75
76 p11<-p11+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
gtb<-grid.arrange(p11, p12, ncol=2, widths=c(2, 1.4))
#Biomass Scaridae
PQL <- glmmPQL(Biomass.Scaridae+1~Fished.Unfished+Polunin.1+Fished.Unfished*Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL1 <- glmmPQL(Biomass.Scaridae+1~Fished.Unfished+Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL2 <- glmmPQL(Biomass.Scaridae+1~Fished.Unfished, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL3 <- glmmPQL(Biomass.Scaridae+1~Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
#Test residuals
qqnorm(log10(resid(PQL))) hist(log10(PQL$residuals))
#Adjusted means
PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
#Plots
p2<-ggplot(PQL.sum2, aes(Fished.Unfished, response, fill=Fished.Unfished)) +geom_bar(stat="identity") +geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4)) + scale_fill_discrete() +
scale_y_continuous(limits=c(0,1500), breaks=seq(0,1500, by = 250))+ labs(x="Zone", y="Scaridae biomass (g/100m2)") + theme_bw()+ guides(fill=FALSE) +theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9),
axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p21<-p2+xlab(NULL)+ylab(NULL)
p22<-ggplot(y=Biomass.Scaridae, x=Polunin.1, data=Per.Period.Saba.1, stat="identity", aes(x = Polunin.1, y = Biomass.Scaridae, fill=Fished.Unfished)) + geom_boxplot() + facet_wrap(~Fished.Unfished) + scale_fill_discrete()+
scale_y_continuous(limits=c(0,7000), breaks=seq(0,7000, by = 1000))+ ylab("Scaridae biomass (g/100M^2)") + xlab("Polunin score") + theme_bw()+ guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p22<-p22+xlab(NULL)+ylab(NULL)+ theme(strip.background = element_blank(), strip.text.x = element_blank())
g1<-grid.arrange(p22, p21, ncol=2, widths=c(2, 1.4), left="Scaridae")
#Biomass Acanthuridae
PQL <- glmmPQL(Biomass.Acanthuridae+1~Fished.Unfished+Polunin.1+Fished.Unfished*Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL1 <- glmmPQL(Biomass.Acanthuridae+1~Fished.Unfished+Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL2 <- glmmPQL(Biomass.Acanthuridae+1~Fished.Unfished, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL3 <- glmmPQL(Biomass.Acanthuridae+1~Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
#Test residuals
qqnorm(log10(resid(PQL))) hist(log10(PQL$residuals))
77
#Adjusted means
PQL.ls1<-lsmeans(PQL1, "Polunin.1", by="Fished.Unfished")
PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum<-summary(PQL.ls1, infer=c(TRUE, TRUE), level=0.95, adjust="bon", by="Fished.Unfished", type="response")
PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
#Plots
p3<-ggplot(PQL.sum2, aes(Fished.Unfished, response,
fill=Fished.Unfished))+geom_bar(stat="identity")+geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4)) + scale_fill_discrete() + scale_y_continuous(limits=c(0,2500), breaks=seq(0,2500, by = 500))+ labs(x="Zone", y="Acanthuridae biomass (g/100m2)") +theme_bw()+
guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p31<-p3+xlab(NULL)+ylab(NULL)
# p1<-ggplot(PQL.sum, aes(Polunin.1, response,
fill=Fished.Unfished))+geom_bar(stat="identity")+geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4)) + facet_wrap(~Fished.Unfished)+scale_fill_discrete() + scale_y_continuous(limits=c(0,10000), breaks=seq(0,10000, by = 1000))+ labs(x="Zone", y="Acanthurridae biomass (g/100m2)") +theme_bw()+ggtitle("B")+ guides(fill=FALSE)
p33<-ggplot(y=Biomass.Acanthuridae, x=Polunin.1, data=Per.Period.Saba.1, stat="identity", aes(x = Polunin.1, y = Biomass.Acanthuridae, fill=Fished.Unfished)) + geom_boxplot() + facet_wrap(~Fished.Unfished) + scale_fill_discrete()+
scale_y_continuous(limits=c(0,7500), breaks=seq(0,7500, by = 1000))+ ylab("Acanthuridae biomass (g/100M^2)") + xlab("Polunin score") + theme_bw()+
guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p33<-p33+xlab(NULL)+ylab(NULL)+ theme(strip.background = element_blank(), strip.text.x = element_blank())
g2<-grid.arrange(p33, p31, ncol=2, widths=c(2, 1.4), left="Acanthuridae")
#Biomass Lutjanidae
PQL <- glmmPQL(Biomass.Lutjanidae+1~Fished.Unfished+Polunin.1+Fished.Unfished*Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL1 <- glmmPQL(Biomass.Lutjanidae+1~Fished.Unfished+Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL2 <- glmmPQL(Biomass.Lutjanidae+1~Fished.Unfished, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL3 <- glmmPQL(Biomass.Lutjanidae+1~Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
#Test residuals
qqnorm(log10(resid(PQL))) hist(log10(PQL$residuals))
#Adjusted means
PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
#Plots
78 p4<-ggplot(PQL.sum2, aes(Fished.Unfished, response, fill=Fished.Unfished))
+geom_bar(stat="identity")+geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4)) + scale_fill_discrete() + scale_y_continuous(limits=c(0,2000), breaks=seq(0,2000, by = 500))+ labs(x="Zone", y="Lutjanidae biomass (g/100m2)") +theme_bw()+ guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9),
axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p41<-p4+xlab(NULL)+ylab(NULL)
p44<-ggplot(y=Biomass.Lutjanidae, x=Polunin.1, data=Per.Period.Saba.1, stat="identity", aes(x = Polunin.1, y = Biomass.Lutjanidae, fill=Fished.Unfished)) + geom_boxplot() + facet_wrap(~Fished.Unfished) + scale_fill_discrete()+
scale_y_continuous(limits=c(0,1500), breaks=seq(0,1500, by = 250))+ ylab("Lutjanidae biomass (g/100M^2)") + xlab("Polunin score") + theme_bw()+ guides(fill=FALSE) +
theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p44<-p44+xlab(NULL)+ylab(NULL)+ theme(strip.background = element_blank(), strip.text.x = element_blank())
g3<-grid.arrange(p44, p41, ncol=2, widths=c(2, 1.4), left="Lutjanidae")
#Biomass Haemulidae
PQL <- glmmPQL(Biomass.Haemulidae+1~Fished.Unfished+Polunin.1+Fished.Unfished*Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL1 <- glmmPQL(Biomass.Haemulidae+1~Fished.Unfished+Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL2 <- glmmPQL(Biomass.Haemulidae+1~Fished.Unfished, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL3 <- glmmPQL(Biomass.Haemulidae+1~Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
#Test residuals
qqnorm(log10(resid(PQL))) hist(log10(PQL$residuals))
#Adjusted means
PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
#Plots
p5<-ggplot(PQL.sum2, aes(Fished.Unfished, response, fill=Fished.Unfished))+
geom_bar(stat="identity")+geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4)) + scale_fill_discrete() + scale_y_continuous(limits=c(0,2000), breaks=seq(0,2000, by = 500))+ labs(x="Zone", y="Haemulidae biomass (g/100m2)") +theme_bw()+ guides(fill=FALSE)+ theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9),
axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p51<-p5+xlab(NULL)+ylab(NULL)
