEPS.AVG,TG.INT_ERE.ALL_GENO.SEL.N100.STEPS.AVG,TG.INT_ERE.ALL_GENO.SEL.N177.STEPS.AVG,TG.INT_ERE.ALL_GENO.SEL.N316.STEPS.AVG,TG.INT_ERE.ALL_GENO.SEL.N562.STEPS.AVG,TG.INT_ERE.ALL_GENO.SEL.N1000.STEPS.AVG,TG.INT_ERE.ALL_GENO.SEL.N1778.STEPS.AVG,TG.INT_ERE.ALL_GENO.SEL.N3162.STEPS.AVG,TG.INT_ERE.ALL_GENO.SEL.N5263.STEPS.AVG,TG.INT_ERE.ALL_GENO.SEL.N10000.STEPS.AVG)
#Collect SDs
ALL.ALL_GENO.STEPS.SD <- c(TG.ALL_ERE.ALL_GENO.STEPS.SD,TG.INT_ERE.ALL_GENO.STEPS.SD,
PG.ALL_ERE.ALL_GENO.STEPS.SD,PG.INT_ERE.ALL_GENO.STEPS.SD,
MG.ALL_ERE.ALL_GENO.STEPS.SD,MG.INT_ERE.ALL_GENO.STEPS.SD,
TH.ALL_ERE.ALL_GENO.STEPS.SD,TH.INT_ERE.ALL_GENO.STEPS.SD,
PH.ALL_ERE.ALL_GENO.STEPS.SD,PH.INT_ERE.ALL_GENO.STEPS.SD,
MH.ALL_ERE.ALL_GENO.STEPS.SD,MH.INT_ERE.ALL_GENO.STEPS.SD)
MG.ALL_ERE.ALL_GENO.SD <- c(MG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.SD,MG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.SD,MG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.SD,MG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.SD,MG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.SD,MG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.SD,MG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.SD,MG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.SD,MG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.SD,MG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.SD,MG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.SD,MG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.SD,MG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.SD,MG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.SD,MG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.SD,MG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.SD)
PG.ALL_ERE.ALL_GENO.SD <- c(PG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.SD,PG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.SD,PG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.SD,PG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.SD,PG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.SD,PG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.SD,PG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.SD,PG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.SD,PG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.SD,PG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.SD,PG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.SD,PG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.SD,PG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.SD,PG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.SD,PG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.SD,PG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.SD)
TG.ALL_ERE.ALL_GENO.SD <- c(TG.ALL_ERE.ALL_GENO.SEL.N1.STEPS.SD,TG.ALL_ERE.ALL_GENO.SEL.N3.STEPS.SD,TG.ALL_ERE.ALL_GENO.SEL.N5.STEPS.SD,TG.ALL_ERE.ALL_GENO.SEL.N10.STEPS.SD,TG.ALL_ERE.ALL_GENO.SEL.N17.STEPS.SD,TG.ALL_ERE.ALL_GENO.SEL.N31.STEPS.SD,TG.ALL_ERE.ALL_GENO.SEL.N56.STEPS.SD,TG.ALL_ERE.ALL_GENO.SEL.N100.STEPS.SD,TG.ALL_ERE.ALL_GENO.SEL.N177.STEPS.SD,TG.ALL_ERE.ALL_GENO.SEL.N316.STEPS.SD,TG.ALL_ERE.ALL_GENO.SEL.N562.STEPS.SD,TG.ALL_ERE.ALL_GENO.SEL.N1000.STEPS.SD,TG.ALL_ERE.ALL_GENO.SEL.N1778.STEPS.SD,TG.ALL_ERE.ALL_GENO.SEL.N3162.STEPS.SD,TG.ALL_ERE.ALL_GENO.SEL.N5263.STEPS.SD,TG.ALL_ERE.ALL_GENO.SEL.N10000.STEPS.SD)
