#Epifaunal invertebrate assemblages associated with branching Pocilloporids in Moorea, French Polynesia



#Flow graph
library(ggplot2)
library(reshape2)

flow<-read.csv("Flow.csv", header=T, strip.white=T)
head(flow)

flow$Date <- as.Date("%m-%d-%y") 

ggplot(flow, aes(Date)) +
  geom_line(aes(y = UP, colour = "red")) + 
  geom_line(aes(y = DN, colour = "blue"))



#Mutualist vs obligate Decapoda and Partial mortality graph

Decapoda<-read.csv("regression.csv", header=T, strip.white=T)

fit1 <- lm(mutualist ~ partial mortality, data =Decapoda)
summary(fit1)

plot(mutualist ~ partial mortality, data =Decapoda)
abline(fit1)
ggplot(Decapoda, aes(x = partial mortality, y = mutualist)) + 
  geom_point() 


fit1 <- lm(obligate ~ partial mortality, data =Decapoda)
summary(fit1)

plot(obligate ~ partial mortality, data =Decapoda)
abline(fit1)
ggplot(Decapoda, aes(x = partial mortality, y = obligate)) + 
  geom_point() 

#Surface Area graph

SA<-read.csv("regression2.csv", header=T, strip.white=T)

#Abundance
fit1 <- lm(Abundance ~ surface area, data =SA)
summary(fit1)

plot(Abundance ~ surface area, data=SA)
abline(fit1)
ggplot(SA, aes(x = surface area, y = Abundance)) + 
  geom_point() 


#Taxon richness
fit1 <- lm(Taxon richness ~ surface area, data =SA)
summary(fit1)

plot(Taxon richness~ surface area, data=SA)
abline(fit1)
ggplot(SA, aes(x = surface area, y = Taxon richness)) + 
  geom_point() 




#GLMMM Abundance of invertebrates 
library(lme4)
library(Matrix)
moorea<-read.csv("moorea.csv", strip.white=T)

data.glmerL5<-glmer.nb(Abundance~partial mortality+(1|Transect), data=moorea)

data.glmerL5<-glmer.nb(Abundance~Colony Height+(1|Transect), data=moorea)

data.glmerL5<-glmer.nb(Abundance~Space between branches +(1|Transect), data=moorea)

data.glmerL5<-glmer.nb(Abundance~Penetration depth+(1|Transect), data=moorea)

data.glmerL5<-glmer.nb(Abundance~upstream/downstream+(1|Transect), data=moorea)

data.glmerL5<-glmer.nb(Abundance~surface area+(1|Transect), data=moorea)

summary(data.hp.glmerL5)

## GLMMM taxon richness
moorea.glm1<-glmer(Taxon.richness~surface area+(1|Transect), data=moorea, family='poisson')

moorea.glm1<-glmer(Taxon.richness~partial mortality+(1|Transect), data=moorea, family='poisson')

moorea.glm1<-glmer(Taxon.richness~Colony Height+(1|Transect), data=moorea, family='poisson')

moorea.glm1<-glmer(Taxon.richness~Space between branches+(1|Transect), data=moorea, family='poisson')

moorea.glm1<-glmer(Taxon.richness~Penetration depth+(1|Transect), data=moorea, family='poisson')

moorea.glm1<-glmer(Taxon.richness~upstream/downstream+(1|Transect), data=moorea, family='poisson')

summary(moorea.glm1)


#Rarefaction curves
library(vegan)
Moo<-read.csv("rarefy2.csv", strip.white=T)
#total number of  Taxon at each site (row of data)
S <- specnumber(Moo)
S

# raremax is the minimum surface areample count achieved over the 36 surface areamples

raremax <- min(rowSums(Moo)) 

raremax
[10]

Srare <- rarefy(Moo, raremax)
#Plot rarefaction results
par(mfrow = c(1,2))
plot(S, Srare, xlab = "Observed No. of  Taxon", 
     ylab = "Rarefied No. of  Taxon",
     main = " plot(rarefy(Moo, raremax))")
abline(0, 1)
rarecurve(Moo, step = 1, 
          surface areample = raremax, 
          col = "blue", 
          cex = 0.6,
          main = "rarecurve()")