Convert to date

exp$date<-as.Date(exp$date, format = c("%m/%d/%Y"))

Calculate percent reproductive apices

exp$total_a<-exp$repro_apices+exp$veg_apices

exp$percentra<-100*(exp$repro_apices/exp$total_a)

Subset data by site

run1<-subset(exp, run== "1")
run2<-subset(exp, run== "2")
run3<-subset(exp, run== "3")

Graph percent reproductive apices

a<-ggplot(data = run1, mapping = aes(x = treatment, y = percentra, group=treatment)) + geom_boxplot()+ylim(50,100) + ggtitle("Run 1")+ theme(plot.title = element_text(size = 12, face = "plain")) +theme(axis.text=element_text(size=12),axis.title=element_text(size=12,face="plain")) + ylab(" ") + xlab(" ") + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank(), axis.line = element_line(colour = "black")) 


b<-ggplot(data = run2, mapping = aes(x = treatment, y = percentra, group=treatment)) + geom_boxplot() +ylim(50,100) +ggtitle("Run 2")+ theme(plot.title = element_text(size = 12, face = "plain")) +theme(axis.text=element_text(size=12),axis.title=element_text(size=12,face="plain")) + ylab(" ") + xlab(" ") + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank(), axis.line = element_line(colour = "black")) 


c<-ggplot(data = run3, mapping = aes(x = treatment, y = percentra, group=treatment)) + geom_boxplot()+ylim(50,100) + ggtitle("Run 2")+ theme(plot.title = element_text(size = 12, face = "plain")) +theme(axis.text=element_text(size=12),axis.title=element_text(size=12,face="plain")) + ylab(" ") + xlab(" ") + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank(), axis.line = element_line(colour = "black")) 


percentrafig<-ggarrange(a,b,c, ncol = 3, nrow = 1)
## Warning: Removed 40 rows containing non-finite values (stat_boxplot).

## Warning: Removed 40 rows containing non-finite values (stat_boxplot).

## Warning: Removed 40 rows containing non-finite values (stat_boxplot).
annotate_figure(percentrafig,
                top = text_grob("Percent Reproductive Apices", color = "black", face = "plain", size = 14), bottom = text_grob("Treatment", color = "black", rot = 0, size=12), left = text_grob("Percent Reproductive Apices", color = "black", rot = 90, size=12))