MG.INT_ERE.ALL_GENO.SD <- c(MG.INT_ERE.ALL_GENO.SEL.N1.STEPS.SD,MG.INT_ERE.ALL_GENO.SEL.N3.STEPS.SD,MG.INT_ERE.ALL_GENO.SEL.N5.STEPS.SD,MG.INT_ERE.ALL_GENO.SEL.N10.STEPS.SD,MG.INT_ERE.ALL_GENO.SEL.N17.STEPS.SD,MG.INT_ERE.ALL_GENO.SEL.N31.STEPS.SD,MG.INT_ERE.ALL_GENO.SEL.N56.STEPS.SD,MG.INT_ERE.ALL_GENO.SEL.N100.STEPS.SD,MG.INT_ERE.ALL_GENO.SEL.N177.STEPS.SD,MG.INT_ERE.ALL_GENO.SEL.N316.STEPS.SD,MG.INT_ERE.ALL_GENO.SEL.N562.STEPS.SD,MG.INT_ERE.ALL_GENO.SEL.N1000.STEPS.SD,MG.INT_ERE.ALL_GENO.SEL.N1778.STEPS.SD,MG.INT_ERE.ALL_GENO.SEL.N3162.STEPS.SD,MG.INT_ERE.ALL_GENO.SEL.N5263.STEPS.SD,MG.INT_ERE.ALL_GENO.SEL.N10000.STEPS.SD)
PG.INT_ERE.ALL_GENO.SD <- c(PG.INT_ERE.ALL_GENO.SEL.N1.STEPS.SD,PG.INT_ERE.ALL_GENO.SEL.N3.STEPS.SD,PG.INT_ERE.ALL_GENO.SEL.N5.STEPS.SD,PG.INT_ERE.ALL_GENO.SEL.N10.STEPS.SD,PG.INT_ERE.ALL_GENO.SEL.N17.STEPS.SD,PG.INT_ERE.ALL_GENO.SEL.N31.STEPS.SD,PG.INT_ERE.ALL_GENO.SEL.N56.STEPS.SD,PG.INT_ERE.ALL_GENO.SEL.N100.STEPS.SD,PG.INT_ERE.ALL_GENO.SEL.N177.STEPS.SD,PG.INT_ERE.ALL_GENO.SEL.N316.STEPS.SD,PG.INT_ERE.ALL_GENO.SEL.N562.STEPS.SD,PG.INT_ERE.ALL_GENO.SEL.N1000.STEPS.SD,PG.INT_ERE.ALL_GENO.SEL.N1778.STEPS.SD,PG.INT_ERE.ALL_GENO.SEL.N3162.STEPS.SD,PG.INT_ERE.ALL_GENO.SEL.N5263.STEPS.SD,PG.INT_ERE.ALL_GENO.SEL.N10000.STEPS.SD)
TG.INT_ERE.ALL_GENO.SD <- c(TG.INT_ERE.ALL_GENO.SEL.N1.STEPS.SD,TG.INT_ERE.ALL_GENO.SEL.N3.STEPS.SD,TG.INT_ERE.ALL_GENO.SEL.N5.STEPS.SD,TG.INT_ERE.ALL_GENO.SEL.N10.STEPS.SD,TG.INT_ERE.ALL_GENO.SEL.N17.STEPS.SD,TG.INT_ERE.ALL_GENO.SEL.N31.STEPS.SD,TG.INT_ERE.ALL_GENO.SEL.N56.STEPS.SD,TG.INT_ERE.ALL_GENO.SEL.N100.STEPS.SD,TG.INT_ERE.ALL_GENO.SEL.N177.STEPS.SD,TG.INT_ERE.ALL_GENO.SEL.N316.STEPS.SD,TG.INT_ERE.ALL_GENO.SEL.N562.STEPS.SD,TG.INT_ERE.ALL_GENO.SEL.N1000.STEPS.SD,TG.INT_ERE.ALL_GENO.SEL.N1778.STEPS.SD,TG.INT_ERE.ALL_GENO.SEL.N3162.STEPS.SD,TG.INT_ERE.ALL_GENO.SEL.N5263.STEPS.SD,TG.INT_ERE.ALL_GENO.SEL.N10000.STEPS.SD)
##Plot
##pdf("Sim.path.length.no.local.pdf")
par(mfrow=c(1,1))
par(pty="s")
barplot(ALL.ALL_GENO.STEPS.AVG,ylim=c(0,13),space=rep(c(0.5,0),6),width=0.5,cex.names=0.5,cex.axis=0.5,cex.main=0.5,col=c(rep(c("darkred","red"),3),rep(c("darkblue","skyblue2"),3)),main="Negative")
error.bar(x = c(0.5,1,1.75,2.25,3,3.5,4.25,4.75,5.5,6,6.75,7.25), y = ALL.ALL_GENO.STEPS.AVG, upper = 1.96*ALL.ALL_GENO.STEPS.SD/sqrt(prod(dim(TG.INT_ERE.ALL_GENO.STEPS.N))-1))
axis(1,c(.75,2,3.25,4.5,5.75,7),c("TG","PG","MG","TH","PH","MH"),cex.axis=0.5)
legend(4.5,12,legend=c("All ERE GC","Common ERE GC","All ERE HD","Common ERE HD"),fill=c("darkred","red","darkblue","skyblue2"),cex=0.5)
plot( log10(c(1,3,5,10,17,31,56,100,177,316,562,1000,1778,3162,5263,10000)), MG.ALL_ERE.ALL_GENO.AVG,pch=19,cex=0.6,ylim=c(1,13),ylab="Average Path Length",xlab="log10(Population Size)",main="Positive+Negative Selection All Starting")
points(log10(c(1,3,5,10,17,31,56,100,177,316,562,1000,1778,3162,5263,10000)), PG.ALL_ERE.ALL_GENO.AVG,pch=19,cex=0.6,col="red")
points(log10(c(1,3,5,10,17,31,56,100,177,316,562,1000,1778,3162,5263,10000)), TG.ALL_ERE.ALL_GENO.AVG,pch=19,cex=0.6,col="blue")
plot( log10(c(1,3,5,10,17,31,56,100,177,316,562,1000,1778,3162,5263,10000)), MG.INT_ERE.ALL_GENO.AVG,pch=19,cex=0.6,ylim=c(1,13),ylab="Average Path Length",xlab="log10(Population Size)",main="Positive+Negative Selection Common Starting")
points(log10(c(1,3,5,10,17,31,56,100,177,316,562,1000,1778,3162,5263,10000)), PG.INT_ERE.ALL_GENO.AVG,pch=19,cex=0.6,col="red")
points(log10(c(1,3,5,10,17,31,56,100,177,316,562,1000,1778,3162,5263,10000)), TG.INT_ERE.ALL_GENO.AVG,pch=19,cex=0.6,col="blue")
##dev.off()
