Does it work if you ignore NAs when calculating the max?

ylim=c(0,max(sm.mean$Total_Ch + 0.1, na.rm=TRUE))

Jean


On Fri, Jun 21, 2013 at 7:30 AM, Tinus Sonnekus <tsonnekus@gmail.com> wrote:

> 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: tsonnekus@gmail.com
>
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