Changes

batchRuns/analyze_codes.r

@@ -6,7 +6,7 @@ library(cowplot)
 library(dplyr)
 #oneLR<-read.csv("v4_param_results.csv")
 #oneLR<-read.csv("v5_param_results.csv")
-oneLR<- read.csv("ParamListGen_results(8).csv")
+oneLR<- read.csv("ParamListGen-1_results.csv")
 straRef<-data.frame(nstrains=ceiling(10^(seq(0.7,2.3,0.15))),rawStrains = 10^(seq(0.7,2.3,0.15)))
 oneLR<-oneLR%>%left_join(straRef,by="nstrains")
 oneLR<-oneLR%>%mutate(resistP = PR/P,
@@ -42,16 +42,16 @@ ggplot(oneLR%>%filter(wildOnly==0,d1>0), aes(log10(adjB),log10(rawStrains)))+
   geom_raster(aes(fill=resistP))+scale_fill_viridis_c()+
   facet_wrap(d1~seasonality, labeller="label_both")
 
-ggplot(oneLR%>%filter(wildOnly==0,d1>0), aes(log10(adjB),red))+
+ggplot(oneLR%>%filter(wildOnly==0,d1>0,cloneCost==0.1), aes(log10(adjB),red))+
   geom_raster(aes(fill=resistP))+scale_fill_viridis_c()+
   facet_wrap(d1~seasonality, labeller="label_both")
 
 ggplot(oneLR%>%filter(wildOnly==0,d1>0.5,cloneCost==0.1), aes(log10(adjB),resistP))+geom_point()+geom_line(aes(color=as.factor(red)))#+facet_wrap(d1~cloneCost, labeller="label_both")
 
 # host populations
-ggplot(oneLR%>%filter(wildOnly==0,d1>0), aes(log10(adjB),log10(rawStrains)))+
-  geom_raster(aes(fill=N))+scale_fill_viridis_c()+
-  facet_wrap(d1~seasonality~, labeller="label_both")
+ggplot(oneLR%>%filter(wildOnly==0,d1>0,prev>0), aes(log10(adjB),red))+
+  geom_raster(aes(fill=resistP))+scale_fill_viridis_c()+
+  facet_wrap(d1~cloneCost, labeller="label_both")
 
 ggplot(oneLR%>%filter(wildOnly==0,d1>0), aes(log10(adjB),N)) + geom_point() + geom_line(aes(color=as.factor(log10(rawStrains))))
 
@@ -91,15 +91,15 @@ ggplot(oneLR%>%drop_na()%>%filter(wildOnly==0,d1>0), aes(log10(adjB*adjPrev*365)
   ylab("percentage of resistance")+facet_grid(d1~seasonality,labeller="label_both")+
   theme_cowplot()
 
-ggplot(oneLR%>%filter(wildOnly==0,d1>0.5), aes(adjB*adjPrev*365,resistP))+
+ggplot(oneLR%>%filter(wildOnly==0,d1>0.5,cloneCost==0.1), aes(adjB*adjPrev*365,resistP))+
   geom_point(aes(color=red))+
   scale_color_viridis_c(option="turbo")+xlab("log10(EIR per year)")+
   ylab("percentage of resistance")+facet_grid(d1~seasonality,labeller="label_both")+
   theme_cowplot()
 
 
 # AU prevalence vs resistance
-ggplot(oneLR%>%filter(wildOnly==0,d1>0),aes(I_AU,resistP))+
+ggplot(oneLR%>%filter(wildOnly==0,d1>0,cloneCost==0.1),aes(I_AU,resistP))+
   geom_point(aes(color=log10(nstrains/adjB),shape=as.factor(seasonality)))+scale_color_viridis_c(option="plasma")+xlab("Prevalance in Asymptomatic")+ylab("percentage of resistance")+
   facet_grid(d1~.,labeller="label_both")+
   theme_cowplot()+
@@ -143,7 +143,46 @@ ggplot(oneLR%>%filter(wildOnly==0,d1>0.5,cloneCost==0.1),aes(adjPrev,resistP))+
   facet_grid(d1~.,labeller="label_both")+
   theme_cowplot()+
   geom_smooth()
-
+
+
+ggplot(oneLR%>%filter(wildOnly==0,d1>0),aes(adjPrev,resistP))+
+  geom_line(aes(color=as.factor(adjB)))+scale_color_viridis_d(option="plasma")+
+  xlab("Prevalance")+ylab("percentage of resistance")+
+  facet_grid(d1~cloneCost,labeller="label_both")+
+  theme_cowplot()
+
+ggplot(oneLR%>%filter(wildOnly==0,d1>0,adjB>=0.1,adjPrev>0,red>0),aes(I_AU,resistP))+
+  geom_point(aes(color=red))+scale_color_viridis_c(option="plasma")+
+  xlab("Prevalance")+ylab("percentage of resistance")+
+  facet_grid(d1~cloneCost,labeller="label_both")+
+  theme_cowplot()
+
+ggplot(oneLR%>%filter(wildOnly==0,d1>0,adjPrev>0,red>0),aes(1/muWU*exp(-red*P_acc_S/(SU+SD)),resistP))+
+  geom_point(aes(color=red))+scale_color_viridis_c(option="plasma")+
+  ylab("percentage of resistance")+
+  facet_grid(d1~cloneCost,labeller="label_both")+
+  theme_cowplot()
+
+oneLR<-oneLR%>%mutate(clearN = 1/(1/muWU*exp(-red*P_acc_N/(NU+ND))+1),
+                      clearS = 1/(1/muWU*exp(-red*P_acc_S/(SU+SD))+1),
+                      clearA = 1/(1/muWU*exp(-red*P_acc_A/(AU+AD))+1),
+                      sympt = ((PW_NU)*(1-exp(-1/8/clearN))+(PW_SU)*(1-exp(-1/8/clearS))+
+                        (PW_AU)*(1-exp(-1/8/clearA))),
+                      aSympt = ((PW_NU)*exp(-1/8/clearN))/clearN+
+                        ((PW_SU)*exp(-1/8/clearS))/clearS+
+                                  ((PW_AU)*exp(-1/8/clearA))/clearA,
+                      noDrug = PW_NU/clearN+PW_SU/clearS+PW_AU/clearA,
+                      symptRatio = (sympt+aSympt)/noDrug)
+
+
+
+ggplot(oneLR%>%filter(wildOnly==0,d1>0,adjPrev>0,red>0),aes(symptRatio,resistP))+
+  geom_point(aes(color=red))+scale_color_viridis_c(option="plasma")+
+  ylab("percentage of resistance")+
+  facet_grid(d1~cloneCost,labeller="label_both")+
+  theme_cowplot()
+
+
 ggplot(oneLR%>%filter(wildOnly==0,d1>0.5,cloneCost==0.1,red!=0),aes(log10(adjB),adjPrev))+geom_point()+geom_line(aes(color=as.factor(red)))