p55<-ggplot(y=Biomass.Haemulidae, x=Polunin.1, data=Per.Period.Saba.1, stat="identity", aes(x = Polunin.1, y = Biomass.Haemulidae, fill=Fished.Unfished)) + geom_boxplot() + facet_wrap(~Fished.Unfished) + scale_fill_discrete()+
scale_y_continuous(limits=c(0,1750), breaks=seq(0,1750, by = 250))+ ylab("Haemulidae biomass (g/100M^2)") + xlab("Polunin score") + theme_bw()+
guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p55<-p55+xlab(NULL)+ylab(NULL)+ theme(strip.background = element_blank(), strip.text.x = element_blank())
79 g4<-grid.arrange(p55, p51, ncol=2, widths=c(2, 1.4), left="Haemulidae")
#Biomass Serranidae
PQL <- glmmPQL(Biomass.Serranidae+1~Fished.Unfished+Polunin.1+Fished.Unfished*Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL1 <- glmmPQL(Biomass.Serranidae+1~Fished.Unfished+Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL2 <- glmmPQL(Biomass.Serranidae+1~Fished.Unfished, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL3 <- glmmPQL(Biomass.Serranidae+1~Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
#Test residuals
qqnorm(log10(resid(PQL))) hist(log10(PQL$residuals))
#Adjusted means
PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
#Plots
p6<-ggplot(PQL.sum2, aes(Fished.Unfished, response,
fill=Fished.Unfished))+geom_bar(stat="identity")+geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4)) + scale_fill_discrete() + scale_y_continuous(limits=c(0,2000), breaks=seq(0,2000, by = 500))+ labs(x="Zone", y="Serranidae biomass (g/100m2)") +theme_bw()+
guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p61<-p6+ylab(NULL)
p66<-ggplot(y=Biomass.Serranidae, x=Polunin.1, data=Per.Period.Saba.1, stat="identity", aes(x = Polunin.1, y = Biomass.Serranidae, fill=Fished.Unfished)) + geom_boxplot() + facet_wrap(~Fished.Unfished) + scale_fill_discrete()+
scale_y_continuous(limits=c(0,3500), breaks=seq(0,35500, by = 500))+ ylab("Serranidae biomass (g/100M^2)") + xlab("Polunin score") + theme_bw()+ guides(fill=FALSE)+
theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p66<- p66+ylab(NULL)+ theme(strip.background = element_blank(), strip.text.x = element_blank())
g5<-grid.arrange(p66, p61, ncol=2, widths=c(2, 1.4), left="Serranidae")
grid.arrange(g1,g2,g3,g4,g5, ncol=1, left=textGrob(label=expression(paste("Biomass per family ", "(g/100",m^2,")"), sep=""),gp=gpar(fontsize=14),rot=90))
#----Density
#Total density
PQL <- glmmPQL(NumFish.Indiv~Fished.Unfished+Polunin.1+Fished.Unfished*Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL1 <- glmmPQL(NumFish.Indiv~Fished.Unfished+Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL2 <- glmmPQL(NumFish.Indiv~Fished.Unfished, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
80 PQL3 <- glmmPQL(NumFish.Indiv~Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1,
verbose=FALSE)
#Test residuals
qqnorm(log10(resid(PQL))) hist(PQL$residuals)
#Adjusted means
PQL.ls1<-lsmeans(PQL, "Polunin.1", by="Fished.Unfished") PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum<-summary(PQL.ls1, infer=c(TRUE, TRUE), level=0.95, adjust="bon", by="Fished.Unfished", type="response") PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
#Plots
p7<-ggplot(PQL.sum, aes(Polunin.1, response, fill=Fished.Unfished))+ geom_bar(stat="identity")
+geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4))+ facet_wrap(~Fished.Unfished) + scale_fill_discrete() + scale_y_continuous(limits=c(0,300), breaks=seq(0,300, by = 50))+ labs(x="Polunin score", y="Total fish density (#/100m2)") +theme_bw()+ guides(fill=FALSE)