##Permutation test for difference in path length for all starting genotype
N <- 10000
TG_PG.ALL_ERE.ALL_GENO.STEPS.p <- permutation.test.matrix(TG.ALL_ERE.ALL_GENO.STEPS.N,PG.ALL_ERE.ALL_GENO.STEPS.N,N)
OBS <- TG.ALL_ERE.ALL_GENO.STEPS.AVG - PG.ALL_ERE.ALL_GENO.STEPS.AVG
sum(OBS < TG_PG.ALL_ERE.ALL_GENO.STEPS.p)/length(TG_PG.ALL_ERE.ALL_GENO.STEPS.p)
TG_MG.ALL_ERE.ALL_GENO.STEPS.p <- permutation.test.matrix(TG.ALL_ERE.ALL_GENO.STEPS.N,MG.ALL_ERE.ALL_GENO.STEPS.N,N)
OBS <- TG.ALL_ERE.ALL_GENO.STEPS.AVG - MG.ALL_ERE.ALL_GENO.STEPS.AVG
sum(OBS < TG_MG.ALL_ERE.ALL_GENO.STEPS.p)/length(TG_MG.ALL_ERE.ALL_GENO.STEPS.p)
PG_MG.ALL_ERE.ALL_GENO.STEPS.p <- permutation.test.matrix(PG.ALL_ERE.ALL_GENO.STEPS.N,MG.ALL_ERE.ALL_GENO.STEPS.N,N)
OBS <- PG.ALL_ERE.ALL_GENO.STEPS.AVG - MG.ALL_ERE.ALL_GENO.STEPS.AVG
sum(OBS < PG_MG.ALL_ERE.ALL_GENO.STEPS.p)/length(PG_MG.ALL_ERE.ALL_GENO.STEPS.p)
TG_PG.INT_ERE.ALL_GENO.STEPS.p <- permutation.test.matrix(TG.INT_ERE.ALL_GENO.STEPS.N,PG.INT_ERE.ALL_GENO.STEPS.N,N)
OBS <- TG.INT_ERE.ALL_GENO.STEPS.AVG - PG.INT_ERE.ALL_GENO.STEPS.AVG
sum(OBS < TG_PG.INT_ERE.ALL_GENO.STEPS.p)/length(TG_PG.INT_ERE.ALL_GENO.STEPS.p)
TG_MG.INT_ERE.ALL_GENO.STEPS.p <- permutation.test.matrix(TG.INT_ERE.ALL_GENO.STEPS.N,MG.INT_ERE.ALL_GENO.STEPS.N,N)
OBS <- TG.INT_ERE.ALL_GENO.STEPS.AVG - MG.INT_ERE.ALL_GENO.STEPS.AVG
sum(OBS < TG_MG.INT_ERE.ALL_GENO.STEPS.p)/length(TG_MG.INT_ERE.ALL_GENO.STEPS.p)
PG_MG.INT_ERE.ALL_GENO.STEPS.p <- permutation.test.matrix(PG.INT_ERE.ALL_GENO.STEPS.N,MG.INT_ERE.ALL_GENO.STEPS.N,N)
OBS <- PG.INT_ERE.ALL_GENO.STEPS.AVG - MG.INT_ERE.ALL_GENO.STEPS.AVG
sum(OBS < PG_MG.INT_ERE.ALL_GENO.STEPS.p)/length(PG_MG.INT_ERE.ALL_GENO.STEPS.p)
TH_PH.ALL_ERE.ALL_GENO.STEPS.p <- permutation.test.matrix(TH.ALL_ERE.ALL_GENO.STEPS.N,PH.ALL_ERE.ALL_GENO.STEPS.N,N)
OBS <- TH.ALL_ERE.ALL_GENO.STEPS.AVG - PH.ALL_ERE.ALL_GENO.STEPS.AVG
sum(OBS < TH_PH.ALL_ERE.ALL_GENO.STEPS.p)/length(TH_PH.ALL_ERE.ALL_GENO.STEPS.p)
TH_MH.ALL_ERE.ALL_GENO.STEPS.p <- permutation.test.matrix(TH.ALL_ERE.ALL_GENO.STEPS.N,MH.ALL_ERE.ALL_GENO.STEPS.N,N)
OBS <- TH.ALL_ERE.ALL_GENO.STEPS.AVG - MH.ALL_ERE.ALL_GENO.STEPS.AVG
sum(OBS < TH_MH.ALL_ERE.ALL_GENO.STEPS.p)/length(TH_MH.ALL_ERE.ALL_GENO.STEPS.p)
PH_MH.ALL_ERE.ALL_GENO.STEPS.p <- permutation.test.matrix(PH.ALL_ERE.ALL_GENO.STEPS.N,MH.ALL_ERE.ALL_GENO.STEPS.N,N)
OBS <- PH.ALL_ERE.ALL_GENO.STEPS.AVG - MH.ALL_ERE.ALL_GENO.STEPS.AVG
sum(OBS < PH_MH.ALL_ERE.ALL_GENO.STEPS.p)/length(PH_MH.ALL_ERE.ALL_GENO.STEPS.p)
TH_PH.INT_ERE.ALL_GENO.STEPS.p <- permutation.test.matrix(TH.INT_ERE.ALL_GENO.STEPS.N,PH.INT_ERE.ALL_GENO.STEPS.N,N)
OBS <- TH.INT_ERE.ALL_GENO.STEPS.AVG - PH.INT_ERE.ALL_GENO.STEPS.AVG
sum(OBS < TH_PH.INT_ERE.ALL_GENO.STEPS.p)/length(TH_PH.INT_ERE.ALL_GENO.STEPS.p)
TH_MH.INT_ERE.ALL_GENO.STEPS.p <- permutation.test.matrix(TH.INT_ERE.ALL_GENO.STEPS.N,MH.INT_ERE.ALL_GENO.STEPS.N,N)
OBS <- TH.INT_ERE.ALL_GENO.STEPS.AVG - MH.INT_ERE.ALL_GENO.STEPS.AVG
sum(OBS < TH_MH.INT_ERE.ALL_GENO.STEPS.p)/length(TH_MH.INT_ERE.ALL_GENO.STEPS.p)
PH_MH.INT_ERE.ALL_GENO.STEPS.p <- permutation.test.matrix(PH.INT_ERE.ALL_GENO.STEPS.N,MH.INT_ERE.ALL_GENO.STEPS.N,N)
OBS <- PH.INT_ERE.ALL_GENO.STEPS.AVG - MH.INT_ERE.ALL_GENO.STEPS.AVG
sum(OBS < PH_MH.INT_ERE.ALL_GENO.STEPS.p)/length(PH_MH.INT_ERE.ALL_GENO.STEPS.p)
##Partition differences into Genetic code/Hamming distance
##Main vs Pairwise vs Third order epistassi
##All starting genotypes vs Common starting genotypes
