From cfa4a3523d58b7a7f0f03c48d976f3dfde174d7d Mon Sep 17 00:00:00 2001 From: Jack Chaillet Date: Tue, 12 Apr 2022 15:19:48 -0400 Subject: [PATCH] Generalized Immunity changes 3 --- batchRuns/ODESGeneralizedImmunity.R | 43 +++++++++++++++-------------- 1 file changed, 22 insertions(+), 21 deletions(-) diff --git a/batchRuns/ODESGeneralizedImmunity.R b/batchRuns/ODESGeneralizedImmunity.R index 235a119..8e943ef 100644 --- a/batchRuns/ODESGeneralizedImmunity.R +++ b/batchRuns/ODESGeneralizedImmunity.R @@ -810,10 +810,10 @@ print(abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)) while((abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)>0.001 )| (abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)>0.001)){ - print(out2[30*365,2:23]) + print(out2[30*365,2:20]) t2<-t2+30*365 - N0 = as.numeric(out2[30*365+1,2:23]) - names(N0)<-colnames(out2[,2:23]) + N0 = as.numeric(out2[30*365+1,2:20]) + names(N0)<-colnames(out2[,2:20]) out2 = ode(y=N0,times=t2,func=SEAI_wildOnly,parms=currentPara) out2<-as_tibble(out2) sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, @@ -830,6 +830,7 @@ out2<-out2%>%mutate(PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, #ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ # facet_wrap(.~variable,scales="free_y") outData<-as.data.frame(cbind(jobid=jobid,wildOnly=1,currentPara,tail(out2,1))) + if(file.exists(outFile)){ write.table(outData, file = outFile, row.names=F, col.names=F,sep=",", @@ -841,7 +842,7 @@ if(file.exists(outFile)){ } -storeOut<-tail(out2,1)[,2:23] +storeOut<-tail(out2,1)[,2:20] # Step 2 treat occasionally, wildOnly----- currentPara$d1<-0.5 @@ -867,10 +868,10 @@ print(abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)) while((abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)>0.001 )| (abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)>0.001)){ - print(out2[30*365,2:23]) + print(out2[30*365,2:20]) t2<-t2+30*365 - N0 = as.numeric(out2[30*365+1,2:23]) - names(N0)<-colnames(out2[,2:23]) + N0 = as.numeric(out2[30*365+1,2:20]) + names(N0)<-colnames(out2[,2:20]) out2 = ode(y=N0,times=t2,func=SEAI_wildOnly,parms=currentPara) out2<-as_tibble(out2) sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, @@ -898,7 +899,7 @@ if(file.exists(outFile)){ } -storeOut<-rbind(storeOut,tail(out2,1)[,2:23]) +storeOut<-rbind(storeOut,tail(out2,1)[,2:20]) # Step 3 full treatment, wildOnly----- currentPara$d1<-1 @@ -924,10 +925,10 @@ print(abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)) while((abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)>0.001 )| (abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)>0.001)){ - print(out2[30*365,2:23]) + print(out2[30*365,2:20]) t2<-t2+30*365 - N0 = as.numeric(out2[30*365+1,2:23]) - names(N0)<-colnames(out2[,2:23]) + N0 = as.numeric(out2[30*365+1,2:20]) + names(N0)<-colnames(out2[,2:20]) out2 = ode(y=N0,times=t2,func=SEAI_wildOnly,parms=currentPara) out2<-as_tibble(out2) sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, @@ -955,7 +956,7 @@ if(file.exists(outFile)){ } -storeOut<-rbind(storeOut,tail(out2,1)[,2:23]) +storeOut<-rbind(storeOut,tail(out2,1)[,2:20]) # Step 4 resistant strains only, no treatment ------ currentPara$d1<-0 @@ -981,10 +982,10 @@ print(abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)) while((abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)>0.001 )| (abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)>0.001)){ - print(out2[30*365,2:23]) + print(out2[30*365,2:20]) t2<-t2+30*365 - N0 = as.numeric(out2[30*365+1,2:23]) - names(N0)<-colnames(out2[,2:23]) + N0 = as.numeric(out2[30*365+1,2:20]) + names(N0)<-colnames(out2[,2:20]) out2 = ode(y=N0,times=t2,func=SEAI_resOnly,parms=currentPara) out2<-as_tibble(out2) sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, @@ -1035,10 +1036,10 @@ print(abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)) while((abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)>0.001 )| (abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)>0.001)){ - print(out2[30*365,2:23]) + print(out2[30*365,2:20]) t2<-t2+30*365 - N0 = as.numeric(out2[30*365+1,2:23]) - names(N0)<-colnames(out2[,2:23]) + N0 = as.numeric(out2[30*365+1,2:20]) + names(N0)<-colnames(out2[,2:20]) out2 = ode(y=N0,times=t2,func=SEAI_p,parms=currentPara) out2<-as_tibble(out2) sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, @@ -1089,10 +1090,10 @@ print(abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)) while((abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)>0.001 )| (abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)>0.001)){ - print(out2[30*365,2:23]) + print(out2[30*365,2:20]) t2<-t2+30*365 - N0 = as.numeric(out2[30*365+1,2:23]) - names(N0)<-colnames(out2[,2:23]) + N0 = as.numeric(out2[30*365+1,2:20]) + names(N0)<-colnames(out2[,2:20]) out2 = ode(y=N0,times=t2,func=SEAI_p,parms=currentPara) out2<-as_tibble(out2) sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD,