vinesRus/R_Code_Vines at master · BenbowLab/vinesRus · GitHub

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## Anazlyze Macroinvertebrate Community Data for Hess Samples in Augusta Creek

##Load Packages
library(vegan)
library(ggplot2)

##Upload file
Hess_Data<-read.csv("/Users/katiekierczynski/Desktop/URP_2016_EAB/SFS/AugustaCkHessMacros.csv")
LM_Data<-read.csv("/Users/katiekierczynski/Desktop/URP_2016_EAB/SFS/AugustaCkLMMacros.csv")

## Remove everything except macros
Hess_Macros<-Hess_Data[,c(6:40)]
row.names(Hess_Macros)<-c("A1","A2","A3","A4","A5","B1","B2","B3","B4","B5","C1","C2","C3","C4","C5","D1","D2","D3","D4","D5","E1","E2","E3","E4","E5","F1","F2","F3","F4","F5")
#colnames(Hess_Macros)<-c(1:35)

LM_Macros<-LM_Data[,c(6:30)]
row.names(LM_Macros)<-c("A1","A2","A3","A4","A5","B1","B2","B3","B4","B5","C1","C2","C3","C4","C5","D1","D2","D3","D4","D5","E1","E2","E3","E4","E5","F1","F2","F3","F4","F5")
#colnames(LM_Macros)<-c(1:35)

## Separate Site Data
Hess_Site<-Hess_Data[,c(1:4)]
LM_Site<-LM_Data[,c(1:4)]

## Separate Pre-trial data
Hess_Data_Pre<-Hess_Data[c(1,2,6,7,11,12,16,17,21,22,26,27),]
Hess_Macros_Pre<-Hess_Data_Pre[,c(6:40)]
row.names(Hess_Macros_Pre)<-c("A1","A2","B1","B2","C1","C2","D1","D2","E1","E2","F1","F2")
##colnames(Hess_Macros_Pre)<-c(1:35)

LM_Data_Pre<-LM_Data[c(1,2,6,7,11,12,16,17,21,22,26,27),]
LM_Macros_Pre<-LM_Data_Pre[,c(6:30)]
row.names(LM_Macros_Pre)<-c("A1","A2","B1","B2","C1","C2","D1","D2","E1","E2","F1","F2")
##colnames(LM_Macros_Pre)<_c(1:29)

## Separate Post-trial data
Hess_Data_Post<-Hess_Data[c(3:5,8:10,13:15,18:20,23:25,28:30),]
Hess_Macros_Post<-Hess_Data_Post[,c(6:40)]
row.names(Hess_Macros_Post)<-c("A3","A4","A5","B3","B4","B5","C3","C4","C5","D3","D4","D5","E3","E4","E5","F3","F4","F5")
##colnames(Hess_Macros_Post)<-c(1:35)

LM_Data_Post<-LM_Data[c(3:5,8:10,13:15,18:20,23:25,28:30),]
LM_Macros_Post<-LM_Data_Post[,c(6:30)]
row.names(LM_Macros_Post)<-c("A3","A4","A5","B3","B4","B5","C3","C4","C5","D3","D4","D5","E3","E4","E5","F3","F4","F5")
##colnames(LM_Macros_Post)<-c(1:29)

## Matrix combining colnames with taxa
taxa<-colnames(Hess_Data[6:40])
taxa
colheader<-c(1:35)
colheader
taxanames<-paste(taxa,colheader)
taxanames

## Set up factor for for Control vs Treatment (Vine vs VineRemoved) for all samples
levels(Hess_Data$Treatment)
stream_site=factor(Hess_Data$Treatment)
stream_site

levels(LM_Data$Treatment)
stream_site_LM=factor(LM_Data$Treatment)
stream_site_LM

## Set up factor for for Control vs Treatment (Vine vs VineRemoved) for Pre-treatment data
levels(Hess_Data_Pre$Treatment)
stream_site_Pre=factor(Hess_Data_Pre$Treatment)
stream_site_Pre

levels(LM_Data_Pre$Treatment)
stream_site_LM_Pre=factor(LM_Data_Pre$Treatment)
stream_site_LM_Pre

## Set up factor for for Control vs Treatment (Vine vs VineRemoved) for Post-treatment data
levels(Hess_Data_Post$Treatment)
stream_site_Post=factor(Hess_Data_Post$Treatment)
stream_site_Post

levels(LM_Data_Post$Treatment)
stream_site_LM_Post=factor(LM_Data_Post$Treatment)
stream_site_LM_Post


## NMDS Analysis all samples
Hess_Macros_NMDS<-metaMDS(Hess_Macros,distance = "bray")
Hess_Macros_NMDS

ordiplot(Hess_Macros_NMDS, type = "n",main="All Invertebrates")
orditorp(Hess_Macros_NMDS,display = "species",col = "red",air = 0.01)
orditorp(Hess_Macros_NMDS,display = "sites")


#Make color schemes
two_col_vec <- c("black", "bisque3")