##With vs without selection
PARTITION <- data.frame(STEPS=c(ALL.ALL_GENO.STEPS.AVG,ALL.ALL_GENO.SEL.STEPS.AVG), MODEL = rep(c("T","T","P","P","M","M"),4),NETWORK = rep(c(rep("G",6),rep("H",6)),2), SET = rep(c(rep(c("A","S"),6)),2), SEL=c(rep("Neg",12),rep("Pos",12)) )
PARTITION$MODEL <- as.factor(PARTITION$MODEL)
PARTITION$NETWORK <- as.factor(PARTITION$NETWORK)
PARTITION$SET <- as.factor(PARTITION$SET)
PARTITION$SEL <- as.factor(PARTITION$SEL)
MODEL.OUT <- lm(STEPS ~ 0 + MODEL*NETWORK*SEL+MODEL*SET + NETWORK*SET + SEL*SET, data=PARTITION)
step(MODEL.OUT)
MODEL.OUT <- lm(STEPS ~ 0 + MODEL*NETWORK*SEL + SEL*SET, data=PARTITION)
##Average path length for each starting genotype
#Individual mean for all starting genotypes
TG.ALL_ERE.IND_GENO.STEPS.AVG <- apply(TG.ALL_ERE.ALL_GENO.STEPS.N,2,mean)
PG.ALL_ERE.IND_GENO.STEPS.AVG <- apply(PG.ALL_ERE.ALL_GENO.STEPS.N,2,mean)
MG.ALL_ERE.IND_GENO.STEPS.AVG <- apply(MG.ALL_ERE.ALL_GENO.STEPS.N,2,mean)
TH.ALL_ERE.IND_GENO.STEPS.AVG <- apply(TH.ALL_ERE.ALL_GENO.STEPS.N,2,mean)
PH.ALL_ERE.IND_GENO.STEPS.AVG <- apply(PH.ALL_ERE.ALL_GENO.STEPS.N,2,mean)
MH.ALL_ERE.IND_GENO.STEPS.AVG <- apply(MH.ALL_ERE.ALL_GENO.STEPS.N,2,mean)
TG.ALL_ERE.IND_GENO.SEL.STEPS.AVG <- apply(TG.ALL_ERE.ALL_GENO.SEL.STEPS.N,2,mean)
PG.ALL_ERE.IND_GENO.SEL.STEPS.AVG <- apply(PG.ALL_ERE.ALL_GENO.SEL.STEPS.N,2,mean)
MG.ALL_ERE.IND_GENO.SEL.STEPS.AVG <- apply(MG.ALL_ERE.ALL_GENO.SEL.STEPS.N,2,mean)
TH.ALL_ERE.IND_GENO.SEL.STEPS.AVG <- apply(TH.ALL_ERE.ALL_GENO.SEL.STEPS.N,2,mean)
PH.ALL_ERE.IND_GENO.SEL.STEPS.AVG <- apply(PH.ALL_ERE.ALL_GENO.SEL.STEPS.N,2,mean)
MH.ALL_ERE.IND_GENO.SEL.STEPS.AVG <- apply(MH.ALL_ERE.ALL_GENO.SEL.STEPS.N,2,mean)
#Individual mean for common starting genotypes
TG.INT_ERE.IND_GENO.STEPS.AVG <- apply(TG.INT_ERE.ALL_GENO.STEPS.N,2,mean)
PG.INT_ERE.IND_GENO.STEPS.AVG <- apply(PG.INT_ERE.ALL_GENO.STEPS.N,2,mean)
MG.INT_ERE.IND_GENO.STEPS.AVG <- apply(MG.INT_ERE.ALL_GENO.STEPS.N,2,mean)
TH.INT_ERE.IND_GENO.STEPS.AVG <- apply(TH.INT_ERE.ALL_GENO.STEPS.N,2,mean)
PH.INT_ERE.IND_GENO.STEPS.AVG <- apply(PH.INT_ERE.ALL_GENO.STEPS.N,2,mean)
MH.INT_ERE.IND_GENO.STEPS.AVG <- apply(MH.INT_ERE.ALL_GENO.STEPS.N,2,mean)
TG.INT_ERE.IND_GENO.SEL.STEPS.AVG <- apply(TG.INT_ERE.ALL_GENO.SEL.STEPS.N,2,mean)
PG.INT_ERE.IND_GENO.SEL.STEPS.AVG <- apply(PG.INT_ERE.ALL_GENO.SEL.STEPS.N,2,mean)
MG.INT_ERE.IND_GENO.SEL.STEPS.AVG <- apply(MG.INT_ERE.ALL_GENO.SEL.STEPS.N,2,mean)
TH.INT_ERE.IND_GENO.SEL.STEPS.AVG <- apply(TH.INT_ERE.ALL_GENO.SEL.STEPS.N,2,mean)
PH.INT_ERE.IND_GENO.SEL.STEPS.AVG <- apply(PH.INT_ERE.ALL_GENO.SEL.STEPS.N,2,mean)
MH.INT_ERE.IND_GENO.SEL.STEPS.AVG <- apply(MH.INT_ERE.ALL_GENO.SEL.STEPS.N,2,mean)
#Collect individual means for all starting genotypes
ALL.ALL_ERE.IND_GENO.STEPS.AVG <- list(TG.ALL_ERE.IND_GENO.STEPS.AVG,
PG.ALL_ERE.IND_GENO.STEPS.AVG,
MG.ALL_ERE.IND_GENO.STEPS.AVG,
TH.ALL_ERE.IND_GENO.STEPS.AVG,
PH.ALL_ERE.IND_GENO.STEPS.AVG,
MH.ALL_ERE.IND_GENO.STEPS.AVG)
ALL.ALL_ERE.IND_GENO.SEL.STEPS.AVG <- list(TG.ALL_ERE.IND_GENO.SEL.STEPS.AVG,
PG.ALL_ERE.IND_GENO.SEL.STEPS.AVG,
MG.ALL_ERE.IND_GENO.SEL.STEPS.AVG,
TH.ALL_ERE.IND_GENO.SEL.STEPS.AVG,
PH.ALL_ERE.IND_GENO.SEL.STEPS.AVG,
MH.ALL_ERE.IND_GENO.SEL.STEPS.AVG)
#Collect individual means for common starting genotypes
ALL.INT_ERE.IND_GENO.STEPS.AVG <- list(TG.INT_ERE.IND_GENO.STEPS.AVG,
PG.INT_ERE.IND_GENO.STEPS.AVG,
MG.INT_ERE.IND_GENO.STEPS.AVG,
TH.INT_ERE.IND_GENO.STEPS.AVG,
PH.INT_ERE.IND_GENO.STEPS.AVG,
