jpeg("Figure7_Prop_Opaque_Amber.jpg",width=4.5,height=6.5,units="in",res=675)
layout(rbind(1,2)); layout.show(2)
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(5.6,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSite.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("J. kosteri")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$asymp.LCL[i],TUKEYSite.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSite.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$rcmpl[i]),lty=1)
}
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(6.3,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSiteA.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("P. roswellensis")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
mtext("(a)",col="black",at=0.65,las=1,side=3,line=+16.0, cex=1.2,font=1)
mtext("(b)",col="black",at=0.65,las=1,side=3,line=-1.4, cex=1.2,font=1)
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$asymp.LCL[i],TUKEYSiteA.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSiteA.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$rcmpl[i]),lty=1)
}
lines(c(-1,7),c(0.41,0.41),lty=3)
dev.off()
# Save the plot
jpeg("Figure7_Prop_Opaque_Amber.jpg",width=4.5,height=6.5,units="in",res=675)
layout(rbind(1,2)); layout.show(2)
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(5.6,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSite.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("J. kosteri")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$asymp.LCL[i],TUKEYSite.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSite.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$rcmpl[i]),lty=1)
}
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(6.3,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSiteA.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("P. roswellensis")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
mtext("(a)",col="black",at=0.65,las=1,side=3,line=+15.0, cex=1.2,font=1)
mtext("(b)",col="black",at=0.65,las=1,side=3,line=-1.4, cex=1.2,font=1)
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$asymp.LCL[i],TUKEYSiteA.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSiteA.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$rcmpl[i]),lty=1)
}
lines(c(-1,7),c(0.41,0.41),lty=3)
dev.off()
# Save the plot
jpeg("Figure7_Prop_Opaque_Amber.jpg",width=4.5,height=6.5,units="in",res=675)
layout(rbind(1,2)); layout.show(2)
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(5.6,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSite.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("J. kosteri")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$asymp.LCL[i],TUKEYSite.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSite.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$rcmpl[i]),lty=1)
}
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(6.3,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSiteA.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("P. roswellensis")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
mtext("(a)",col="black",at=0.65,las=1,side=3,line=+15.0, cex=1.0,font=1)
mtext("(b)",col="black",at=0.65,las=1,side=3,line=-1.4, cex=1.2,font=1)
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$asymp.LCL[i],TUKEYSiteA.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSiteA.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$rcmpl[i]),lty=1)
}
lines(c(-1,7),c(0.41,0.41),lty=3)
dev.off()
# Save the plot
jpeg("Figure7_Prop_Opaque_Amber.jpg",width=4.5,height=6.5,units="in",res=675)
layout(rbind(1,2)); layout.show(2)
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(5.6,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSite.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("J. kosteri")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$asymp.LCL[i],TUKEYSite.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSite.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$rcmpl[i]),lty=1)
}
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(6.3,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSiteA.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("P. roswellensis")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
mtext("(a)",col="black",at=0.65,las=1,side=3,line=+15.0, cex=0.9,font=1)
mtext("(b)",col="black",at=0.65,las=1,side=3,line=-1.4, cex=1.2,font=1)
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$asymp.LCL[i],TUKEYSiteA.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSiteA.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$rcmpl[i]),lty=1)
}
lines(c(-1,7),c(0.41,0.41),lty=3)
dev.off()
# Save the plot
jpeg("Figure7_Prop_Opaque_Amber.jpg",width=4.5,height=6.5,units="in",res=675)
layout(rbind(1,2)); layout.show(2)
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(5.6,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSite.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("J. kosteri")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$asymp.LCL[i],TUKEYSite.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSite.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$rcmpl[i]),lty=1)
}
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(6.3,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSiteA.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("P. roswellensis")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
mtext("(a)",col="black",at=0.63,las=1,side=3,line=+15.1, cex=0.85,font=1)
mtext("(b)",col="black",at=0.65,las=1,side=3,line=-1.4, cex=1.2,font=1)
