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MalariaResistance/.Rhistory

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mutate(changeRate = (resistP-lead(resistP))/(resistP))
p27<-ggplot(policy%>% filter(d1>0,varyCost==1,P>1,resistP<1,mixCost==0.9,cloneCost==0.1) )+
aes(time/365, resistP, group=No, color=rawStrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
p27
colnames(p27)
colnames(policy)
unique(policy$time)
policy%>%filter(time==0)
t0feat <- policy%>%filter(time==0)%>%select(jobid,No,d1,resistP)
t0feat
t0feat <- policy%>%filter(time==0)%>%ungroup()%>%select(jobid,No,d1,resistP)
t0feat
colnames(t0feat)[4]<-"t0resistP"
policy <- policy %>% left_join(t0feat)
ggplot(policy%>% filter(d1>0,varyCost==1,P>1,resistP<1,mixCost==0.9,cloneCost==0.1) )+
aes(time/365, resistP, group=No, color=rawStrains,t0resistP>0.9)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(policy%>% filter(d1>0,varyCost==1,P>1,resistP<1,mixCost==0.9,cloneCost==0.1,t0resistP>0.9) )+
aes(time/365, resistP, group=No, color=rawStrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(policy%>% filter(d1>0,varyCost==1,P>1,resistP<1,mixCost==0.9,cloneCost==0.1,t0resistP>0.9) )+
aes(time/365, resistP, group=No, color=adjB)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(policy%>% filter(d1>0,varyCost==1,P>1,resistP<1,mixCost==0.9,cloneCost==0.1,t0resistP>0.9) )+
aes(time/365, resistP, group=No, color=adjPrev)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(policy%>% filter(d1>0,varyCost==1,P>1,
resistP<1,mixCost==0.9,cloneCost==0.1) )+
aes(time/365, resistP, group=No, color=adjPrev)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(nstrain~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(policy%>% filter(d1>0,varyCost==1,P>1,
resistP<1,mixCost==0.9,cloneCost==0.1) )+
aes(time/365, resistP, group=No, color=adjPrev)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(nstrains~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(policy%>% filter(d1>0,varyCost==1,P>1,
resistP<1,mixCost==0.9,cloneCost==0.1) )+
aes(time/365, resistP, group=No, color=adjB)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(nstrains~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(policy%>% filter(d1>0,varyCost==1,P>100,
resistP<1,mixCost==0.9,cloneCost==0.1) )+
aes(time/365, resistP, group=No, color=adjB)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(nstrains~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(policy%>% filter(d1>0,varyCost==1,P>100,
resistP<1,mixCost==0.9,cloneCost==0.1,t0resistP>0.9) )+
aes(time/365, resistP, group=No, color=adjB)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(nstrains~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(policy%>% filter(d1>0,varyCost==1,P>100,
resistP<=1,mixCost==0.9,cloneCost==0.1,t0resistP>0.9) )+
aes(time/365, resistP, group=No, color=adjB)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(nstrains~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(policy%>% filter(d1>0,varyCost==1,P>1,resistP<1,mixCost==0.9,cloneCost==0.1) )+
aes(time/365, resistP, group=No, color=rawStrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(ResistanceEfficacy~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
unique(policy$ResistanceEfficacy)
unique(policy$muRU)
meanRes <- policy%>% filter(d1>0,prev_order<10,
resistP<=1)%>%
group_by(time,mixCost,cloneCost,varyCost,d1,nstrains)%>%
summarize(meanRes = mean(resistP,na.rm=T))
meanRes
ggplot(meanRes)+
aes(time/365, meanRes, group=No, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(nstrains~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
meanRes <- policy%>% filter(d1>0,prev_order<10,
resistP<=1)%>%
group_by(time,mixCost,cloneCost,varyCost,treatment,nstrains)%>%
summarize(meanRes = mean(resistP,na.rm=T))
ggplot(meanRes)+
aes(time/365, meanRes, group=No, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(nstrains~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
meanRes <- policy%>% filter(d1>0,prev_order<10,
resistP<=1)%>%
group_by(No,time,mixCost,cloneCost,varyCost,treatment,nstrains)%>%
summarize(meanRes = mean(resistP,na.rm=T))
ggplot(meanRes)+
aes(time/365, meanRes, group=No, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(nstrains~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(meanRes)+
