diff --git a/Woody_Debris.R b/Woody_Debris.R
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-#Analysis of woody debris survey
-
-#Upload libraries
-library(ggplot2)
-library(nlme)
-library(nlme)
-library(lme4)
-library(lmerTest)
-#Upload data
-EAB_ILWD<-read.csv("~/Documents/MSU/Research/Surveying/Stream_Woody_Debris.csv", sep=",", header = T)
-#Create new variable for location
-EAB_ILWD$LocationID<-factor(paste(EAB_ILWD$Stream, EAB_ILWD$Gap, EAB_ILWD$Basket))
-#Create new variable for Area
-EAB_ILWD$Area<-as.numeric(2*pi*((EAB_ILWD$Diameter)/2)*EAB_ILWD$In_Stream_Length+2*pi*(EAB_ILWD$Diameter/2)^2)
-#Cast data into new data sheet with counts for each location
-EAB_LWD<-aggregate(EAB_ILWD$Area, by=list(EAB_ILWD$LocationID,EAB_ILWD$Species,EAB_ILWD$Basket,EAB_ILWD$Stream), FUN=sum)
-#Create Watershed variable
-EAB_LWD$Watershed<-as.character(EAB_LWD$Group.4)
-EAB_LWD$Watershed[EAB_LWD$Watershed == "Augusta Creek"]<-"Kalamazoo"
-EAB_LWD$Watershed[EAB_LWD$Watershed == "Seven Mile Creek"]<-"Kalamazoo"
-EAB_LWD$Watershed[EAB_LWD$Watershed == "Frayer Creek"]<-"Grand"
-EAB_LWD$Watershed[EAB_LWD$Watershed == "Sessions Creek"]<-"Grand"
-EAB_LWD$Watershed[EAB_LWD$Watershed == "Spring Creek"]<-"Clinton"
-EAB_LWD$Watershed[EAB_LWD$Watershed == "Stoney Creek"]<-"Clinton"
-#Create transect length variable
-EAB_LWD$Length<-as.character(EAB_LWD$Group.1)
-EAB_LWD$Length[EAB_LWD$Length == "Augusta Creek 1 Upstream"]<-"32"
-EAB_LWD$Length[EAB_LWD$Length == "Augusta Creek 1 Gap"]<-"71"
-EAB_LWD$Length[EAB_LWD$Length == "Augusta Creek 1 Downstream"]<-"30"
-EAB_LWD$Length[EAB_LWD$Length == "Augusta Creek 2 Upstream"]<-"38"
-EAB_LWD$Length[EAB_LWD$Length == "Augusta Creek 2 Gap"]<-"114"
-EAB_LWD$Length[EAB_LWD$Length == "Augusta Creek 2 Downstream"]<-"20"
-EAB_LWD$Length[EAB_LWD$Length == "Seven Mile Creek 1 Upstream"]<-"20"
-EAB_LWD$Length[EAB_LWD$Length == "Seven Mile Creek 1 Gap"]<-"33"
-EAB_LWD$Length[EAB_LWD$Length == "Seven Mile Creek 1 Downstream"]<-"21"
-EAB_LWD$Length[EAB_LWD$Length == "Seven Mile Creek 2 Upstream"]<-"29"
-EAB_LWD$Length[EAB_LWD$Length == "Seven Mile Creek 2 Gap"]<-"31"
-EAB_LWD$Length[EAB_LWD$Length == "Seven Mile Creek 2 Downstream"]<-"20"
-EAB_LWD$Length[EAB_LWD$Length == "Frayer Creek 1 Upstream"]<-"20"
-EAB_LWD$Length[EAB_LWD$Length == "Frayer Creek 1 Gap"]<-"104"
-EAB_LWD$Length[EAB_LWD$Length == "Frayer Creek 1 Downstream"]<-"87"
-EAB_LWD$Length[EAB_LWD$Length == "Frayer Creek 2 Upstream"]<-"36"
-EAB_LWD$Length[EAB_LWD$Length == "Frayer Creek 2 Gap"]<-"29"
-EAB_LWD$Length[EAB_LWD$Length == "Frayer Creek 2 Downstream"]<-"45"
-EAB_LWD$Length[EAB_LWD$Length == "Sessions Creek 1 Upstream"]<-"28"
-EAB_LWD$Length[EAB_LWD$Length == "Sessions Creek 1 Gap"]<-"26"
-EAB_LWD$Length[EAB_LWD$Length == "Sessions Creek 1 Downstream"]<-"20"
-EAB_LWD$Length[EAB_LWD$Length == "Sessions Creek 2 Upstream"]<-"20"
-EAB_LWD$Length[EAB_LWD$Length == "Sessions Creek 2 Gap"]<-"20"