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$asymp.LCL[i],TUKEYSiteA.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSiteA.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$rcmpl[i]),lty=1)
}
lines(c(-1,7),c(0.41,0.41),lty=3)
dev.off()
# Save the plot
jpeg("Figure7_Prop_Opaque_Amber.jpg",width=4.5,height=6.5,units="in",res=675)
layout(rbind(1,2)); layout.show(2)
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(5.6,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSite.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("J. kosteri")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$asymp.LCL[i],TUKEYSite.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSite.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$rcmpl[i]),lty=1)
}
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(6.3,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSiteA.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("P. roswellensis")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
mtext("(a)",col="black",at=0.61,las=1,side=3,line=+15.2, cex=0.83,font=1)
mtext("(b)",col="black",at=0.65,las=1,side=3,line=-1.4, cex=1.2,font=1)
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$asymp.LCL[i],TUKEYSiteA.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSiteA.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$rcmpl[i]),lty=1)
}
lines(c(-1,7),c(0.41,0.41),lty=3)
dev.off()
# Save the plot
jpeg("Figure7_Prop_Opaque_Amber.jpg",width=4.5,height=6.5,units="in",res=675)
layout(rbind(1,2)); layout.show(2)
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(5.6,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSite.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("J. kosteri")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$asymp.LCL[i],TUKEYSite.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSite.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$rcmpl[i]),lty=1)
}
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(6.3,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSiteA.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("P. roswellensis")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
mtext("(a)",col="black",at=0.61,las=1,side=3,line=+15.2, cex=0.83,font=1)
mtext("(b)",col="black",at=0.61,las=1,side=3,line=-1.4, cex=0.83,font=1)
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$asymp.LCL[i],TUKEYSiteA.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSiteA.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$rcmpl[i]),lty=1)
}
lines(c(-1,7),c(0.41,0.41),lty=3)
dev.off()
# Save the plot
jpeg("Figure7_Prop_Opaque_Amber.jpg",width=4.5,height=6.5,units="in",res=675)
layout(rbind(1,2)); layout.show(2)
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(5.6,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSite.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("J. kosteri")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$asymp.LCL[i],TUKEYSite.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSite.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$rcmpl[i]),lty=1)
}
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(6.3,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSiteA.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("P. roswellensis")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
mtext("(a)",col="black",at=0.61,las=1,side=3,line=+15.2, cex=0.83,font=1)
mtext("(b)",col="black",at=0.61,las=1,side=3,line=-1.2, cex=0.83,font=1)
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$asymp.LCL[i],TUKEYSiteA.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSiteA.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$rcmpl[i]),lty=1)
}
lines(c(-1,7),c(0.41,0.41),lty=3)
dev.off()
# Save the plot
jpeg("Figure7_Prop_Opaque_Amber.jpg",width=4.5,height=6.5,units="in",res=675)
layout(rbind(1,2)); layout.show(2)
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(5.6,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSite.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("J. kosteri")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$asymp.LCL[i],TUKEYSite.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSite.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSite.plot$data$the.emmean[i],TUKEYSite.plot$data$rcmpl[i]),lty=1)
}
par(cex.lab=1.1)
par(font.lab=2)
par(cex.main=1.6)
par(font.main=2)
par(cex.axis=1.1)
par(lwd=2)
par(mar=c(6.3,6,2,2))
# axes=FALSE takes away the axis so you can customize them with code below.
plot(1:5,TUKEYSiteA.plot$data$the.emmean,axes=FALSE,pch="",ylab=expression(~bold("Proporiton")~bolditalic("P. roswellensis")),ylim=c(0,1),xlim=c(0.5,5.5),xlab="")
mtext("(a)",col="black",at=0.61,las=1,side=3,line=+15.2, cex=0.83,font=1)
mtext("(b)",col="black",at=0.61,las=1,side=3,line=-1.15, cex=0.83,font=1)
box()
polygon(x=c(1.5,1.5,3.5,3.5),y=c(-0.2,1.2,1.2,-0.1),col=adjustcolor("gray",alpha.f=0.31),border=NA)
# axis make new axis with customizations.
# yaxp=c(0,1.6,8) sets the ticks.
axis(2,ylim=c(0,1),col="black",las=1,yaxp=c(0,1,10))
axis(1,at=1:5,labels=c("Bitter\nCreek","Rio Hondo\nMidstream","Rio Hondo\nSpring-vents","Sago\nSprings","Snail\nUnit"),col="black",las=2,cex=2)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$asymp.LCL[i],TUKEYSiteA.plot$data$asymp.UCL[i]),lty=1,lwd=15,col="grey")
}
points(1:5,TUKEYSiteA.plot$data$the.emmean,pch=19)
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$lcmpl[i]),lty=1)
}
for (i in 1:5){
lines(rep(i,2),c(TUKEYSiteA.plot$data$the.emmean[i],TUKEYSiteA.plot$data$rcmpl[i]),lty=1)
}
lines(c(-1,7),c(0.41,0.41),lty=3)
dev.off()
