#CPUE differences among sites#### otter_crab<- read.csv("Crab_data_otter_estuary.csv") str(otter_crab) library(ggplot2) library(nlme) #linear mixed models package #linear mixed model testing for differences between estuary, location is a random factor otter_lme<- lme(CPUE ~ 1 + Site, random = ~1|Location,data = otter_crab,na.action=na.omit) summary(otter_lme) anova(otter_lme) #Multiple comparison test require(multcomp) comp.site <- glht(otter_lme, linfct=mcp(Site="Tukey")) print(summary(comp.site)) #Linear model for CPUE, no replication of site at Drakes so can't treat site as random? otter_lm<- lm(CPUE ~ 1 + Otter + Site,data = otter_crab,na.action=na.omit) summary(otter_lm) anova(otter_lm) #Multiple comparison test require(multcomp) comp.site <- glht(otter_lm, linfct=mcp(Site="Tukey")) print(summary(comp.site)) #plot of crab biomass between Elkhorn 2016, SF Bay 2016 & 2017, Drakes 2016 mytheme<-theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) otter_crab$Site=factor(otter_crab$Site, levels=levels(otter_crab$Site)[c(1,4,3,2)]) CPUE_plot<-ggplot(otter_crab, aes(x=Site, y=CPUE)) + geom_boxplot() + theme_bw() +xlab("Site") + ylab("Edible crab biomass (g FW CPUE)")+ annotate("text",x=3, y=3500, label= "Otter: P < 0.0005; Site: P < 0.0005")+ annotate("text",x=1, y=3500, label= "a")+ annotate("text",x=2, y=2400, label= "b")+ annotate("text",x=3, y=1000, label= "c")+ annotate("text",x=4, y=500, label= "c")+ mytheme +geom_point(position = position_jitter(height = 0, width = 0.06), alpha = 0.5, size = 3) CPUE_plot #Crab sizes#### drakes_crab_size<- read.csv("Crab_data_2016_size.csv") str(drakes_crab_size) #C antennarius #linear mixed model testing for differences between estuary, location is a random factor drakes_crab_size2 <- subset(drakes_crab_size, Species=="R antennarium") drakes_Cant_lme<- lme(Size_mm ~ 1 + Site, random = ~1|Location,data = drakes_crab_size2,na.action=na.omit) summary(drakes_Cant_lme) anova(drakes_Cant_lme) #Multiple comparison test require(multcomp) comp.site <- glht(drakes_Cant_lme, linfct=mcp(Site="Tukey")) print(summary(comp.site)) #Linear model for C antennarius, no replication of site at Drakes and SF Bay so can't treat site as random? drakes_crab_size2 <- subset(drakes_crab_size, Species=="C antennarius") drakes_Cant_lm<- lm(Size_mm ~ Otter + Site,data = drakes_crab_size2,na.action=na.omit) summary(drakes_Cant_lm) anova(drakes_Cant_lm) #Multiple comparison test require(multcomp) comp.site <- glht(drakes_Cant_lm, linfct=mcp(Site="Tukey")) print(summary(comp.site)) #C productus #linear mixed model testing for differences between estuary, location is a random factor drakes_crab_size3 <- subset(drakes_crab_size, Species=="C productus") drakes_Cprod_lme<- lme(Size_mm ~ 1 + Site, random = ~1|Location,data = drakes_crab_size3,na.action=na.omit) summary(drakes_Cprod_lme) anova(drakes_Cprod_lme) #Multiple comparison test require(multcomp) comp.site <- glht(drakes_Cprod_lme, linfct=mcp(Site="Tukey")) print(summary(comp.site)) #Linear model for C productus, no replication of site at Drakes and SF Bay so can't treat site as random? drakes_crab_size3 <- subset(drakes_crab_size, Species=="C productus") drakes_Cprod_lm<- lm(Size_mm ~ Otter + Site,data = drakes_crab_size3,na.action=na.omit) summary(drakes_Cprod_lm) anova(drakes_Cprod_lm) #Multiple comparison test require(multcomp) comp.site <- glht(drakes_Cprod_lm, linfct=mcp(Site="Tukey")) print(summary(comp.site)) #Crab size plot####+theme_bw(base_size=18)+ mytheme<-theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) +theme_bw(base_size=18)+ drakes_crab_size$Site=factor(drakes_crab_size$Site, levels=levels(drakes_crab_size$Site)[c(1,5,4,2,3)]) size_plot<-ggplot(drakes_crab_size, aes(x=Site, y=Size_mm)) + geom_boxplot(aes(fill=Species)) + theme_bw() + theme(legend.position = c(0.9, 0.2)) +xlab("Site") + ylab("Carapice width (mm)") + annotate("text",x=2.5, y=120, label= "Otter effect: R antennarium & C productus; P < 0.0005")+ annotate("text",x=0.75, y=110, label= "a")+ annotate("text",x=1.75, y=82, label= "b")+ annotate("text",x=2.75, y=70, label= "bc")+ annotate("text",x=3.75, y=65, label= "c")+ annotate("text",x=4.75, y=120, label= "a")+ annotate("text",x=1.25, y=110, label= "x")+ annotate("text",x=2.25, y=82, label= "xy")+ annotate("text",x=3.25, y=70, label= "y")+ annotate("text",x=4.25, y=65, label= "y")+ annotate("text",x=5.25, y=120, label= "x")+ mytheme size_plot