p71<-p7+ylab(NULL)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
# ggplot(PQL.sum2, aes(Fished.Unfished, response, fill=Fished.Unfished))+ geom_bar(stat="identity") +
geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4)) + scale_fill_discrete() + scale_y_continuous(limits=c(0,120), breaks=seq(0,120, by = 20))+ labs(x="Zone", y="Total fish density (#/100m2)") +theme_bw()+ggtitle("B")+ guides(fill=FALSE)
p77<-ggplot(y=NumFish.Indiv, x=Polunin.1, data=Per.Period.Saba.1, stat="identity", aes(x = Polunin.1, y = NumFish.Indiv, fill=Fished.Unfished)) + geom_boxplot() + facet_wrap(~Fished.Unfished) + scale_fill_discrete()+
scale_y_continuous(limits=c(0,300), breaks=seq(0,300, by = 50))+ ylab(expression(paste("Total fish density ",
"(#/100",m^2,")", sep=""))) + xlab("Polunin score") + theme_bw()+ guides(fill=FALSE)
p77<-p77+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
gtd<-grid.arrange(p77, p71, ncol=2)
#Scaridae density
PQL <- glmmPQL(NumFish.Scaridae+1~Fished.Unfished+Polunin.1+Fished.Unfished*Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL1 <- glmmPQL(NumFish.Scaridae+1~Fished.Unfished+Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL2 <- glmmPQL(NumFish.Scaridae+1~Fished.Unfished, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL3 <- glmmPQL(NumFish.Scaridae+1~Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
#Test residuals
qqnorm(log10(resid(PQL))) hist(PQL$residuals)
#Adjusted means
PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
81
#Plots
p8<-ggplot(PQL.sum2, aes(Fished.Unfished, response,
fill=Fished.Unfished))+geom_bar(stat="identity")+geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4)) + scale_fill_discrete() + scale_y_continuous(limits=c(0,7), breaks=seq(0,7, by = 1))+ labs(x="Zone", y="Scaridae density (#/100m2)") +theme_bw()+ guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p81<-p8+xlab(NULL)+ylab(NULL)
p88<-ggplot(y=NumFish.Scaridae, x=Polunin.1, data=Per.Period.Saba.1, stat="identity", aes(x = Polunin.1, y = NumFish.Scaridae, fill=Fished.Unfished)) + geom_boxplot() + facet_wrap(~Fished.Unfished)+ scale_fill_discrete()+
scale_y_continuous(limits=c(0,20), breaks=seq(0,20, by = 4)) + ylab("Scaridae density (#/100M^2)") + xlab("Polunin score") + theme_bw()+ guides(fill=FALSE) + theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9),
axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p88<-p88+xlab(NULL)+ylab(NULL)+ theme(strip.background = element_blank(), strip.text.x = element_blank())
gd1<-grid.arrange(p88, p81, ncol=2, widths=c(2, 1.4), left="Scaridae")
#Acanthuridae density
PQL <- glmmPQL(NumFish.Acanthuridae+1~Fished.Unfished+Polunin.1+Fished.Unfished*Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL1 <- glmmPQL(NumFish.Acanthuridae+1~Fished.Unfished+Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL2 <- glmmPQL(NumFish.Acanthuridae+1~Fished.Unfished, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL3 <- glmmPQL(NumFish.Acanthuridae+1~Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
#Test residuals
qqnorm(log10(resid(PQL))) hist(PQL$residuals)
#Adjusted means
PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
#Plots
p9<-ggplot(PQL.sum2, aes(Fished.Unfished, response,