-EAB_LWD$Length[EAB_LWD$Length == "Sessions Creek 2 Downstream"]<-"40"
-EAB_LWD$Length[EAB_LWD$Length == "Spring Creek 1 Upstream"]<-"54"
-EAB_LWD$Length[EAB_LWD$Length == "Spring Creek 1 Gap"]<-"202"
-EAB_LWD$Length[EAB_LWD$Length == "Spring Creek 1 Downstream"]<-"73"
-EAB_LWD$Length[EAB_LWD$Length == "Spring Creek 2 Upstream"]<-"36"
-EAB_LWD$Length[EAB_LWD$Length == "Spring Creek 2 Gap"]<-"34"
-EAB_LWD$Length[EAB_LWD$Length == "Spring Creek 2 Downstream"]<-"58"
-#Delete stoney creek
-EAB_LWDS<-EAB_LWD[-c(52,53,54,55,56),]
-#Create new dataset for total woody debris
-EAB_TWD<-aggregate(EAB_LWDS$x, by=list(EAB_LWDS$Group.4,EAB_LWDS$Group.1,EAB_LWDS$Group.3,EAB_LWDS$Watershed, EAB_LWDS$Length), FUN=sum)
-EAB_TWD$TWDAREA<-as.numeric(EAB_TWD$Group.5)
-#Create new variable for total woody debris density
-EAB_TWD$TWD_Density<-as.numeric(EAB_TWD$x/EAB_TWD$TWDAREA)
-#order for watershed
-EAB_TWD$Watershed<-factor(EAB_TWD$Group.4, levels=c("Kalamazoo", "Grand", "Clinton"))
-#order for stream location
-EAB_TWD$GapLocation<-factor(EAB_TWD$Group.3, levels=c("Upstream", "Gap", "Downstream"))
-#Plot for total woody debris density
-ggplot(EAB_TWD, aes(x=GapLocation, y=TWD_Density, fill=Watershed)) + 
-  geom_boxplot() +
-  ylab("TWD area per m in stream") +
-  xlab("Gap Location")+
-  theme_classic()+
-  theme(axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),
-        axis.text.x=element_text(size=14),axis.text.y = element_text(size=14),
-        legend.title=element_text(size=20),legend.text = element_text(size=16))+
-  scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))
-#Some basic stats
-anova(lmer(TWD_Density ~ GapLocation + (1|Watershed), EAB_TWD))
-
-
-################################
-#Create new variable for ash woody debris density
-EAB_LWD$AWD_Density<-as.numeric(EAB_LWD$Number_Ash_LWD/EAB_LWD$Transect_Length_m)
-#Create new variable for ratio of ash to total woody debris
-EAB_LWD$Ash_Ratio<-as.numeric(EAB_LWD$Number_Ash_LWD/EAB_LWD$Total_LWD)
-#Create new variable for ash density percent
-EAB_LWD$AshPer<-as.numeric(EAB_LWD$AWD_Density/EAB_LWD$TWD_Density)
-#order for upstream, gap, downstream
-str(EAB_LWD)
-EAB_LWD$Gap_location<- factor(EAB_LWD$Gap_location, levels=c("Upstream", "Gap", "Downstream"))
-#make gap number a factor
-EAB_LWD$Gap_number<-as.factor(EAB_LWD$Gap_number)
-#order for watershed
-EAB_LWD$Watershed<-factor(EAB_LWD$Watershed, levels=c("Kalamazoo", "Grand", "Clinton"))
-
-#Plots for percent ash
-#Create box plots
-ggplot(EAB_LWD, aes(x=Gap_location, y=Ash_Ratio, fill=Watershed)) + 
-  geom_boxplot() +
-  ylab("Percent Ash") +
-  xlab("Gap Location")+
-  theme_classic()+
-  theme(axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),
-        axis.text.x=element_text(size=14),axis.text.y = element_text(size=14),
-        legend.title=element_text(size=20),legend.text = element_text(size=16))+
-  scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))
-
-
-#Create heat maps
-#using geom_tile