#NMDS plot for stream_site Treatment vs Control all samples
with(Hess_Macros_NMDS, points(Hess_Macros_NMDS, display="sites", col=two_col_vec[stream_site], pch=19, pt.bg=two_col_vec))
with(Hess_Macros_NMDS, legend("topleft", legend=levels(stream_site), bty="n", col=two_col_vec, pch=19, pt.bg=two_col_vec))
with(Hess_Macros_NMDS, ordiellipse(Hess_Macros_NMDS, stream_site, kind="se", conf=0.95, lwd=2, col="black", show.groups = "Treatment"))
with(Hess_Macros_NMDS, ordiellipse(Hess_Macros_NMDS, stream_site, kind="se", conf=0.95, lwd=2, col="bisque3", show.groups = "Control"))


## NMDS Analysis Pre-treatment samples
Hess_Macros_Pre_NMDS<-metaMDS(Hess_Macros_Pre,distance = "bray")
Hess_Macros_Pre_NMDS

ordiplot(Hess_Macros_Pre_NMDS, type = "n",main="Pre-Treatment Invertebrates")
orditorp(Hess_Macros_Pre_NMDS,display = "species",col = "red",air = 0.01)
orditorp(Hess_Macros_Pre_NMDS,display = "sites")


#NMDS plot for stream_site Treatment vs Control Pre-treatment samples
with(Hess_Macros_Pre_NMDS, points(Hess_Macros_Pre_NMDS, display="sites", col=two_col_vec[stream_site_Pre], pch=19, pt.bg=two_col_vec))
with(Hess_Macros_Pre_NMDS, legend("topleft", legend=levels(stream_site_Pre), bty="n", col=two_col_vec, pch=19, pt.bg=two_col_vec))
with(Hess_Macros_Pre_NMDS, ordiellipse(Hess_Macros_Pre_NMDS, stream_site_Pre, kind="se", conf=0.95, lwd=2, col="black", show.groups = "Treatment"))
with(Hess_Macros_Pre_NMDS, ordiellipse(Hess_Macros_Pre_NMDS, stream_site_Pre, kind="se", conf=0.95, lwd=2, col="bisque3", show.groups = "Control"))


## NMDS Analysis Post-treatment samples
Hess_Macros_Post_NMDS<-metaMDS(Hess_Macros_Post,distance = "bray")
Hess_Macros_Post_NMDS

ordiplot(Hess_Macros_Post_NMDS, type = "n",main="Post-Treatment Invertebrates")
orditorp(Hess_Macros_Post_NMDS,display = "species",col = "red",air = 0.01)
orditorp(Hess_Macros_Post_NMDS,display = "sites")


#NMDS plot for stream_site Treatment vs Control Post-treatment samples
with(Hess_Macros_Post_NMDS, points(Hess_Macros_Post_NMDS, display="sites", col=two_col_vec[stream_site_Post], pch=19, pt.bg=two_col_vec))
with(Hess_Macros_Post_NMDS, legend("topleft", legend=levels(stream_site_Post), bty="n", col=two_col_vec, pch=19, pt.bg=two_col_vec))
with(Hess_Macros_Post_NMDS, ordiellipse(Hess_Macros_Post_NMDS, stream_site_Post, kind="se", conf=0.95, lwd=2, col="black", show.groups = "Treatment"))
with(Hess_Macros_Post_NMDS, ordiellipse(Hess_Macros_Post_NMDS, stream_site_Post, kind="se", conf=0.95, lwd=2, col="bisque3", show.groups = "Control"))


## Alternate NMDS plot all data
ordiplot(Hess_Macros_NMDS,type="n",main="All Invertebrates")
ordihull(Hess_Macros_NMDS,groups=stream_site,draw="polygon",col="grey90",label=F)
orditorp(Hess_Macros_NMDS,display="species",col="red",air=0.01)
orditorp(Hess_Macros_NMDS,display="sites")


## Alternate NMDS plot Pre-treatment data
ordiplot(Hess_Macros_Pre_NMDS,type="n",main="Pre-Treatment Invertebrates")
ordihull(Hess_Macros_Pre_NMDS,groups=stream_site_Pre,draw="polygon",col="grey90",label=F)
orditorp(Hess_Macros_Pre_NMDS,display="species",col="red",air=0.01)
orditorp(Hess_Macros_Pre_NMDS,display="sites")


## Alternate NMDS plot Post-treatment ata
ordiplot(Hess_Macros_Post_NMDS,type="n",main="Post-Treatment Invertebrates")
ordihull(Hess_Macros_Post_NMDS,groups=stream_site_Post,draw="polygon",col="grey90",label=F)
orditorp(Hess_Macros_Post_NMDS,display="species",col="red",air=0.01)
orditorp(Hess_Macros_Post_NMDS,display="sites")


#Permanova for stream_site Treatment vs. Control
adonis(Hess_Macros ~ stream_site, data=Hess_Site, permutations=999)

adonis(LM_Macros ~ stream_site_LM, data= LM_Site, permutations = 999)
## Check for interaction with Date
adonis(Hess_Macros~stream_site*Hess_Site$Date,data=Hess_Site,permutations = 999)

adonis(LM_Macros~stream_site_LM*LM_Site$Date,data=LM_Site,permutations = 999)
##Permanova with Date as covariate
adonis(Hess_Macros~Hess_Site$Date,data=Hess_Site,permutations = 999)

adonis(LM_Macros~LM_Site$Date,data=LM_Site,permutations = 999)
## Check for interaction with Date
adonis(Hess_Macros~Hess_Site$Date*stream_site,data=Hess_Site,permutations = 999)

adonis(LM_Macros~LM_Site$Date*stream_site_LM,data=LM_Site,permutations = 999)