Added Example Time Series Code

ResistanceTimeSeries.R

@@ -0,0 +1,117 @@
+t4 = seq(from=0,to=4*365,by=1)
+CQvec = c(1,1,1,1,0.54,0.54,0.54,0.54,0.5,0.5,0.5,0.5,0.18,0.18,0.18,0.18,0.01,0.01,0.01,0.01)
+CQvecGhana = c(1,1,1,1,0.3,0.3,0.3,0.3,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.1,0.1,0.1,0.1)
+CQvecnull = c(0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02)
+CQvecmax = c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1)
+eqstagSU = matrix(data=0,nrow=21,ncol=15)
+eqstagSD = matrix(data=0,nrow=21,ncol=15)
+eqstagRU = matrix(data=0,nrow=21,ncol=15)
+eqstagRD = matrix(data=0,nrow=21,ncol=15)
+eqstagNU = matrix(data=0,nrow=21,ncol=15)
+eqstagND = matrix(data=0,nrow=21,ncol=15)
+eqstagXU = matrix(data=0,nrow=21,ncol=15)
+eqstagXD = matrix(data=0,nrow=21,ncol=15)
+eqstagAU = matrix(data=0,nrow=21,ncol=15)
+eqstagAD = matrix(data=0,nrow=21,ncol=15)
+eqosc = matrix(data=0,nrow=21,ncol=15)
+eqstagf = matrix(data=0,nrow=21,ncol=15)
+for (k in 1:15){
+  wr=1-0.6
+  bavgnull = 10^bavgvaluesverynarrow[k]
+  eqstagSU[1,k] = out3eqSU[k]
+  #eqstagSU[1,k] = (1-out3eq2[k])*1000
+  eqstagSD[1,k] = out3eqSD[k]
+  #eqstagSD[1,k] = (1-out3eq2[k])*1000
+  eqstagRU[1,k] = out3eqRU[k]
+  #eqstagRU[1,k] = out3eq2[k]*1000
+  eqstagRD[1,k] = out3eqRD[k]
+  #eqstagRD[1,k] = out3eq2[k]*1000
+  eqstagf[1,k] = (eqstagRU[1,k]+eqstagRD[1,k])/(eqstagSU[1,k]+eqstagSD[1,k]+eqstagRU[1,k]+eqstagRD[1,k])
+  eqstagNU[1,k] = out3eqNU[k]
+  #eqstagNU[1,k] = 333
+  eqstagND[1,k] = out3eqND[k]
+  #eqstagND[1,k] = 333
+  eqstagXU[1,k] = out3eqXU[k]
+  #eqstagXU[1,k] = 333
+  eqstagXD[1,k] = out3eqXD[k]
+  #eqstagXD[1,k] = 333
+  eqstagAU[1,k] = out3eqAU[k]
+  #eqstagAU[1,k] = 333
+  eqstagAD[1,k] = out3eqAD[k]
+  #eqstagAD[1,k] = 333
+  eqosc[1,k] = out3osc[k]
+  #eqosc[1,k] = bavgnull+(bavgnull*L)
+  for (i in 1:20){
+    CQ=CQvec[i]
+    #N0 = c(eqstagSU[i,k],eqstagSD[i,k],eqstagRU[i,k],eqstagRD[i,k],333,333,333,333,333,333,(bavgnull)+(bavgnull*L))
+    N0 = c(eqstagSU[i,k],eqstagSD[i,k],eqstagRU[i,k],eqstagRD[i,k],eqstagNU[i,k],eqstagND[i,k],eqstagXU[i,k],eqstagXD[i,k],eqstagAU[i,k],eqstagAD[i,k],eqosc[i,k])
+    p2 = list(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,bavgnull=bavgnull,CQ=CQ)
+    out8 = ode(y=N0,times=t4,func=SEAI,parms=p2)
+    #eqstag[i+1] = (out8[,4]+out8[,5])/(out8[,2]+out8[,3]+out8[,4]+out8[,5])
