From 75164f9d18e9244811b8f3759c5fb7646a92a2c7 Mon Sep 17 00:00:00 2001 From: Jack Chaillet Date: Mon, 15 Nov 2021 13:55:01 -0500 Subject: [PATCH] updated 11/15/2021 --- ODESRecombination-copy.R | 95 ++++++++++++++++++++++++---------------- 1 file changed, 57 insertions(+), 38 deletions(-) diff --git a/ODESRecombination-copy.R b/ODESRecombination-copy.R index d6d8da9..c6121cf 100644 --- a/ODESRecombination-copy.R +++ b/ODESRecombination-copy.R @@ -13,7 +13,7 @@ SEAI<-function(t,y,p){ SD = y[8] AU = y[9] AD = y[10] - gamma = y[11] + x = y[11] with(as.list(p),{ #gammainit = vector() @@ -154,18 +154,27 @@ SEAI<-function(t,y,p){ I = 1-exp(-m)#(1-((PSU+PSD+PRU+PRD)/(N*K))) 1-exp(-m) ratr = ((PRU+PRD)*wr)/(PSU+PSD+((PRU+PRD)*wr)) ratr1 = (PRU+PRD)/(PSU+PSD+PRU+PRD) - rats = (PSU+PSD)/(PSU+PSD+PRU+PRD) - P1 = ratr1 + rats = (PSU+PSD)/(PSU+PSD+((PRU+PRD)*wr)) + #P1 = ratr1 #ps = 0.34 #gammainit = (ratr1*1)+(rats*ps) #gamma = (ratr1*1)+(rats*((gammainit - ratr1)/rats)) - A = ((1+gamma)/2)^2 - cr = (PSU+PSD)/N - B = (1-(1/cr))*(gamma^2) - sigma1 = (ratr1*A)+(rats*B) - sigma2 = (rats*(1-A))+(ratr1*(1-B)) + #A = ((1+gamma)/2)^2 #prob that recombinant is resistant given RxS recombination + #lambda = (PSU+PSD)/N + #cr = 1-((lambda*exp(-lambda))/(1-exp(-m)))#-exp(-lambda))#/(1-exp(-m))) + #B = (1-(1/cr))*(gamma^2) #prob that recombinant is resistant given SxS recombination + #rats1 = (PSU+PSD-1)/(PSU+PSD+((PRU+PRD)*wr)) + #B = cr*(gamma^2) + #sigma1 = (ratr*A)+(rats*B) + #sigma2 = (rats*(1-A)) eps = (PSD+PSU+((PRD+PRU)*(wr)))/(PSD+PSU+PRD+PRU) + r = 0.5*(1-(((m*exp(-m)))/(1-exp(-m)))) + upsilon = (1/K)*(K-((PSU+PSD+PRU+PRD)/N)) + delR = b*upsilon*(PRU+PRD)*wr#*I + delS = b*upsilon*(PSU+PSD)*ws#*I + delP = delS +delR + n=2 #TauRN1=((P1*((1-d1)+(d1*TauRD1)))-(d1*TauRD1))/(1-d1) #calculate TauRN1 from equation A4 #FUNC2<-function(smallp,E,S,Tau1,x1,f1,c1,h1,freqc1,freqh1){ # for(k in 1:cmax){ @@ -190,7 +199,7 @@ SEAI<-function(t,y,p){ #gammainit3 = 0.471481 #gamma2final = gamma2[numsteps] - #PSU to PRU: sigma1*b*(PSU/N)*ws*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) + #PSU to PRU: (sigma1*b*(PSU/N)*ws*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) #PSU to PRD: (sigma1*b*(PSU/N)*ws*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) #PSD to PRU: (sigma1*b*(PSD/N)*ws*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) #PSD to PRD: (sigma1*b*(PSD/N)*ws*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) @@ -202,10 +211,17 @@ SEAI<-function(t,y,p){ #PSU to PSU: ((1-sigma1)*b*(PSU/N)*ws*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) #PRD to PRD: ((1-sigma2)*b*(PRD/N)*wr*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) #PRU to PRU: ((1-sigma2)*b*(PRU/N)*wr*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - dPSU.dt = -((1-sigma1)*b*(PSU/N)*ws*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma2*b*(PRD/N)*wr*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma2*b*(PRU/N)*wr*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (b*(PSU/N)*ws*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (b*(PSD/N)*ws*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (muSU)*(PSU)#-(del*att*(1/N)*(NU+SU+AU)*PSU) - dPSD.dt = -((1-sigma1)*b*(PSD/N)*ws*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma2*b*(PRD/N)*wr*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma2*b*(PRU/N)*wr*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))- (b*(PSU/N)*ws*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (b*(PSD/N)*ws*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (muSD)*(PSD)#-(del*att*(1/N)*(ND+SD+AD)*PSD) - dPRU.dt = -((1-sigma2)*b*(PRU/N)*wr*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma1*b*(PSD/N)*ws*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma1*b*(PSU/N)*ws*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))- (b*(PRU/N)*wr*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (b*(PRD/N)*wr*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (muRU)*(PRU)#-(del*att*(1/N)*(NU+SU+AU)*PRU) - dPRD.dt = -((1-sigma2)*b*(PRD/N)*wr*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma1*b*(PSD/N)*ws*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma1*b*(PSU/N)*ws*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))- (b*(PRU/N)*wr*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (b*(PRD/N)*wr*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (muRD)*(PRD)#-(del*att*(1/N)*(ND+SD+AD)*PRD) + #dPSU.dt = -((1-sigma1)*b*((PSU+PSD)/N)*ws*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma2*b*(PRD/N)*wr*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma2*b*(PRU/N)*wr*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (b*(PSU/N)*ws*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (b*(PSD/N)*ws*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (muSU)*(PSU)#-(del*att*(1/N)*(NU+SU+AU)*PSU) + #dPSD.dt = -((1-sigma1)*b*((PSU+PSD)/N)*ws*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma2*b*(PRD/N)*wr*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma2*b*(PRU/N)*wr*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))- (b*(PSU/N)*ws*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (b*(PSD/N)*ws*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (muSD)*(PSD)#-(del*att*(1/N)*(ND+SD+AD)*PSD) + #dPRU.dt = -((1-sigma2)*b*((PRU+PRD)/N)*wr*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma1*b*(PSD/N)*ws*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma1*b*(PSU/N)*ws*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))- (b*(PRU/N)*wr*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (b*(PRD/N)*wr*(NU+SU+AU)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (muRU)*(PRU)#-(del*att*(1/N)*(NU+SU+AU)*PRU) + #dPRD.dt = -((1-sigma2)*b*((PRU+PRD)/N)*wr*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma1*b*(PSD/N)*ws*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))-(sigma1*b*(PSU/N)*ws*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K))- (b*(PRU/N)*wr*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (b*(PRD/N)*wr*(ND+SD+AD)*(1/K)*(((PSU+PSD+PRU+PRD)/N)-K)) - (muRD)*(PRD)#-(del*att*(1/N)*(ND+SD+AD)*PRD) + dPSU.dt = ((NU+SU+AU)/N)*((1-r)*delS+r*delP*((1-x)^n))-muSU*PSU + dPSD.dt = ((ND+SD+AD)/N)*((1-r)*delS+r*delP*((1-x)^n))-muSD*PSD + dPRU.dt = ((NU+SU+AU)/N)*((1-r)*delR+r*delP*(x^n))-muRU*PRU + dPRD.dt = ((ND+SD+AD)/N)*((1-r)*delR+r*delP*(x^n))-muRD*PRD + e = ((NU+SU+AU)/N)*((1-r)*delS+r*delP*((1-x)^n))-muSU*PSU+((ND+SD+AD)/N)*((1-r)*delS+r*delP*((1-x)^n))-muSD*PSD+((NU+SU+AU)/N)*((1-r)*delR+r*delP*(x^n))-muRU*PRU+((ND+SD+AD)/N)*((1-r)*delR+r*delP*(x^n))-muRD*PRD + er = ((NU+SU+AU)/N)*((1-r)*delR+r*delP*(x^n))-muRU*PRU+((ND+SD+AD)/N)*((1-r)*delR+r*delP*(x^n))-muRD*PRD + es = ((NU+SU+AU)/N)*((1-r)*delS+r*delP*((1-x)^n))-muSU*PSU+((ND+SD+AD)/N)*((1-r)*delS+r*delP*((1-x)^n))-muSD*PSD #dNU.dt = (del*(AU+AD))+(ND/Tau)-(b*I*eps*NU*(d+rho1))-(muNU*NU) - (del*att*NU) dNU.dt = del+(ND/Tau)-(b*I*eps*NU*(d1+rho1))-(muNU*NU*I*b*eps) - (del*att*NU) dND.dt = (b*I*eps*NU*d1)-(ND/Tau)-(ratr*b*I*eps*ND*rho2)-(muND*ratr*ND*I*b*eps) - (del*att*ND) @@ -215,12 +231,15 @@ SEAI<-function(t,y,p){ dAU.dt = (AD/Tau)+(b*I*eps*SU*rho3)-(b*I*eps*omega1*AU*d3) - (del*att*AU) #dAD.dt = rat*(AU+AD)*(1-((AU+AD)/L))+(b*I*eps*SD*rho4)+(b*I*eps*omega1*AU*d)-(AD/Tau) - (del*att*AD) dAD.dt = (ratr*b*I*eps*SD*rho4)+(b*I*eps*omega1*AU*d3)-(AD/Tau) - (del*att*AD) - dgamma.dt = (1/(PSU+PSD+PRU+PRD))*((1-gamma)/(rats))*(dPRD.dt+dPRU.dt) - return(list(c(dPSU.dt,dPSD.dt,dPRU.dt,dPRD.dt,dNU.dt,dND.dt,dSU.dt,dSD.dt,dAU.dt,dAD.dt,dgamma.dt))) + #dgamma.dt = (1/(PSU+PSD+((1-S)*(PRU+PRD))))*((1/rats)-(gamma))*(dPRD.dt+dPRU.dt) + #dgamma.dt = ratr + rats*((gamma)-ratr)-((1/(PSU+PSD+((1-S)*(PRU+PRD))))*(dPRD.dt+dPRU.dt)*((gamma)-ratr)) + #dgamma.dt = -(dPRD.dt+dPRU.dt)/(dPSD.dt+dPSU.dt) + dx.dt = (1/((PSU+PSD+PRU+PRD)+(e)))*((er)-(x*(e))+((es)*((x*(PSD+PSD+PRU+PRD)-(PRU+PRD))/(PSU+PSD)))) + return(list(c(dPSU.dt,dPSD.dt,dPRU.dt,dPRD.dt,dNU.dt,dND.dt,dSU.dt,dSD.dt,dAU.dt,dAD.dt,dx.dt))) }) } -b = 1 +b = 10^(-1.5) nstrains = 150 @@ -239,7 +258,7 @@ omega2 = omega1 #prob of appearance of new antigen only in resistant strains L = 10000 ws = 1 -wr = 1-0.15 +wr = 1-0.6 S = 1-wr #muSU = 1 muSU=1/250#0.001 @@ -250,7 +269,7 @@ muRD = muSU#0.001 #muRU = 1 muRU = muSU#0.001 Tau = 20#/365 -d1 = 0.87*0.3 +d1 = 0.87#*0.3 d2 = d1#/6 d3 = d1#/10 #m = 3 @@ -258,7 +277,7 @@ K=10 p2 = list(b=b,ws=ws,wr=wr,muSU=muSU,muSD=muSD,muRD=muRD,muRU=muRU,Tau=Tau,d1=d1,d2=d2,d3=d3,del=del,muND=muND,muNU=muNU,rho1=rho1,rho2=rho2,rho3=rho3,rho4=rho4,omega1=omega1,omega2=omega2,L=L,att=att, K=K) tmax=40000 -t2 = seq(from=0,to=tmax,by=10) +t2 = seq(from=0,to=tmax,by=1) P1 = 0.5 TauRN1=((P1*((1-d1)+(d1*TauRD1)))-(d1*TauRD1))/(1-d1) #calculate TauRN1 from equation A4 @@ -285,7 +304,7 @@ gammainit2=(Recomb$root) print(gammainit2) -N0 = c(500,500,500,500,333,333,333,333,333,333,0.34) +N0 = c(10000,10000,1,1,333,333,333,333,333,333,0.34) out2 = ode(y=N0,times=t2,func=SEAI,parms=p2) P<-rowSums(out2[,2:5]) N<-rowSums(out2[,6:11]) @@ -297,11 +316,11 @@ eps<-(PS+wr*PR)/N plot(out2[,1],I,type="l", xlab="Time", ylab="I") plot(out2[,1],I*eps,type="l", xlab="Time", ylab="I*eps") -plot(out2[,1],(out2[,2]),type="l", xlab="Time", ylab="Population", main = paste("b=",b,", d=",d1)) +plot(out2[,1],(out2[,2]),ylim=c(0,max(out2[,2])),type="l", xlab="Time", ylab="Population", main = paste("b=",b,", d=",d1)) lines(out2[,1],(out2[,3]),col="RED") legend("bottomright",legend=c("PSU","PSD"),bty="n",lwd = c(2,1),col=c("BLACK","RED")) -plot(out2[,1],(out2[,4]),type="l", xlab = "Time", ylab="Population", main = "b=0.2239*365,d=0.30") +plot(out2[,1],(out2[,4]),type="l", ylim=c(0,max(out2[,4])),xlab = "Time", ylab="Population", main = "b=0.2239*365,d=0.30") lines(out2[,1],(out2[,5]),col="RED") legend("bottomright",legend=c("PRU","PRD"),bty="n",lwd = c(2,1),col=c("BLACK","RED")) @@ -322,21 +341,21 @@ legend("bottomright",legend=c("SU","SD"),bty="n",lwd=c(2,1),col=c("BLACK","RED") plot(out2[,1],out2[,10],type="l",xlab="Time",ylab="Asymptomatic Population (A)", main="b=0.2239*365,d=0.30") lines(out2[,1],out2[,11],col="RED") - +plot(out2[,1],out2[,12],type="l") I1 = (1/(K*(out3[,6]+out3[,7]+out3[,8]+out3[,9]+out3[,10]+out3[,11])))*(-(((out3[,3]+out3[,2]+out3[,4] + out3[,5])/(out3[,6]+out3[,7]+out3[,8]+out3[,9]+out3[,10]+out3[,11]))-K)) plot(out2[,1],I1) -#out3eq = vector(mode = "numeric", length = 8) -out3eq2 = vector(mode = "numeric", length = 17) +#out3eq = vector(mode = "numeric", length = 17) +out3eq2 = vector(mode = "numeric", length = 11) #out3eq3 = vector(mode = "numeric", length = 8) #out3eq4 = vector(mode = "numeric", length = 8) -#out3eq5 = vector(mode="numeric", length=8) +#out3eq5 = vector(mode="numeric", length=23) #out3eq6 = vector(mode="numeric", length=8) #out4 = vector(mode="numeric", length=22) #bvalues = c(0,0.0001,0.0005,0.05,0.10,0.15,0.20,0.25,0.27,0.30,0.32,0.35,0.37,0.40,0.45,0.50,0.55,0.60,0.70,0.80,0.90,1) -bvalues = c(-2, -1.5, -1,-0.9,-0.8,-0.6,-0.4,-0.2,-0.1,0,0.2,0.4,0.6,0.8,1,1.5,2)#,2,3,4) +bvalues = c(-2,-1.5, -1,-0.9,-0.8,-0.6,-0.4,-0.2,-0.1,0,0.2)#,0.4)#,0.6,0.8,1)#,1.5,2)#,2,3,4) #bvalues = c(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24) #bvalues = seq(from=-2.5,to=0.5,by=1) wrvalues = c(0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1) @@ -346,7 +365,7 @@ muSUvalues = c(0,0.10,0.15,0.20,0.25,0.27,0.30,0.32,0.35,0.37,0.40,0.45,0.50,0.5 