MH.INT_ERE.IND_GENO.STEPS.AVG)
ALL.INT_ERE.IND_GENO.SEL.STEPS.AVG <- list(TG.INT_ERE.IND_GENO.SEL.STEPS.AVG,
PG.INT_ERE.IND_GENO.SEL.STEPS.AVG,
MG.INT_ERE.IND_GENO.SEL.STEPS.AVG,
TH.INT_ERE.IND_GENO.SEL.STEPS.AVG,
PH.INT_ERE.IND_GENO.SEL.STEPS.AVG,
MH.INT_ERE.IND_GENO.SEL.STEPS.AVG)
##Plot
#par(mfrow=c(3,2))
#par(pty="s")
#par(mar=c(4,4,4,4))
#hist(TG.ALL_ERE.IND_GENO.STEPS.AVG,breaks=seq(0,30,2),xlab="TG Steps Avg",main="All ERE-specific"); abline(v=mean(TG.ALL_ERE.IND_GENO.STEPS.AVG,na.rm=TRUE),col="red")
#hist(TH.ALL_ERE.IND_GENO.STEPS.AVG,breaks=seq(0,20,2),xlab="TH Steps Avg",main="All ERE-specific"); abline(v=mean(TH.ALL_ERE.IND_GENO.STEPS.AVG,na.rm=TRUE),col="red")
#hist(PG.ALL_ERE.IND_GENO.STEPS.AVG,breaks=seq(0,30,2),xlab="PG Steps Avg",main="All ERE-specific"); abline(v=mean(PG.ALL_ERE.IND_GENO.STEPS.AVG,na.rm=TRUE),col="red")
#hist(PH.ALL_ERE.IND_GENO.STEPS.AVG,breaks=seq(0,20,2),xlab="PH Steps Avg",main="All ERE-specific"); abline(v=mean(PH.ALL_ERE.IND_GENO.STEPS.AVG,na.rm=TRUE),col="red")
#hist(MG.ALL_ERE.IND_GENO.STEPS.AVG,breaks=seq(0,30,2),xlab="MG Steps Avg",main="All ERE-specific"); abline(v=mean(MG.ALL_ERE.IND_GENO.STEPS.AVG,na.rm=TRUE),col="red")
#hist(MH.ALL_ERE.IND_GENO.STEPS.AVG,breaks=seq(0,20,2),xlab="MH Steps Avg",main="All ERE-specific"); abline(v=mean(MH.ALL_ERE.IND_GENO.STEPS.AVG,na.rm=TRUE),col="red")
#
#hist(TG.ALL_ERE.IND_GENO.SEL.STEPS.AVG,breaks=seq(0,15,2),xlab="TG SEL.STEPS Avg",main="All ERE-specific"); abline(v=mean(TG.ALL_ERE.IND_GENO.SEL.STEPS.AVG,na.rm=TRUE),col="red")
#hist(TH.ALL_ERE.IND_GENO.SEL.STEPS.AVG,breaks=seq(0,10,2),xlab="TH SEL.STEPS Avg",main="All ERE-specific"); abline(v=mean(TH.ALL_ERE.IND_GENO.SEL.STEPS.AVG,na.rm=TRUE),col="red")
#hist(PG.ALL_ERE.IND_GENO.SEL.STEPS.AVG,breaks=seq(0,15,2),xlab="PG SEL.STEPS Avg",main="All ERE-specific"); abline(v=mean(PG.ALL_ERE.IND_GENO.SEL.STEPS.AVG,na.rm=TRUE),col="red")
#hist(PH.ALL_ERE.IND_GENO.SEL.STEPS.AVG,breaks=seq(0,10,2),xlab="PH SEL.STEPS Avg",main="All ERE-specific"); abline(v=mean(PH.ALL_ERE.IND_GENO.SEL.STEPS.AVG,na.rm=TRUE),col="red")
#hist(MG.ALL_ERE.IND_GENO.SEL.STEPS.AVG,breaks=seq(0,15,2),xlab="MG SEL.STEPS Avg",main="All ERE-specific"); abline(v=mean(MG.ALL_ERE.IND_GENO.SEL.STEPS.AVG,na.rm=TRUE),col="red")
#hist(MH.ALL_ERE.IND_GENO.SEL.STEPS.AVG,breaks=seq(0,10,2),xlab="MH SEL.STEPS Avg",main="All ERE-specific"); abline(v=mean(MH.ALL_ERE.IND_GENO.SEL.STEPS.AVG,na.rm=TRUE),col="red")
#
#hist(TG.INT_ERE.IND_GENO.STEPS.AVG,breaks=seq(0,30,2),xlab="TG Steps Avg",main="Common ERE-specific"); abline(v=mean(TG.INT_ERE.IND_GENO.STEPS.AVG,na.rm=TRUE),col="red")
#hist(TH.INT_ERE.IND_GENO.STEPS.AVG,breaks=seq(0,20,2),xlab="TH Steps Avg",main="Common ERE-specific"); abline(v=mean(TH.INT_ERE.IND_GENO.STEPS.AVG,na.rm=TRUE),col="red")
#hist(PG.INT_ERE.IND_GENO.STEPS.AVG,breaks=seq(0,30,2),xlab="PG Steps Avg",main="Common ERE-specific"); abline(v=mean(PG.INT_ERE.IND_GENO.STEPS.AVG,na.rm=TRUE),col="red")
#hist(PH.INT_ERE.IND_GENO.STEPS.AVG,breaks=seq(0,20,2),xlab="PH Steps Avg",main="Common ERE-specific"); abline(v=mean(PH.INT_ERE.IND_GENO.STEPS.AVG,na.rm=TRUE),col="red")
#hist(MG.INT_ERE.IND_GENO.STEPS.AVG,breaks=seq(0,30,2),xlab="MG Steps Avg",main="Common ERE-specific"); abline(v=mean(MG.INT_ERE.IND_GENO.STEPS.AVG,na.rm=TRUE),col="red")
#hist(MH.INT_ERE.IND_GENO.STEPS.AVG,breaks=seq(0,20,2),xlab="MH Steps Avg",main="Common ERE-specific"); abline(v=mean(MH.INT_ERE.IND_GENO.STEPS.AVG,na.rm=TRUE),col="red")
