Hi all,
So this code works for three of the six seamounts. The problem I am
encountering is the fact that some of the seamounts doesn't have all the
depth categories (i.e missing the deep category) and thus gives me this
error "Error in plot.window(...) : need finite 'ylim' values."
How can I fix this so that if a depth category is missing that it won't
result in an error. If I change ylim=c(0,max(sm.mean$Total_Ch + 0.1)), to
something like this ylim=c(0,6)), then it works but the I don't like scale.
Please help and thank you.
> head(SChla)
Seamount Station Depth Pico Nano Micro Total_Ch dbar
1 Atlantis 1217 Surface 0.0639 0.1560 0.0398 0.2597 2.082
2 Atlantis 1217 Shallow 0.0305 0.1250 0.0740 0.2295 24.524
3 Atlantis 1217 Deep 0.1660 0.3560 0.0734 0.5954 49.573
4 Atlantis 1217 Fmax 0.1740 0.5200 0.1830 0.8770 79.595
5 Atlantis 1217 Below 0.0235 0.0486 0.0242 0.0963 199.067
6 Atlantis 1225 Surface 0.0764 0.1490 0.0333 0.2587 0.409
# Get the unique seamounts
as.character(unique(SChla$Seamount))
sm <- as.character(unique(SChla$Seamount))
for ( i in sm[1:6]) {
SM.mean <- subset(SChla,Seamount==i,
select=c(Seamount, Station, Depth, Pico, Nano, Micro, Total_Ch))
sm.mean <- with(SM.mean, aggregate(cbind(Pico, Nano, Micro, Total_Ch),
list(Depth),FUN=mean))
sm.mean <-
sm.mean[order(order(c("Surface","Shallow","Deep","Fmax","Below"))),]
yy <- matrix(c(sm.mean$Pico,sm.mean$Nano, sm.mean$Micro),5,3,byrow=FALSE,
dimnames = list(c("Below", "Deep", "Fmax", "Shallow", "Surface"),
c("Pico", "Nano", "Micro")))
yy <- t(yy)
jpeg(filename = paste(i,"
Seamount.jpg"),res=300,width=15,height=10,units="cm")
barp(yy , ylim=c(0,max(sm.mean$Total_Ch + 0.1)), col=c("light
green","green","dark green"),
xlab="Depth (m)",
legend.pos = 0.6,
ylab= expression (paste("Chlorophyll ", italic(" a ") ~~ (mu*g ~
l^{-1}))),,
names.arg=c("Surface","Shallow","Deep","Fmax","Below"))
points(sm.mean$Total_Ch, pch = 19)
lines(sm.mean$Total_Ch)
title(i)
legend("topleft",c("Pico","Nano","Micro", "Total"),bty="n",
col=c("light green","green","dark green","black"),
pch=c(15,15,15,19,-1),
lty = c(0,0,0,1))
}
dev.off()
Regards,
Tinus
--
M.J. Sonnekus
PhD Candidate (The Phytoplankton of the southern Agulhas Current Large
Marine Ecosystem (ACLME))
Department of Botany
South Campus
Nelson Mandela Metropolitan University
PO Box 77000
Port Elizabeth
South Africa
6031
Cell: 082 080 9638
E-mail: tsonne...@gmail.com
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