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batchRuns/analyze_codes.r

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+setwd("~/Dropbox/research/current/resistance/MalariaResistance/batchRuns/")
+library(tidyverse)
+library(cowplot)
+oneLR<-read.csv("v4_param_results.csv")
+#oneLR<-read.csv("v5_param_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,
+                      adjB = bavgnull*(0.5819519*(seasonality>0) + (seasonality==0)),
+                      rNU = (PW_NU+PR_NU)/(NU+1),
+                      rND = (PW_ND+PR_ND)/(ND+1),
+                      rSU = (PW_SU+PR_SU)/(SU+1),
+                      rSD = (PW_SD+PR_SD)/(SD+1),
+                      rAU = (PW_AU+PR_AU)/(AU+1),
+                      rAD = (PW_AD+PW_AD)/(AD+1),
+                      I_NU = 1-exp(-rNU),
+                      I_ND = 1-exp(-rND),
+                      I_SU = 1-exp(-rSU),
+                      I_SD = 1-exp(-rSD),
+                      I_AU = 1-exp(-rAU),
+                      I_AD = 1-exp(-rAD),
+                      adjPrev = (I_NU*NU+I_ND*ND+I_SU*SU+I_SD*SD+I_AU*AU+I_AD*AD)/N
+                      )
+
+
+
+# resistant prevalence as a function of biting rate and strains
+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")
+
+# prevalence as a function of starting conditions
+ggplot(oneLR%>%drop_na()%>%filter(nstrains%in%c(10,20,80,159),d1==1), 
+       aes(log10(adjB),adjPrev,
+           color=as.factor(wildOnly),shape = as.factor(d1)))+
+  geom_point()+
+  geom_line()+
+  facet_grid(nstrains~seasonality,scales="free")+theme_light()
+
+# EIR vs. resistance
+ggplot(oneLR%>%drop_na()%>%filter(wildOnly==0,d1>0), aes(log10(adjB*adjPrev*365),resistP))+
+  geom_point(aes(color=log(nstrains),shape=as.factor(seasonality)))+
+  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))+
+  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()
+
+# prevalence vs resistance
+ggplot(oneLR%>%filter(wildOnly==0,d1>0),aes(adjPrev,resistP))+
+  geom_point(aes(color=log10(nstrains/adjB),shape=as.factor(seasonality)))+scale_color_viridis_c(option="plasma")+
+  xlab("Prevalance")+ylab("percentage of resistance")+
+  facet_grid(d1~.,labeller="label_both")+
+  theme_cowplot()
+
+
+
+
+
+