delvalues = c(10,20,40,50,60,70,90,100,150,200,250,300,350,400,450,500,550,600,700,800,900,1000) rho3values = c(0.0005,0.002,0.004,0.005,0.007,0.008,0.01,0.02,0.04,0.05,0.06,0.07,0.08,0.09,0.10,0.11) omegavalues = c(0.01,0.012,0.014,0.016,0.018,0.02,0.022,0.024,0.026,0.028,0.030,0.032,0.034,0.036,0.038,0.040)#,0.042,0.044,0.046,0.048,0.050,0.052) -for (i in 1:17){ +for (i in 1:11){ #del=delvalues[i] b=10^(bvalues[i]) #wr=wrvalues[i] @@ -357,7 +376,7 @@ for (i in 1:17){ p2 = list(b=b,ws=ws,muSU=muSU,muSD=muSD,muRD=muRD,muRU=muRU,Tau=Tau,d1=d1,d2=d2,d3=d3,del=del,muND=muND,muNU=muNU,rho1=rho1,rho2=rho2,rho3=rho3,rho4=rho4,omega1=omega1,omega2=omega2,L=L,att=att) out3 = ode(y=N0,times=t2,func=SEAI,parms=p2) #out3eq[i] = out3[3999,3]+out3[3999,2] +out3[3999,4] + out3[3999,5] - out3eq2[i] = (out3[3999,4]+out3[3999,5])/(out3[3999,2] + out3[3999,3] + out3[3999,4] + out3[3999,5]) + out3eq2[i] = (out3[39999,4]+out3[39999,5])/(out3[39999,2] + out3[39999,3] + out3[39999,4] + out3[39999,5]) #out3eq3[i] = (out3[3999,6]+out3[3999,7])/(out3[3999,6]+out3[3999,7]+out3[3999,8]+out3[3999,9]+out3[3999,10]+out3[3999,11]) #out3eq4[i] = (out3[3999,8]+out3[3999,9])/(out3[3999,6]+out3[3999,7]+out3[3999,8]+out3[3999,9]+out3[3999,10]+out3[3999,11]) #out3eq5[i] =(out3[3999,10]+out3[3999,11])/(out3[3999,6]+out3[3999,7]+out3[3999,8]+out3[3999,9]+out3[3999,10]+out3[3999,11]) @@ -372,15 +391,15 @@ plot(bvalues,out3eq2) #print(out3eq2) print(out3eq2) -mat6 = matrix(data=0,nrow=11,ncol=17) -#mat7 = matrix(data=0,nrow=22,ncol=22) -#mat8 = matrix(data=0,nrow=22,ncol=22) -#mat9 = matrix(data=0,nrow=22,ncol=22) -#mat10 = matrix(data=0,nrow=22,ncol=22) -#mat11 = matrix(data=0,nrow=22,ncol=22) -#mat12 = matrix(data=0,nrow=22,ncol=22) +mat6 = matrix(data=0,nrow=11,ncol=11) +#mat7 = matrix(data=0,nrow=11,ncol=17) +#mat8 = matrix(data=0,nrow=11,ncol=11) +#mat9 = matrix(data=0,nrow=11,ncol=18) +#mat10 = matrix(data=0,nrow=11,ncol=18) +#mat11 = matrix(data=0,nrow=11,ncol=18) +#mat12 = matrix(data=0,nrow=11,ncol=18) for (i in 1:11){ - for (j in 1:17){ + for (j in 1:11){ #d = dvalues[i] # A = Avalues[j] #rho3=rho3values[i] @@ -394,7 +413,7 @@ for (i in 1:11){ # mat[i,j] = (out5[3999,4] + out5[3999,5])/PTotal #mat2[i,j] = (out5[3999,2] + out5[3999,3] + out5[3999,4] + out5[3999,5])/6000 #mat3[i,j] = out5[3999,6]/out5[3999,7] - mat6[i,j] = (out5[3999,4]+out5[3999,5])/(out5[3999,2] + out5[3999,3] + out5[3999,4] + out5[3999,5]) + mat6[i,j] = (out5[39999,4]+out5[39999,5])/(out5[39999,2] + out5[39999,3] + out5[39999,4] + out5[39999,5]) #mat7[i,j] = out5[3999,2]+out5[3999,3]+out5[3999,4]+out5[3999,5] #mat8[i,j]=(out5[3999,10]+out5[3999,11])/(out5[3999,6]+out5[3999,7]+out5[3999,8]+out5[3999,9]+out5[3999,10]+out5[3999,11]) #mat9[i,j] = (out5[3999,8]+out5[3999,9])/(out5[3999,6]+out5[3999,7]+out5[3999,8]+out5[3999,9]+out5[3999,10]+out5[3999,11])