fill=Fished.Unfished))+geom_bar(stat="identity")+geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4)) + scale_fill_discrete() + scale_y_continuous(limits=c(0,20), breaks=seq(0,20, by = 5))+ labs(x="Zone", y="Acanthurdae density (#/100m2)") +theme_bw()+ guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p91<-p9+xlab(NULL)+ylab(NULL)
p99<-ggplot(y=NumFish.Acanthuridae, x=Polunin.1, data=Per.Period.Saba.1, stat="identity", aes(x = Polunin.1, y = NumFish.Acanthuridae, fill=Fished.Unfished)) + geom_boxplot() + facet_wrap(~Fished.Unfished)+ scale_fill_discrete()+
scale_y_continuous(limits=c(0,60), breaks=seq(0,60, by = 10)) + ylab("Acanthuridae density (#/100M^2)") + xlab("Polunin score") + theme_bw()+ guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p99<-p99+xlab(NULL)+ylab(NULL)+ theme(strip.background = element_blank(), strip.text.x = element_blank())
gd2<-grid.arrange(p99, p91, ncol=2, widths=c(2,1.4), left="Acanthuridae")
82
#Lutjanidae density
PQL <- glmmPQL(NumFish.Lutjanidae+1~Fished.Unfished+Polunin.1+Fished.Unfished*Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL1 <- glmmPQL(NumFish.Lutjanidae+1~Fished.Unfished+Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL2 <- glmmPQL(NumFish.Lutjanidae+1~Fished.Unfished, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL3 <- glmmPQL(NumFish.Lutjanidae+1~Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
#Test residuals
qqnorm(log10(resid(PQL))) hist(PQL$residuals)
#Adjusted means
PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
#Plots
p10<-ggplot(PQL.sum2, aes(Fished.Unfished, response,
fill=Fished.Unfished))+geom_bar(stat="identity")+geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4)) + scale_fill_discrete() + scale_y_continuous(limits=c(0,7), breaks=seq(0,7, by = 1))+ labs(x="Zone", y="Lutjanidae density (#/100m2)") +theme_bw()+ guides(fill=FALSE)+ theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p101<-p10+xlab(NULL)+ylab(NULL)
p110<-ggplot(y=NumFish.Lutjanidae, x=Polunin.1, data=Per.Period.Saba.1, stat="identity", aes(x = Polunin.1, y = NumFish.Lutjanidae, fill=Fished.Unfished)) + geom_boxplot() + facet_wrap(~Fished.Unfished)+ scale_fill_discrete()+
scale_y_continuous(limits=c(0,12), breaks=seq(0,12, by = 2)) + ylab("Lutjanidae density (#/100M^2)") + xlab("Polunin score") + theme_bw()+ guides(fill=FALSE)+ theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p110<-p110+xlab(NULL)+ylab(NULL)+ theme(strip.background = element_blank(), strip.text.x = element_blank())
gd3<-grid.arrange(p110, p101, ncol=2, widths=c(2,1.4), left="Lutjanidae")
#Haemulidae density
PQL <- glmmPQL(NumFish.Haemulidae+1~Fished.Unfished+Polunin.1+Fished.Unfished*Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL1 <- glmmPQL(NumFish.Haemulidae+1~Fished.Unfished+Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL2 <- glmmPQL(NumFish.Haemulidae+1~Fished.Unfished, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL3 <- glmmPQL(NumFish.Haemulidae+1~Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
#Test residuals
qqnorm(log10(resid(PQL))) hist(PQL$residuals)
#Adjusted means
PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
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#Plots
p11<-ggplot(PQL.sum2, aes(Fished.Unfished, response,
fill=Fished.Unfished))+geom_bar(stat="identity")+geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4)) + scale_fill_discrete() + scale_y_continuous(limits=c(0,20), breaks=seq(0,20, by = 5))+ labs(x="Zone", y="Haemulidae density (#/100m2)") +theme_bw()+ guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p111<-p11+xlab(NULL)+ylab(NULL)