#
#hist(TG.INT_ERE.IND_GENO.SEL.STEPS.AVG,breaks=seq(0,15,2),xlab="TG SEL.STEPS Avg",main="Common ERE-specific"); abline(v=mean(TG.INT_ERE.IND_GENO.SEL.STEPS.AVG,na.rm=TRUE),col="red")
#hist(TH.INT_ERE.IND_GENO.SEL.STEPS.AVG,breaks=seq(0,10,2),xlab="TH SEL.STEPS Avg",main="Common ERE-specific"); abline(v=mean(TH.INT_ERE.IND_GENO.SEL.STEPS.AVG,na.rm=TRUE),col="red")
#hist(PG.INT_ERE.IND_GENO.SEL.STEPS.AVG,breaks=seq(0,15,2),xlab="PG SEL.STEPS Avg",main="Common ERE-specific"); abline(v=mean(PG.INT_ERE.IND_GENO.SEL.STEPS.AVG,na.rm=TRUE),col="red")
#hist(PH.INT_ERE.IND_GENO.SEL.STEPS.AVG,breaks=seq(0,10,2),xlab="PH SEL.STEPS Avg",main="Common ERE-specific"); abline(v=mean(PH.INT_ERE.IND_GENO.SEL.STEPS.AVG,na.rm=TRUE),col="red")
#hist(MG.INT_ERE.IND_GENO.SEL.STEPS.AVG,breaks=seq(0,15,2),xlab="MG SEL.STEPS Avg",main="Common ERE-specific"); abline(v=mean(MG.INT_ERE.IND_GENO.SEL.STEPS.AVG,na.rm=TRUE),col="red")
#hist(MH.INT_ERE.IND_GENO.SEL.STEPS.AVG,breaks=seq(0,10,2),xlab="MH SEL.STEPS Avg",main="Common ERE-specific"); abline(v=mean(MH.INT_ERE.IND_GENO.SEL.STEPS.AVG,na.rm=TRUE),col="red")
#
#par(mfrow=c(2,2))
#boxplot(ALL.ALL_ERE.IND_GENO.STEPS.AVG, notch=TRUE,names=c("TG","PG","MG","TH","PH","MH"),boxwex=0.5,cex.axis=0.5,pch=19,cex=0.2,ylim=c(0,25),cex.main=0.5,main="Average Path Length for each ERE - All ERE Neg Sel")
#boxplot(ALL.ALL_ERE.IND_GENO.SEL.STEPS.AVG,notch=TRUE,names=c("TG","PG","MG","TH","PH","MH"),boxwex=0.5,cex.axis=0.5,pch=19,cex=0.2,ylim=c(0,30),cex.main=0.5,main="Average Path Length for each ERE - All ERE Pos Sel")
#boxplot(ALL.INT_ERE.IND_GENO.STEPS.AVG, notch=TRUE,names=c("TG","PG","MG","TH","PH","MH"),boxwex=0.5,cex.axis=0.5,pch=19,cex=0.2,ylim=c(0,25),cex.main=0.5,main="Average Path Length for each ERE - Common ERE Neg Sel")
#boxplot(ALL.INT_ERE.IND_GENO.SEL.STEPS.AVG,notch=TRUE,names=c("TG","PG","MG","TH","PH","MH"),boxwex=0.5,cex.axis=0.5,pch=19,cex=0.2,ylim=c(0,15),cex.main=0.5,main="Average Path Length for each ERE - Common ERE Pos Sel")
##Differences in path length between models
#Only uses common ERE-specific genotypes
#Path length differences for individual genotypes for common starting genotypes
TG_PG.INT_ERE.IND_GENO.STEPS.DIFF <- TG.INT_ERE.IND_GENO.STEPS.AVG - PG.INT_ERE.IND_GENO.STEPS.AVG
TG_MG.INT_ERE.IND_GENO.STEPS.DIFF <- TG.INT_ERE.IND_GENO.STEPS.AVG - MG.INT_ERE.IND_GENO.STEPS.AVG
PG_MG.INT_ERE.IND_GENO.STEPS.DIFF <- PG.INT_ERE.IND_GENO.STEPS.AVG - MG.INT_ERE.IND_GENO.STEPS.AVG
TH_PH.INT_ERE.IND_GENO.STEPS.DIFF <- TH.INT_ERE.IND_GENO.STEPS.AVG - PH.INT_ERE.IND_GENO.STEPS.AVG
TH_MH.INT_ERE.IND_GENO.STEPS.DIFF <- TH.INT_ERE.IND_GENO.STEPS.AVG - MH.INT_ERE.IND_GENO.STEPS.AVG
PH_MH.INT_ERE.IND_GENO.STEPS.DIFF <- PH.INT_ERE.IND_GENO.STEPS.AVG - MH.INT_ERE.IND_GENO.STEPS.AVG
TG_PG.INT_ERE.IND_GENO.SEL.STEPS.DIFF <- TG.INT_ERE.IND_GENO.SEL.STEPS.AVG - PG.INT_ERE.IND_GENO.SEL.STEPS.AVG
TG_MG.INT_ERE.IND_GENO.SEL.STEPS.DIFF <- TG.INT_ERE.IND_GENO.SEL.STEPS.AVG - MG.INT_ERE.IND_GENO.SEL.STEPS.AVG
PG_MG.INT_ERE.IND_GENO.SEL.STEPS.DIFF <- PG.INT_ERE.IND_GENO.SEL.STEPS.AVG - MG.INT_ERE.IND_GENO.SEL.STEPS.AVG
TH_PH.INT_ERE.IND_GENO.SEL.STEPS.DIFF <- TH.INT_ERE.IND_GENO.SEL.STEPS.AVG - PH.INT_ERE.IND_GENO.SEL.STEPS.AVG
TH_MH.INT_ERE.IND_GENO.SEL.STEPS.DIFF <- TH.INT_ERE.IND_GENO.SEL.STEPS.AVG - MH.INT_ERE.IND_GENO.SEL.STEPS.AVG
PH_MH.INT_ERE.IND_GENO.SEL.STEPS.DIFF <- PH.INT_ERE.IND_GENO.SEL.STEPS.AVG - MH.INT_ERE.IND_GENO.SEL.STEPS.AVG