-#Base plot
-AWD<-ggplot(EAB_LWD, aes(x=Watershed, y=Gap_location, fill=Ash_Ratio))
-AWD+
-  geom_tile()+
-  xlab("Watershed")+
-  scale_x_discrete(limits=c("Kalamazoo", "Grand", "Clinton"))+
-  ylab("Gap Location")+
-  labs(fill="Percent Ash
-Woody Debris")+
-  scale_fill_gradient(low="#f7fcf5", high="#00441b")+
-  theme_classic()+
-  theme(axis.title = element_text(size = rel(2)))+
-  theme(axis.text = element_text(size = rel(1.5)))+
-  theme(legend.title = element_text(size=rel(1.5)))+
-  theme(legend.text = element_text(size=rel(1)))
-
-#Stats for percent ash in stream
-
-#test for normality of distribution
-shapiro.test(EAB_LWD$AshPer)
-#We reject the null hypothesis and determine not normally distributed
-#Transform arcsin function
-EAB_LWD$arcsinAshPer<-asin(EAB_LWD$AshPer)
-shapiro.test(EAB_LWD$arcsinAshPer)
-#test for outliers
-dotchart(EAB_LWD$arcsinAshPer)
-#appears to be one outlier
-plot(EAB_LWD$arcsinAsh_Ratio)
-identify(EAB_LWD$arcsinAsh_Ratio)
-#Create new data frame with outlier deleted (augusta creek gap 2 downstream)
-EAB_LWD_NO<-EAB_LWD[-c(12),]
-
-AR<-glmer(Ash_Ratio ~ Gap_location + Watershed + Gap_number + (1|Stream_name), family=binomial, data = EAB_LWD_NO)
-summary(AR)
-#no significance, possibly too few data points
-
-drop1(AR)
-#run model again without gap_number
-AR1<-glmer(Ash_Ratio ~ Gap_location + Watershed + (1|Stream_name), family=binomial, data = EAB_LWD_NO)
-summary(AR1)
-
-drop1(AR1)
-
-#try model with transformed data
-ART<-lm(arcsinAsh_Ratio ~ Gap_location + Watershed, data = EAB_LWD_NO)
-summary(ART)
-alias(ART)
-anova(lmer(arcsinAsh_Ratio ~ Gap_location + (1|Gap_number/Stream_name), EAB_LWD))
-
-#Now look at decay levels
-ggplot(EAB_LWD, aes(x=Gap_location, y=Average_Decay_Level, fill=Watershed)) + 
-  geom_boxplot() +
-  ylab("Decay Level") +
-  xlab("Gap Location")+
-  theme_classic()+
-  theme(axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),
-        axis.text.x=element_text(size=14),axis.text.y = element_text(size=14),
-        legend.title=element_text(size=20),legend.text = element_text(size=16))+
-  scale_fill_manual(values=c("#999999", "#E69F00", "#56B4E9"))
-
-#Stats for decay level
-#test for normality of distribution
-shapiro.test(EAB_LWD$Average_Decay_Level)
-#Not normal
-anova(lmer(Average_Decay_Level ~ Gap_location + (1|Gap_number/Stream_name), EAB_LWD))
-
-#analyze ash density
-#Create line plots
-anova(lmer(AWD_Density ~ Gap_location + (1|Gap_number/Stream_name), EAB_LWD))
-ggplot(EAB_LWD, aes(x=Gap_location, y=AWD_Density, colour=Watershed)) + 
-  geom_boxplot() +
-  ylab("Ash Density") +
-  xlab("Gap Location")+
-  theme_classic()+
-  theme(axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),
-        axis.text.x=element_text(size=14),axis.text.y = element_text(size=14),
-        legend.title=element_text(size=20),legend.text = element_text(size=16))+
-  scale_color_manual(values=wes_palette(n=3, name="GrandBudapest"))