+    eqstagSU[i+1,k] = out8[1*365,2]
+    eqstagSD[i+1,k] = out8[1*365,3]
+    eqstagRU[i+1,k] = out8[1*365,4]
+    eqstagRD[i+1,k] = out8[1*365,5]
+    eqstagNU[i+1,k] = out8[1*365,6]
+    eqstagND[i+1,k] = out8[1*365,7]
+    eqstagXU[i+1,k] = out8[1*365,8]
+    eqstagXD[i+1,k] = out8[1*365,9]
+    eqstagAU[i+1,k] = out8[1*365,10]
+    eqstagAD[i+1,k] = out8[1*365,11]
+    eqosc[i+1,k] = out8[1*365,12]
+    eqstagf[i+1,k] = (eqstagRU[i+1,k]+eqstagRD[i+1,k])/(eqstagSU[i+1,k]+eqstagSD[i+1,k]+eqstagRU[i+1,k]+eqstagRD[i+1,k])
+  }
+}
+plot(eqstagf[,1],ylim=c(0,1),type='l',xlim=c(0,21))
+lines(eqstagf[,2])
+lines(eqstagf[,3])
+lines(eqstagf[,4])
+lines(eqstagf[,5])
+lines(eqstagf[,6])
+lines(eqstagf[,7])
+lines(eqstagf[,8])
+lines(eqstagf[,9])
+lines(eqstagf[,10])
+lines(eqstagf[,11])
+lines(eqstagf[,12])
+lines(eqstagf[,13])
+lines(eqstagf[,14])
+lines(eqstagf[,15])
+abline(h=1,col="BLUE")
+abline(h=mean((WWARN_ACT_Partner_Drug_Mol_Surveyor_Data$present)/(WWARN_ACT_Partner_Drug_Mol_Surveyor_Data$tested)),col="RED")
+abline(h=mean((`WWARN_ACT_Partner_Drug_Mol_Surveyor_Data(1)`$present)/(`WWARN_ACT_Partner_Drug_Mol_Surveyor_Data(1)`$tested)),col="GREEN")
+plot(WWARN_ACT_Partner_Drug_Mol_Surveyor_Data$study.start-1998,(WWARN_ACT_Partner_Drug_Mol_Surveyor_Data$present)/(WWARN_ACT_Partner_Drug_Mol_Surveyor_Data$tested))
+plot(`WWARN_ACT_Partner_Drug_Mol_Surveyor_Data(1)`$study.start-2005,(`WWARN_ACT_Partner_Drug_Mol_Surveyor_Data(1)`$present)/(`WWARN_ACT_Partner_Drug_Mol_Surveyor_Data(1)`$tested))
+
+plot(analysis_PointsGhana$year,analysis_PointsGhana$value)
+
+lines(eqstagf[,16])
+lines(eqstagf[,17])
+lines(eqstagf[,18])
+lines(eqstagf[,19])
+lines(eqstagf[,20])#,col="RED")
+lines(eqstagf[,21])
+lines(eqstagf[,22])#,col="GREEN")
+lines(eqstagf[,23])
+
+
+times = matrix(data=0,nrow=21,ncol=23)
+for (i in 1:21){
+  for(j in 1:23){
+    times[i,j] = i
+  }
+}
+print(times)
+timesvec = c(times)
+print(timesvec)
+
+
+trajectory = eqstagf
+trajectoryvec = c(trajectory)
+trajectory2 = cbind(timesvec,vec7t2,trajectoryvec)
+trajectories.df <- as.data.frame(trajectory2)#,row.names = columns, col.names=rows)
+rownames(trajectories.df)
+times=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20)
+
+
+ggplot(data=trajectories.df,mapping=aes(x=timesvec,y=trajectoryvec))+geom_line(aes(color=as.factor(vec7t2)))#+xlim(2,21)