=========msBayes Acc/Rej script
tail -1 ~/BirdCOI/obsSS_Pulse1_26.txt > ~/BirdCOI/BirdCOIObsTAIL_Pulse1_26
tail -1 ~/BirdCOI/obsSS_Pulse2_23.txt > ~/BirdCOI/BirdCOIObsTAIL_Pulse2_23
tail -1 ~/BirdCOI/obsSS_Pulse3_22.txt > ~/BirdCOI/BirdCOIObsTAIL_Pulse3_22


##how to calculate the columns: 6+n*2:5+n*5,6+n*6:5+n*7
###58:135, 162:187<--26
###52:120, 144:166 <--23
###50:115, 138:159 <--22

cd ~/msbayes/trunk/src/


./msReject ~/BirdCOI/BirdCOIObsTAIL_Pulse1_26 ~/BirdCOI/bigprior_Psi6_Pulse1_13_II 0.01 58  59  60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79  80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 > ~/BirdCOI/BirdCOIPosteriorSortHEADLESS_Pulse1_26
./msReject ~/BirdCOI/BirdCOIObsTAIL_Pulse2_23 ~/BirdCOI/bigprior_Psi6_Pulse2_12_II 0.01  52  53  54  55  56  57  58  59  60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79  80  81  82  83  84  85  86  87  88  89 90  91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 > ~/BirdCOI/BirdCOIPosteriorSortHEADLESS_Pulse2_23
./msReject ~/BirdCOI/BirdCOIObsTAIL_Pulse3_22 ~/BirdCOI/bigprior_Psi6_Pulse3_12_II 0.01 50 51 52  53  54  55  56  57  58  59  60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79  80  81  82  83  84  85  86  87  88  89 90  91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 > ~/BirdCOI/BirdCOIPosteriorSortHEADLESS_Pulse3_22

cd ~/BirdCOI


=========R script for pulse1_26

library(abc)
source("loc2plot_d.r")

cols<-c(58:135, 162:187)  ### columns to compute. see line 8 - 9 for pulse 2 and 3.
pairs<-26
MZ_OBS<- scan(("BirdCOIObsTAIL_Pulse1_26"),nlines=1)
OBS<-matrix(MZ_OBS,ncol=length(MZ_OBS),byrow=T)
Prior<-c(scan("BirdCOIPosteriorSortHEADLESS_Pulse1_26",nlines=10000))
POSTVEC<-matrix(Prior,ncol=length(MZ_OBS)+1,byrow=T)  


Z1noLL6 <- try(abc(OBS[1,cols], POSTVEC[,2], POSTVEC[,cols], tol=0.1,method="neuralnet", kernel="epanechnikov", numnet = 15, sizenet = 3,lambda = c(0.0001,0.001,0.01), trace = TRUE,maxit = 500),T)
TDnoLLRmode6 <- loc1stats(Z1noLL6$adj.values, prob=0.95)[1]
TDnoLLRmode6

Z1noLL8 <- try(abc(OBS[1,cols], POSTVEC[,5], POSTVEC[,cols], tol=0.1,method="neuralnet", kernel="epanechnikov", numnet = 15, sizenet = 3,lambda = c(0.0001,0.001,0.01), trace = TRUE,maxit = 500),T)
TDnoLLRmode8 <- loc1stats(Z1noLL8$adj.values, prob=0.95)[1]
TDnoLLRmode8

Z1noLL9 <- try(abc(OBS[1,cols], POSTVEC[,5], POSTVEC[,cols], tol=0.1,method="loclinear"),T)
TDnoLLRmode9 <- loc1stats(Z1noLL9$adj.values, prob=0.95)[1]
TDnoLLRmode9

######BF######
postm1<-length(which(Z1noLL6$adj.values<1.5))/1000
nnp<-(postm1/(1-postm1))*(pairs-1)
postm2<-length(which(Z1noLL8$adj.values<0.01))/1000
nno<-(postm2/(1-postm2))*(pairs-1)

postm3<-length(which(Z1noLL9$adj.values<0.01))/1000
llo<-(postm3/(1-postm3))*(pairs-1)
nnp
nno
llo

sort(Z1noLL6$adj.values)[1]
sort(Z1noLL6$adj.values)[1000]
sort(Z1noLL8$adj.values)[1]
sort(Z1noLL8$adj.values)[1000]
sort(Z1noLL9$adj.values)[1]
sort(Z1noLL9$adj.values)[1000]

pdf('BirdCOI_REAL_II_psi3_Pulse1_26_abc_Neuralnet_tol0.1.pdf')
hist(Z1noLL6$adj.values,xlim=c(0,16),main="Psi Neuralnet")
hist(Z1noLL8$adj.values,xlim=c(0,0.2),main="Omega Neuralnet")
hist(Z1noLL9$adj.values,xlim=c(-0.05,0.15),main="Omega Loclinear")
dev.off()