p1111<-ggplot(y=NumFish.Haemulidae, x=Polunin.1, data=Per.Period.Saba.1, stat="identity", aes(x = Polunin.1, y = NumFish.Haemulidae, fill=Fished.Unfished)) + geom_boxplot() + facet_wrap(~Fished.Unfished)+ scale_fill_discrete()+
scale_y_continuous(limits=c(0,8), breaks=seq(0,8, by = 2)) + ylab("Haemulidae density (#/100M^2)") + xlab("Polunin score") + theme_bw()+ guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9),
axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p1111<-p1111+xlab(NULL)+ylab(NULL)+ theme(strip.background = element_blank(), strip.text.x = element_blank())
gd4<-grid.arrange(p1111, p111, ncol=2, widths=c(2,1.4), left="Haemulidae")
#Serranidae density
PQL <- glmmPQL(NumFish.Serranidae+1~Fished.Unfished+Polunin.1+Fished.Unfished*Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL1 <- glmmPQL(NumFish.Serranidae+1~Fished.Unfished+Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL2 <- glmmPQL(NumFish.Serranidae+1~Fished.Unfished, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL3 <- glmmPQL(NumFish.Serranidae+1~Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
#Test residuals
qqnorm(log10(resid(PQL))) hist(PQL$residuals)
#Adjusted means
PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
#Plots
p12<-ggplot(PQL.sum2, aes(Fished.Unfished, response,
fill=Fished.Unfished))+geom_bar(stat="identity")+geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4)) + scale_fill_discrete() + scale_y_continuous(limits=c(0,6), breaks=seq(0,6, by = 1))+ labs(x="Zone", y="Serranidae density (#/100m2)") +theme_bw()+ guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p121<-p12+ylab(NULL)
p1212<-ggplot(y=NumFish.Serranidae, x=Polunin.1, data=Per.Period.Saba.1, stat="identity", aes(x = Polunin.1, y = NumFish.Serranidae, fill=Fished.Unfished)) + geom_boxplot() + facet_wrap(~Fished.Unfished)+ scale_fill_discrete()+
scale_y_continuous(limits=c(0,20), breaks=seq(0,20, by = 5)) + ylab("Serranidae density (#/100M^2)") + xlab("Polunin score") + theme_bw()+ guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p1212<-p1212+ylab(NULL)+ theme(strip.background = element_blank(), strip.text.x = element_blank())
gd5<-grid.arrange(p1212, p121, ncol=2, widths=c(2,1.4), left="Serranidae")
84 grid.arrange(gd1,gd2,gd3,gd4,gd5, ncol=1, left=textGrob(label=expression(paste("Density per family ", "(#/100",m^2,")"), sep=""),gp=gpar(fontsize=14),rot=90))
#---Benthic cover
#Coral cover
PQL <- glmmPQL(Coral.cover/100~Fished.Unfished+Polunin.1+Fished.Unfished*Polunin.1, ~1 | Location, family=quasibinomial(link="logit"), data=Per.Period.Saba.1, verbose=FALSE)
PQL1 <- glmmPQL(Coral.cover/100~Fished.Unfished+Polunin.1, ~1 | Location, family=quasibinomial(link="logit"), data=Per.Period.Saba.1, verbose=FALSE)
PQL2 <- glmmPQL(Coral.cover/100~Fished.Unfished, ~1 | Location, family=quasibinomial(link="logit"), data=Per.Period.Saba.1, verbose=FALSE)
PQL3 <- glmmPQL(Coral.cover/100~Polunin.1, ~1 | Location, family=quasibinomial(link="logit"), data=Per.Period.Saba.1, verbose=FALSE)
#Test residuals
qqnorm(log10(resid(PQL))) hist(PQL$residuals)
#Adjusted means
PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
#Plots
p01<-ggplot(PQL.sum2, aes(Fished.Unfished, prob*100,
fill=Fished.Unfished))+geom_bar(stat="identity")+geom_errorbar(aes(ymin=lower.CL*100, ymax=upper.CL*100, width=.4)) + scale_fill_discrete() + scale_y_continuous(limits=c(0,10), breaks=seq(0,10, by = 2))+ labs(x="Zone", y="Coral cover (%)") +theme_bw()+ guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9),
axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p011<-p01+xlab(NULL)+ylab(NULL)
p0111<-ggplot(y=Coral.cover, x=Polunin.1, data=Per.Period.Saba.1, stat="identity", aes(x = Polunin.1, y = Coral.cover, fill=Fished.Unfished)) + geom_boxplot() + facet_wrap(~Fished.Unfished)+ scale_fill_discrete()+
scale_y_continuous(limits=c(0,16), breaks=seq(0,16, by = 2)) + ylab("Coral cover (%)") + xlab("Polunin score") + theme_bw()+ guides(fill=FALSE) +theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p0111<-p0111+xlab(NULL)+ylab(NULL) + theme(strip.background = element_blank(), strip.text.x = element_blank())
gcc<-grid.arrange(p0111, p011, ncol=2, widths=c(2,1.4), left="Coral \n cover (%)")
#Macroalgae cover
PQL <- glmmPQL(Macroalgae.cover/100~Fished.Unfished+Polunin.1+Fished.Unfished*Polunin.1, ~1 | Location, family=quasibinomial(link="logit"), data=Per.Period.Saba.1, verbose=FALSE)
PQL1 <- glmmPQL(Macroalgae.cover/100~Fished.Unfished+Polunin.1, ~1 | Location, family=quasibinomial(link="logit"), data=Per.Period.Saba.1, verbose=FALSE)
PQL2 <- glmmPQL(Macroalgae.cover/100~Fished.Unfished, ~1 | Location, family=quasibinomial(link="logit"), data=Per.Period.Saba.1, verbose=FALSE)
PQL3 <- glmmPQL(Macroalgae.cover/100~Polunin.1, ~1 | Location, family=quasibinomial(link="logit"), data=Per.Period.Saba.1, verbose=FALSE)
#Test residuals
qqnorm(log10(resid(PQL))) hist(PQL$residuals)
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#Adjusted means
PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
#Plots
p02<-ggplot(PQL.sum2, aes(Fished.Unfished, prob*100,
fill=Fished.Unfished))+geom_bar(stat="identity")+geom_errorbar(aes(ymin=lower.CL*100, ymax=upper.CL*100, width=.4)) + scale_fill_discrete() + scale_y_continuous(limits=c(0,24), breaks=seq(0,24, by = 4))+ labs(x="Zone", y="Macroalgae cover (%)") +theme_bw()+ guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p022<-p02+xlab(NULL)+ylab(NULL)
p0222<-ggplot(y=Macroalgae.cover, x=Polunin.1, data=Per.Period.Saba.1, stat="identity", aes(x = Polunin.1, y = Macroalgae.cover, fill=Fished.Unfished)) + geom_boxplot() + facet_wrap(~Fished.Unfished)+ scale_fill_discrete()+
scale_y_continuous(limits=c(0,60), breaks=seq(0,60, by = 10)) + ylab("Macroalgae cover (%)") + xlab("Polunin score") + theme_bw()+ guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9),
axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p0222<-p0222+xlab(NULL)+ylab(NULL)+ theme(strip.background = element_blank(), strip.text.x = element_blank())
gmc<-grid.arrange(p0222, p022, ncol=2, widths=c(2,1.4), left="Macroalgae \n cover (%)")
#Macroalgae height
PQL <- glmmPQL(Algae.height~Fished.Unfished+Polunin.1+Fished.Unfished*Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL1 <- glmmPQL(Algae.height~Fished.Unfished+Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL2 <- glmmPQL(Algae.height~Fished.Unfished, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL3 <- glmmPQL(Algae.height~Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
#Test residuals
qqnorm(log10(resid(PQL))) hist(PQL$residuals)
#Adjusted means
PQL.ls1<-lsmeans(PQL, "Polunin.1", by="Fished.Unfished") PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum<-summary(PQL.ls1, infer=c(TRUE, TRUE), level=0.95, adjust="bon", by="Fished.Unfished", type="response") PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