aes(time/365, meanRes, group=No, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(meanRes%>%filter(mixCost==0.9,cloneCost==0.1,varyCost==1))+
aes(time/365, meanRes, group=No, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
meanRes%>%filter(mixCost==0.9,cloneCost==0.1,varyCost==1)
3947/8
3947/2
View(meanRes)
meanRes%>%filter(time==10*365)
meanRes%>%filter(time==10*365,treatment==1)
meanRes%>%filter(time==10*365,treatment=="Treatment: 63.2%")
meanRes%>%filter(time==10*365,treatment=="Treatment: 63.2%",mixCost==0.9,cloneCost==0.1,varyCost==1)
insp <- policy%>%filter(No %in% c(90,102))
insp <- policy%>%filter(No %in% c(90,102),time==0)
View(insp)
insp <- policy%>%filter(No %in% c(90,102),time==0,d1==0.2)
View(insp)
View(insp)
meanRes <- policy%>% filter(d1>0,prev_order<10,
resistP<=1)%>%
group_by(time,mixCost,cloneCost,varyCost,treatment,nstrains)%>%
summarize(meanRes = mean(resistP,na.rm=T))
ggplot(meanRes%>%filter(mixCost==0.9,cloneCost==0.1,varyCost==1))+
aes(time/365, meanRes, group=nstrains, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(meanRes%>%filter(mixCost==0.9,cloneCost==0.1,varyCost==1))+
aes(time/365, meanRes, group=nstrains, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=nstrains))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
meanRes <- policy%>% filter(d1>0,prev_order<10,
resistP<=1)%>%
group_by(time,mixCost,cloneCost,varyCost,treatment,nstrains)%>%
summarize(meanRes = mean(resistP,na.rm=T),
sd = sd(resistP,na.rm=T))
meanRes <- policy%>% filter(d1>0,prev_order<10,
resistP<=1)%>%
group_by(time,mixCost,cloneCost,varyCost,treatment,nstrains)%>%
summarize(meanRes = mean(resistP,na.rm=T),
sdRes = sd(resistP,na.rm=T))
ggplot(meanRes%>%filter(mixCost==0.9,cloneCost==0.1,varyCost==1))+
aes(time/365, meanRes, group=nstrains, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_errorbar(aes(ymin = meanRes-sdRes,ymax=meanRes+sdRes))+
geom_path(aes(group=nstrains))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
meanRes <- policy%>% filter(d1>0,prev_order<10,
resistP<=1)%>%
group_by(time,mixCost,cloneCost,varyCost,treatment,nstrains)%>%
summarize(ss = n(),
meanRes = mean(resistP,na.rm=T),
sdRes = sd(resistP,na.rm=T)/sqrt(ss))
ggplot(meanRes%>%filter(mixCost==0.9,cloneCost==0.1,varyCost==1))+
aes(time/365, meanRes, group=nstrains, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_errorbar(aes(ymin = meanRes-sdRes,ymax=meanRes+sdRes))+
geom_path(aes(group=nstrains))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
meanRes <- policy%>% filter(d1>0,prev_order<5,
resistP<=1)%>%
group_by(time,mixCost,cloneCost,varyCost,treatment,nstrains)%>%
summarize(ss = n(),
meanRes = mean(resistP,na.rm=T),
sdRes = sd(resistP,na.rm=T)/sqrt(ss))
ggplot(meanRes%>%filter(mixCost==0.9,cloneCost==0.1,varyCost==1))+
aes(time/365, meanRes, group=nstrains, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_errorbar(aes(ymin = meanRes-sdRes,ymax=meanRes+sdRes))+
geom_path(aes(group=nstrains))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
meanRes <- policy%>% filter(d1>0,prev_order<5,
resistP<=1)%>%
group_by(time,mixCost,cloneCost,varyCost,treatment,nstrains)%>%
summarize(ss = n(),
meanRes = mean(resistP,na.rm=T),
sdRes = sd(resistP,na.rm=T))
ggplot(meanRes%>%filter(mixCost==0.9,cloneCost==0.1,varyCost==1))+
aes(time/365, meanRes, group=nstrains, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_errorbar(aes(ymin = meanRes-sdRes,ymax=meanRes+sdRes))+
geom_path(aes(group=nstrains))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
meanRes <- policy%>% filter(d1>0,prev_order<10,
resistP<=1)%>%
group_by(time,mixCost,cloneCost,varyCost,treatment,nstrains)%>%
summarize(ss = n(),
meanRes = mean(resistP,na.rm=T),
sdRes = sd(resistP,na.rm=T))
ggplot(meanRes%>%filter(mixCost==0.9,cloneCost==0.1,varyCost==1))+
aes(time/365, meanRes, group=nstrains, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=nstrains))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(meanRes%>%filter(mixCost==0.9,cloneCost==0.3,varyCost==1))+
aes(time/365, meanRes, group=nstrains, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=nstrains))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(meanRes%>%filter(mixCost==0.1,cloneCost==0.1,varyCost==1))+
