####This code is for SIAR analysis of individual animals to compare their consumption of 5 sources
setwd("C:/Stikine/Stikine grizzly isotope paper/SIAR")
library(siar)
graphics.off()

##Load Data for CNS
##The file below excludes the samples that were likely not annual samples
consumers_annual<-read.table("Annual values for annual and uncertain samples.txt",header=TRUE)
sources_CNS<-read.table("sources.txt",header=TRUE)
corrections_CNS<-read.table("corrections.txt",header=TRUE)

##run model
model1<-siarmcmcdirichletv4(consumers_annual, sources_CNS, corrections_CNS)

##create plots
##The line below plots the data similar to figure 1 but figure 1 includes all the data
siarplotdata(model1)
siarhistograms(model1)
siarproportionbygroupplot(model1)
siarproportionbysourceplot(model1,grp=1)

##view data
siarhdrs(model1)

###Make summarized data
##THANKS TO CLAYTON LAMB FOR WRITING THIS CODE
out<-model1$output
Source_Group<-colnames(out)
mean_diet<-data.frame()
library(coda)
##Loop
for(i in 1:length(Source_Group)){
  mean<-mean(out[,i])
  ##calculate highest density intervals for error bars
  lower<-HPDinterval(mcmc(out[,i]))[1]
  upper<-HPDinterval(mcmc(out[,i]))[2]
  a<-data.frame(Source_Group=Source_Group[[i]],
                mean=mean,
                lower95CI=lower,
                upper95CI=upper
                )
  

  mean_diet<-rbind(mean_diet,a)
}

###Extract group from Source_Group column
b<-as.character(mean_diet$Source_Group)

mean_diet$Group<-substr(b, nchar(b)-1, nchar(b))
mean_diet$Source<-substr(b, 1, nchar(b)-2)


####add new group names
mean_diet$Groups<-NA
mean_diet$Groups<-ifelse(mean_diet$Group=="G1","Interior Female",mean_diet$Groups)
mean_diet$Groups<-ifelse(mean_diet$Group=="G2","Interior Male",mean_diet$Groups)
mean_diet$Groups<-ifelse(mean_diet$Group=="G3","Coast Female",mean_diet$Groups)
mean_diet$Groups<-ifelse(mean_diet$Group=="G4","Coast Male",mean_diet$Groups)

####add Sex
mean_diet$Sex<-NA
mean_diet$Sex<-ifelse(mean_diet$Group%in%c("G1","G3"),"Female",mean_diet$Sex)
mean_diet$Sex<-ifelse(mean_diet$Group%in%c("G2","G4"),"Male",mean_diet$Sex)


####add Ecotype
mean_diet$Ecotype<-NA
mean_diet$Ecotype<-ifelse(mean_diet$Group%in%c("G1","G2"),"Interior",mean_diet$Ecotype)
mean_diet$Ecotype<-ifelse(mean_diet$Group%in%c("G3","G4"),"Coast",mean_diet$Ecotype)


####REMOVE SD1 - SD3
mean_diet<-subset(mean_diet,!Source%in%c("SD1","SD2","SD3"))

##PLOT MEAN DIET FRACTIONS FOR COAST AND INTERIOR BY SEX
##THESE ARE NOT IN THE PAPER
##PLOT1

library(ggplot2)
limits <- aes(ymax = upper95CI , ymin=lower95CI)
dodge <- position_dodge(width=0.9)

p <- ggplot(mean_diet, aes(fill=Groups, y=mean, x=Source))+ geom_bar(position=dodge, stat="identity") +
  theme_grey(base_size = 18) +
  theme(axis.title.y=element_text(vjust=1.5),axis.title.x=element_text(vjust=-0.8))+
  xlab("SOURCE") +
  ylab("PROPORTION") +geom_errorbar(limits, position=dodge, width=0.25)+
  geom_errorbar(limits, position=dodge, width=0.25) +
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), 
        panel.background = element_blank(), axis.line = element_line(colour = "black"))

pdf(file="C://Stikine//Stikine grizzly isotope paper//SIAR//ISO_Proportion_ByEcotypePlusSex.pdf", width=11, height=6)
print(p)
dev.off()


##PLOT2
##### Growth
dodge <- position_dodge(width=0.4)
  
p = ggplot(mean_diet, aes(fill=Sex,y=mean, x=Source, color=Sex)) + geom_point(position=dodge, stat="identity",size=3.4)+
  geom_errorbar(aes(ymax = upper95CI , ymin=lower95CI), width=.1,position=dodge)+
  theme_bw() + theme(panel.grid.major = element_blank(), 
                     panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"),
                     axis.title.x  = element_text( vjust=-0.3, size=25),
                     axis.text.x  = element_text(  size=13),
                     axis.title.y  = element_text( vjust=1.5, size=25),
                     axis.text.y  = element_text(  size=16),
                     strip.text = element_text(size=20)) +
  ylab("Proportion")+
  xlab("Source")

pdf(file="C://Stikine//Stikine grizzly isotope paper//SIAR//ISO_Proportion_ByEcotype.pdf", width=11, height=6)
print(p + facet_wrap(~ Ecotype) )
dev.off()