#Collect path length differences for individual genotypes for common starting genotypes
ALL.INT_ERE.IND_GENO.STEPS.DIFF <- list(TG_PG.INT_ERE.IND_GENO.STEPS.DIFF,
TG_MG.INT_ERE.IND_GENO.STEPS.DIFF,
PG_MG.INT_ERE.IND_GENO.STEPS.DIFF,
TH_PH.INT_ERE.IND_GENO.STEPS.DIFF,
TH_MH.INT_ERE.IND_GENO.STEPS.DIFF,
PH_MH.INT_ERE.IND_GENO.STEPS.DIFF)
ALL.INT_ERE.IND_GENO.SEL.STEPS.DIFF <- list(TG_PG.INT_ERE.IND_GENO.SEL.STEPS.DIFF,
TG_MG.INT_ERE.IND_GENO.SEL.STEPS.DIFF,
PG_MG.INT_ERE.IND_GENO.SEL.STEPS.DIFF,
TH_PH.INT_ERE.IND_GENO.SEL.STEPS.DIFF,
TH_MH.INT_ERE.IND_GENO.SEL.STEPS.DIFF,
PH_MH.INT_ERE.IND_GENO.SEL.STEPS.DIFF)
##Plot
#par(mfrow=c(3,2))
#hist(TG_PG.INT_ERE.IND_GENO.STEPS.DIFF,seq(-7,7,1),xlab="TG - PG Avg Dist.",main="Common ERE"); abline(v=mean(TG_PG.INT_ERE.IND_GENO.STEPS.DIFF),col="red")
#hist(TH_PH.INT_ERE.IND_GENO.STEPS.DIFF,seq(-7,7,1),xlab="TH - PH Avg Dist.",main="Common ERE"); abline(v=mean(TH_PH.INT_ERE.IND_GENO.STEPS.DIFF),col="red")
#hist(PG_MG.INT_ERE.IND_GENO.STEPS.DIFF,seq(-7,7,1),xlab="PG - MG Avg Dist.",main="Common ERE"); abline(v=mean(PG_MG.INT_ERE.IND_GENO.STEPS.DIFF),col="red")
#hist(PH_MH.INT_ERE.IND_GENO.STEPS.DIFF,seq(-7,7,1),xlab="PH - MH Avg Dist.",main="Common ERE"); abline(v=mean(PH_MH.INT_ERE.IND_GENO.STEPS.DIFF),col="red")
#hist(TG_MG.INT_ERE.IND_GENO.STEPS.DIFF,seq(-7,7,1),xlab="TH - MH Avg Dist.",main="Common ERE"); abline(v=mean(TG_MG.INT_ERE.IND_GENO.STEPS.DIFF),col="red")
#hist(TH_MH.INT_ERE.IND_GENO.STEPS.DIFF,seq(-7,7,1),xlab="TG - MG Avg Dist.",main="Common ERE"); abline(v=mean(TH_MH.INT_ERE.IND_GENO.STEPS.DIFF),col="red")
#
#hist(TG_PG.INT_ERE.IND_GENO.SEL.STEPS.DIFF,seq(-8,8,1),xlab="TG - PG Avg Dist.",main="Common ERE"); abline(v=mean(TG_PG.INT_ERE.IND_GENO.SEL.STEPS.DIFF),col="red")
#hist(TH_PH.INT_ERE.IND_GENO.SEL.STEPS.DIFF,seq(-8,8,1),xlab="TH - PH Avg Dist.",main="Common ERE"); abline(v=mean(TH_PH.INT_ERE.IND_GENO.SEL.STEPS.DIFF),col="red")
#hist(PG_MG.INT_ERE.IND_GENO.SEL.STEPS.DIFF,seq(-8,8,1),xlab="PG - MG Avg Dist.",main="Common ERE"); abline(v=mean(PG_MG.INT_ERE.IND_GENO.SEL.STEPS.DIFF),col="red")
#hist(PH_MH.INT_ERE.IND_GENO.SEL.STEPS.DIFF,seq(-8,8,1),xlab="PH - MH Avg Dist.",main="Common ERE"); abline(v=mean(PH_MH.INT_ERE.IND_GENO.SEL.STEPS.DIFF),col="red")
#hist(TG_MG.INT_ERE.IND_GENO.SEL.STEPS.DIFF,seq(-8,8,1),xlab="TH - MH Avg Dist.",main="Common ERE"); abline(v=mean(TG_MG.INT_ERE.IND_GENO.SEL.STEPS.DIFF),col="red")
#hist(TH_MH.INT_ERE.IND_GENO.SEL.STEPS.DIFF,seq(-8,8,1),xlab="TG - MG Avg Dist.",main="Common ERE"); abline(v=mean(TH_MH.INT_ERE.IND_GENO.SEL.STEPS.DIFF),col="red")
#
#par(mfrow=c(2,1))
#boxplot(ALL.INT_ERE.IND_GENO.STEPS.DIFF,notch=TRUE,names=c("TG-PG","TG-MG","PG-MG","TH-PH","TH-MH","PH-MH"),boxwex=0.5,pch=19,cex=0.3,ylim=c(-8,8),cex.axis=0.5,cex.main=0.5,las=2,main="Average Path Length Difference for each Common ERE genotype Neg Sel")
#abline(h=0)
#boxplot(ALL.INT_ERE.IND_GENO.SEL.STEPS.DIFF,notch=TRUE,names=c("TG-PG","TG-MG","PG-MG","TH-PH","TH-MH","PH-MH"),boxwex=0.5,pch=19,cex=0.3,ylim=c(-8,8),cex.axis=0.5,cex.main=0.5,las=2,main="Average Path Length Difference for each Common ERE genotype Pos Sel")
#abline(h=0)
#
#par(mfrow=c(2,1))
#plot(jitter(c(rep(1:3,each=97),rep(4:6,each=59))),unlist(ALL.INT_ERE.IND_GENO.STEPS.DIFF),pch=19,cex=0.3,cex.axis=0.5,las=2,xaxt="n",xlab="",ylab="",cex.main=0.5,main="Average Path Length Difference for each Common ERE genotype Neg Sel")
#axis(1,1:6,c("TG-PG","TG-MG","PG-MG","TH-PH","TH-MH","PH-MH"),cex.axis=0.5,las=2)