aes(time/365, meanRes, group=nstrains, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=nstrains))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(meanRes%>%filter(mixCost==0.1,cloneCost==0.1,varyCost==1))+
aes(time/365, meanRes, group=nstrains, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=nstrains))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(meanRes%>%filter(mixCost==0.3,cloneCost==0.1,varyCost==1))+
aes(time/365, meanRes, group=nstrains, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=nstrains))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggplot(meanRes%>%filter(mixCost==0.9,cloneCost==0.1,varyCost==1))+
aes(time/365, meanRes, group=nstrains, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=nstrains))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
meanRes <- policy%>% filter(d1>0,prev_order<10,
resistP<=1)%>%
group_by(time,mixCost,cloneCost,varyCost,treatment,nstrains)%>%
summarize(ss = n(),
meanRes = mean(resistP,na.rm=T),
sdRes = sd(resistP,na.rm=T))
p27<-ggplot(meanRes%>%filter(mixCost==0.9,cloneCost==0.1,varyCost==1))+
aes(time/365, meanRes, group=nstrains, color=nstrains)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Numberof\nStrains")+
geom_path(aes(group=nstrains))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggsave("Figures/fig5_policy.tiff",p27, width=8,height=4)
ggsave("Figures/fig5_policy.png",p27, width=8,height=4)
ggsave("Figures/fig5_policy.pdf",p27, width=8,height=4)
GIpolicy<-read.csv("GI_GIpolicy/GI_GIpolicy_results.csv")
GIpolicy<-read.csv("GI_policy/GI_policy_results.csv")
GIpolicy<-GIpolicy%>%mutate(PW_NU=round(PW_NU),
PW_SU=round(PW_SU),
PW_AU=round(PW_AU),
PW_ND=round(PW_ND),
PW_SD=round(PW_SD),
PW_AD=round(PW_AD),
PR_NU=round(PR_NU),
PR_SU=round(PR_SU),
PR_AU=round(PR_AU),
PR_ND=round(PR_ND),
PR_SD=round(PR_SD),
PR_AD=round(PR_AD))
head(GIpolicy)
#straRef<-data.frame(nstrains=ceiling(10^(seq(0.7,2.75,0.15))),rawStrains = 10^(seq(0.7,2.75,0.15)))
#GIpolicy<-GIpolicy%>%left_join(straRef,by="nstrains")
GIpolicy$treatment<-factor(GIpolicy$d1,levels=c(0,0.05,0.2),labels=c("No Treatment","Treatment: 63.2%","Treatment: 98.2%"))
GIpolicy <- GIpolicy %>% mutate(case = paste(cloneCost,mixCost,sep=";"))
GIpolicy<-GIpolicy%>%mutate(PR = round(PR_NU+PR_ND+PR_SU+PR_SD+PR_AU+PR_AD),
PW = round(PW_NU+PW_ND+PW_SU+PW_SD+PW_AU+PW_AD),
P = round(PR+PW),
N = NU+ND+SU+SD+AU+AD,
resistP = PR/P,
adjB = bavgnull*(0.5819519*(seasonality>0) + (seasonality==0)),
rNU = (PW_NU+PR_NU)/(NU+1),
rND = (PW_ND+PR_ND)/(ND+1),
rSU = (PW_SU+PR_SU)/(SU+1),
rSD = (PW_SD+PR_SD)/(SD+1),
rAU = (PW_AU+PR_AU)/(AU+1),
rAD = (PW_AD+PW_AD)/(AD+1),
I_NU = 1-exp(-rNU),
I_ND = 1-exp(-rND),
I_SU = 1-exp(-rSU),
I_SD = 1-exp(-rSD),
I_AU = 1-exp(-rAU),
I_AD = 1-exp(-rAD),
adjPrev = (I_NU*NU+I_ND*ND+I_SU*SU+I_SD*SD+I_AU*AU+I_AD*AD)/N
)
GIpolicy$resistP[is.nan(GIpolicy$resistP)]<-0
addRateName <- function(string){
paste("Daily Treatment Rate:",string)
}
ggplot(GIpolicy%>% filter(d1>0,varyCost==1,mixCost==0.9,cloneCost==0.1,PR>0) )+
aes(time/365, resistP, group=No, color=adjB)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Transmission\nPotential")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
p28<-ggplot(GIpolicy%>% filter(d1>0,varyCost==1,mixCost==0.9,cloneCost==0.1,PR>0) )+
aes(time/365, resistP, group=No, color=adjB)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Transmission\nPotential")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
ggsave("Figures/figS8_GIpolicy.tiff",p28, width=8,height=4)
ggsave("Figures/figS8_GIpolicy.png",p28, width=8,height=4)
ggsave("Figures/figS8_GIpolicy.pdf",p28, width=8,height=4)
max(policy$time)/365
p28<-ggplot(GIpolicy%>% filter(d1>0,varyCost==1,mixCost==0.9,cloneCost==0.1,adjPrev>0) )+
aes(time/365, resistP, group=No, color=adjB)+
geom_point(size=2)+scale_color_viridis_c(option="magma",trans="log10",name = "Transmission\nPotential")+
geom_path(aes(group=No))+
xlab("Year")+ylab("Frequency of Resistance")+
scale_x_continuous( breaks=breaks_pretty(n = 5))+
facet_grid(.~treatment)+
theme_cowplot()+
theme(
legend.title = element_text(size=10),
legend.text = element_text(size=10))
p28
ggsave("Figures/figS8_GIpolicy.tiff",p28, width=8,height=4)
ggsave("Figures/figS8_GIpolicy.png",p28, width=8,height=4)
ggsave("Figures/figS8_GIpolicy.pdf",p28, width=8,height=4)