#Plots
p03<-ggplot(PQL.sum2, aes(Fished.Unfished, response,
fill=Fished.Unfished))+geom_bar(stat="identity")+geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4)) + scale_fill_discrete() + scale_y_continuous(limits=c(0,3), breaks=seq(0,3, by = 0.5))+ labs(x="Zone", y="Macroalgae height (cm)") +theme_bw()+ guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9), axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p033<-p03+xlab(NULL)+ylab(NULL)
p0333<-ggplot(y=Algae.height, x=Polunin.1, data=Per.Period.Saba.1, stat="identity", aes(x = Polunin.1, y = Algae.height, fill=Fished.Unfished)) + geom_boxplot() + facet_wrap(~Fished.Unfished)+ scale_fill_discrete()+
86 scale_y_continuous(limits=c(0,10), breaks=seq(0,10, by = 2)) + ylab("Macroalgae height (cm)") + xlab("Polunin score") + theme_bw()+ guides(fill=FALSE)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9),
axis.title.x=element_text(size=11), axis.text.x=element_text(size=9))
p0333<-p0333+xlab(NULL)+ylab(NULL)+ theme(strip.background = element_blank(), strip.text.x = element_blank())
gmh<-grid.arrange(p0333, p033, ncol=2, widths=c(2,1.4), left="Macroalgae \n height (cm)")
#Complexity
PQL2 <- glmmPQL(Polunin~Fished.Unfished, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba, verbose=FALSE)
#Adjusted means
PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
#Plots
phc<-ggplot(PQL.sum2, aes(Fished.Unfished, response,
fill=Fished.Unfished))+geom_bar(stat="identity")+geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4)) + scale_fill_discrete() + scale_y_continuous(limits=c(0,4), breaks=seq(0,4, by = 1))+ labs(x="Zone", y="Habitat complexity (polunin)") +theme_bw()+ guides(fill=FALSE)
phc<-phc+ylab(NULL)+theme(axis.title.y=element_text(size=11),axis.text.y=element_text(size=9),
axis.title.x=element_text(size=11), axis.text.x=element_text(size=9), legend.title = element_text(size=11), legend.text = element_text(size = 9))
p2<-ggplot(y=Polunin, x=Fished.Unfished, data=Per.Period.Saba.1, stat="identity", aes(x = Fished.Unfished, y = Polunin, fill=Fished.Unfished)) + geom_boxplot() + scale_fill_discrete()+ scale_y_continuous(limits=c(0,4), breaks=seq(0,4, by = 1)) + ylab("Habitat complexity (polunin)") + xlab("Zone") + theme_bw()+ggtitle("A")+ guides(fill=FALSE)
grid.arrange(p2, p1, ncol=2, widths=c(1,1))
#Coral recruits
PQL <- glmmPQL(NumRecruits.Indiv+1~Fished.Unfished+Polunin.1+Fished.Unfished*Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL1 <- glmmPQL(NumRecruits.Indiv+1~Fished.Unfished+Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL2 <- glmmPQL(NumRecruits.Indiv+1~Fished.Unfished, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
PQL3 <- glmmPQL(NumRecruits.Indiv+1~Polunin.1, ~1 | Location, family=gaussian(link="log"), data=Per.Period.Saba.1, verbose=FALSE)
#Test residuals
qqnorm(log10(resid(PQL))) hist(PQL$residuals)
#Adjusted means
PQL.ls2<-lsmeans(PQL2, "Fished.Unfished")
PQL.sum2<-summary(PQL.ls2, infer=c(TRUE, TRUE), level=0.95, type="response")
#Plots
p04<-ggplot(PQL.sum2, aes(Fished.Unfished, response,
fill=Fished.Unfished))+geom_bar(stat="identity")+geom_errorbar(aes(ymin=lower.CL, ymax=upper.CL, width=.4)) + scale_fill_discrete() + scale_y_continuous(limits=c(0,8), breaks=seq(0,8, by = 2))+ labs(x="Zone", y="Density coral recruits (#/100m2)") +theme_bw()+ guides(fill=FALSE)