#abline(h=0)
#plot(jitter(c(rep(1:3,each=97),rep(4:6,each=59))),unlist(ALL.INT_ERE.IND_GENO.SEL.STEPS.DIFF),pch=19,cex=0.3,cex.axis=0.5,las=2,xaxt="n",xlab="",ylab="",cex.main=0.5,main="Average Path Length Difference for each Common ERE genotype Pos Sel")
#axis(1,1:6,c("TG-PG","TG-MG","PG-MG","TH-PH","TH-MH","PH-MH"),cex.axis=0.5,las=2)
#abline(h=0)
##Permutation test for difference in path length for each starting genotype
N.GENOTYPES <- ncol(TG.INT_ERE.ALL_GENO.STEPS.N)
N.PERMUTATIONS <- 10000
N.SIMULATIONS <- 1000
#TG_PG.INT_ERE.IND_GENO.STEPS.p <- sapply(1:N.GENOTYPES,FUN = function(x) {
# OUT <- sapply(1:N.PERMUTATIONS,FUN = function(y) {
# SAMPLE <- sample(1:N.SIMULATIONS,N.SIMULATIONS/2,replace = FALSE)
# S1 <- mean(c(TG.INT_ERE.ALL_GENO.STEPS.N[ SAMPLE,x],PG.INT_ERE.ALL_GENO.STEPS.N[-SAMPLE,x]))
# S2 <- mean(c(TG.INT_ERE.ALL_GENO.STEPS.N[-SAMPLE,x],PG.INT_ERE.ALL_GENO.STEPS.N[ SAMPLE,x]))
# return(S1-S2)
# })
# OBS <- mean(TG.INT_ERE.ALL_GENO.STEPS.N[,x]) - mean(PG.INT_ERE.ALL_GENO.STEPS.N[,x])
# return(sum(OBS < OUT)/length(OUT))
#}); names(TG_PG.INT_ERE.IND_GENO.STEPS.p) <- names(TG_PG.INT_ERE.IND_GENO.STEPS.DIFF)
#
#TG_MG.INT_ERE.IND_GENO.STEPS.p <- sapply(1:N.GENOTYPES,FUN = function(x) {
# OUT <- sapply(1:N.PERMUTATIONS,FUN = function(y) {
# SAMPLE <- sample(1:N.SIMULATIONS,N.SIMULATIONS/2,replace = FALSE)
# S1 <- mean(c(TG.INT_ERE.ALL_GENO.STEPS.N[ SAMPLE,x],MG.INT_ERE.ALL_GENO.STEPS.N[-SAMPLE,x]))
# S2 <- mean(c(TG.INT_ERE.ALL_GENO.STEPS.N[-SAMPLE,x],MG.INT_ERE.ALL_GENO.STEPS.N[ SAMPLE,x]))
# return(S1-S2)
# })
# OBS <- mean(TG.INT_ERE.ALL_GENO.STEPS.N[,x]) - mean(MG.INT_ERE.ALL_GENO.STEPS.N[,x])
# return(sum(OBS < OUT)/length(OUT))
#}); names(TG_MG.INT_ERE.IND_GENO.STEPS.p) <- names(TG_MG.INT_ERE.IND_GENO.STEPS.DIFF)
#
#PG_MG.INT_ERE.IND_GENO.STEPS.p <- sapply(1:N.GENOTYPES,FUN = function(x) {
# OUT <- sapply(1:N.PERMUTATIONS,FUN = function(y) {
# SAMPLE <- sample(1:N.SIMULATIONS,N.SIMULATIONS/2,replace = FALSE)
# S1 <- mean(c(PG.INT_ERE.ALL_GENO.STEPS.N[ SAMPLE,x],MG.INT_ERE.ALL_GENO.STEPS.N[-SAMPLE,x]))
# S2 <- mean(c(PG.INT_ERE.ALL_GENO.STEPS.N[-SAMPLE,x],MG.INT_ERE.ALL_GENO.STEPS.N[ SAMPLE,x]))
# return(S1-S2)
# })
# OBS <- mean(PG.INT_ERE.ALL_GENO.STEPS.N[,x]) - mean(MG.INT_ERE.ALL_GENO.STEPS.N[,x])
# return(sum(OBS < OUT)/length(OUT))
#}); names(PG_MG.INT_ERE.IND_GENO.STEPS.p) <- names(PG_MG.INT_ERE.IND_GENO.STEPS.DIFF)
#
#N.GENOTYPES <- ncol(TH.INT_ERE.ALL_GENO.STEPS.N)
#
#TH_PH.INT_ERE.IND_GENO.STEPS.p <- sapply(1:N.GENOTYPES,FUN = function(x) {
# OUT <- sapply(1:N.PERMUTATIONS,FUN = function(y) {
# SAMPLE <- sample(1:N.SIMULATIONS,N.SIMULATIONS/2,replace = FALSE)
# S1 <- mean(c(TH.INT_ERE.ALL_GENO.STEPS.N[ SAMPLE,x],PH.INT_ERE.ALL_GENO.STEPS.N[-SAMPLE,x]))
# S2 <- mean(c(TH.INT_ERE.ALL_GENO.STEPS.N[-SAMPLE,x],PH.INT_ERE.ALL_GENO.STEPS.N[ SAMPLE,x]))
# return(S1-S2)
# })
# OBS <- mean(TH.INT_ERE.ALL_GENO.STEPS.N[,x]) - mean(PH.INT_ERE.ALL_GENO.STEPS.N[,x])
# return(sum(OBS < OUT)/length(OUT))
#}); names(TH_PH.INT_ERE.IND_GENO.STEPS.p) <- names(TH_PH.INT_ERE.IND_GENO.STEPS.DIFF)
#
#TH_MH.INT_ERE.IND_GENO.STEPS.p <- sapply(1:N.GENOTYPES,FUN = function(x) {
# OUT <- sapply(1:N.PERMUTATIONS,FUN = function(y) {
# SAMPLE <- sample(1:N.SIMULATIONS,N.SIMULATIONS/2,replace = FALSE)
# S1 <- mean(c(TH.INT_ERE.ALL_GENO.STEPS.N[ SAMPLE,x],MH.INT_ERE.ALL_GENO.STEPS.N[-SAMPLE,x]))
# S2 <- mean(c(TH.INT_ERE.ALL_GENO.STEPS.N[-SAMPLE,x],MH.INT_ERE.ALL_GENO.STEPS.N[ SAMPLE,x]))