setwd("SET working Directory") #Load raw data files isopod_sterile <- read.csv("Sterile-Isopods.csv") isopod_soil <- read.csv("Isopods_InSoil.csv") millipede_sterile <- read.csv("Sterile-Millipedes.csv") millipede_soil <- read.csv("Millipede_InSoil.csv") #Load packages library("survival", lib.loc="/Library/Frameworks/R.framework/Versions/3.6/Resources/library") library("survminer", lib.loc="/Library/Frameworks/R.framework/Versions/3.6/Resources/library") ####ISOPOD ANALYSIS #Begin with sterile isopod analysis attach(isopod_sterile) ##Survival Code sterileiso = survdiff(formula=Surv(Day,Status)~Treatment, data= isopod_sterile) sterileiso #Pairwise comparisons pairiso <- pairwise_survdiff(Surv(Day, Status) ~ Treatment, data = isopod_sterile) pairiso #Preliminary Plot plot(fit, col=c(1:4), xlab="Time (Days)", ylab="Survival Probability") legend("bottomleft", inset = .05, title = "Treatments",legend= c("Contol","Captan","Strep"),c(1:4) ,fill = c(1:4)) #Run this code to run plotting function fit=survfit(Surv(isopod_sterile$Day,isopod_sterile$Status)~isopod_sterile$Treatment) summary(fit) ####Plots png(file="IsopodSterile_SurvivalCurve.png", width = 6000, height = 4800, res = 1200) ggsurvplot( fit, data = isopod_sterile, size = 1, # change line size palette = c("saddlebrown","green4","black"),# custom color palettes conf.int = TRUE, # Add confidence interval ylim = c(0.6,1.00), pval = FALSE, # Add p-value risk.table = FALSE, # Add risk table risk.table.col = "strata",# Risk table color by groups legend.labs = c("Antifungal","Control","Antibacterial"), # Change legend labels risk.table.height = .4 # Useful to change when you have multiple groups ) fit dev.off() ##Now run on Isopods in soil environments #Begin with sterile isopod analysis attach(isopod_soil) ##Survival Code soiliso = survdiff(formula=Surv(Day,Status)~Treatment, data= isopod_soil) soiliso #Pairwise comparisons pairiso <- pairwise_survdiff(Surv(Day, Status) ~ Treatment, data = isopod_soil) pairiso #Preliminary Plot plot(fit, col=c(1:4), xlab="Time (Days)", ylab="Survival Probability") legend("bottomleft", inset = .05, title = "Treatments",legend= c("Contol","Captan","Strep"),c(1:4) ,fill = c(1:4)) #Run this code to run plotting function fit=survfit(Surv(isopod_soil$Day,isopod_soil$Status)~isopod_soil$Treatment) summary(fit) ####Plots png(file="IsopodInSoil_SurvivalCurve.png", width = 6000, height = 4800, res = 1200) ggsurvplot( fit, data = isopod_soil, size = 1, # change line size palette = c("saddlebrown","green4","black"),# custom color palettes conf.int = TRUE, # Add confidence interval ylim = c(0.6,1.00), pval = FALSE, # Add p-value risk.table = FALSE, # Add risk table risk.table.col = "strata",# Risk table color by groups legend.labs = c("Antifungal","Control","Antibacterial"), # Change legend labels risk.table.height = .4 # Useful to change when you have multiple groups ) fit dev.off() #####MILLIPEDE ANALYSIS #Begin with sterile millipede analysis attach(millipede_sterile) ##Survival Code sterileiso = survdiff(formula=Surv(Week,Status)~Treatment, data= millipede_sterile) sterileiso #Pairwise comparisons pairiso <- pairwise_survdiff(Surv(Week, Status) ~ Treatment, data = millipede_sterile) pairiso #Preliminary Plot plot(fit, col=c(1:4), xlab="Time (Weeks)", ylab="Survival Probability") legend("bottomleft", inset = .05, title = "Treatments",legend= c("Contol","Captan","Strep"),c(1:4) ,fill = c(1:4)) #Run this code to run plotting function fit=survfit(Surv(millipede_sterile$week,millipede_sterile$Status)~millipede_sterile$Treatment) summary(fit) ####Plots png(file="millipedeSterile_SurvivalCurve.png", width = 6000, height = 4800, res = 1200) ggsurvplot( fit, data = millipede_sterile, size = 1, # change line size palette = c("saddlebrown","green4","black"),# custom color palettes conf.int = TRUE, # Add confidence interval ylim = c(0.6,1.00), pval = FALSE, # Add p-value risk.table = FALSE, # Add risk table risk.table.col = "strata",# Risk table color by groups legend.labs = c("Antifungal","Control","Antibacterial"), # Change legend labels risk.table.height = .4 # Useful to change when you have multiple groups ) fit dev.off() ##Now run on millipedes in soil environments attach(millipede_soil) ##Survival Code soiliso = survdiff(formula=Surv(week,Status)~Treatment, data= millipede_soil) soiliso #Pairwise comparisons pairiso <- pairwise_survdiff(Surv(week, Status) ~ Treatment, data = millipede_soil) pairiso #Preliminary Plot plot(fit, col=c(1:4), xlab="Time (weeks)", ylab="Survival Probability") legend("bottomleft", inset = .05, title = "Treatments",legend= c("Contol","Captan","Strep"),c(1:4) ,fill = c(1:4)) #Run this code to run plotting function fit=survfit(Surv(millipede_soil$week,millipede_soil$Status)~millipede_soil$Treatment) summary(fit) ####Plots png(file="millipedeInSoil_SurvivalCurve.png", width = 6000, height = 4800, res = 1200) ggsurvplot( fit, data = millipede_soil, size = 1, # change line size palette = c("saddlebrown","green4","black"),# custom color palettes conf.int = TRUE, # Add confidence interval ylim = c(0.6,1.00), pval = FALSE, # Add p-value risk.table = FALSE, # Add risk table risk.table.col = "strata",# Risk table color by groups legend.labs = c("Antifungal","Control","Antibacterial"), # Change legend labels risk.table.height = .4 # Useful to change when you have multiple groups ) fit dev.off()