#Loading required packages
library(survival)
library(survminer)
library(tidyverse)
library(dplyr)
library(doBy)
library(psych)

#Loading Data 
AllSpeciesSurvival <- read.csv("AllSpeciesSurvival.csv")
str(AllSpeciesSurvival)
levels(AllSpeciesSurvival$Species)
AllSpeciesSurvival$Species

#Reorganizing data 
AllSpeciesSurvival$Treatment<-as.factor(AllSpeciesSurvival$Treatment)
AllSpeciesSurvival$Treatment<-relevel(AllSpeciesSurvival$Treatment,ref="Control")
AllSpeciesSurvival$Species <- factor(AllSpeciesSurvival$Species, levels = c("NOVI", "NOVI Eft", "AQCE","NOME","CHPE","NOPE","OSSE","ANAE","ENKL","EUBI","PSRU","EUWI","TAGR","SCHO","ENXA"))

#Creating a survival object
All_Species_Survfit<-survfit(Surv(Days.Survival,Dead)~Treatment+Species,data=AllSpeciesSurvival)
summary(All_Species_Survfit)

#Plotting survival curves
AllSpeciesSurvivalPlot<-ggsurvplot_facet(All_Species_Survfit,AllSpeciesSurvival,facet.by=c("Species"),surv.scale="percent",
                                         palette=c("black","green","blue","gold3","red"),scales='free_x',
                                         xlab="Days Survival Post Exposure",ylab="Percent Survival",legend.title="",
                                         legend.labs = c("Control","5x10e3","5x10e4","5x10e5","5x10e6"),font.x=c(face="bold"),
                                         panel.labs.font.x = list(color = "black",face="bold"),
                                         panel.labs.font = list(color = "black",face="bold"),short.panel.labs = T)

AllSpeciesSurvivalPlot
#Changing text features of figure
ggpar(AllSpeciesSurvivalPlot,
      font.x = c(12, "bold"),
      font.y = c(12, "bold"),
      font.caption = c(12, "bold"), 
      font.legend = c(12, "bold"), 
      font.tickslab = c(12, "bold"),
      panel.labs.font=c(12,"bold"))

#Determening average days survival across all species
SpeciesSurvivalDays<-subset(AllSpeciesSurvival,Dead=="1")
describe(SpeciesSurvivalDays)