Maintaining specific order when using aggregate or change order on axis

Hi,

Thanks for the reply. I know the order is abit confusing, but here is abit more background info to the depths.

For the various depths the ships's ctd sampled.?

surface = ctd @ surface e.g 5m
shallow = between surface and fmax e.g. 25m
deep =?between surface and fmax, but deeper than shallow e.g 50m
fmax = ctd sampled at maximum flouresence ?e.g 100m
below = below the fmax e.g. 200m

The problem I can't really assign a?specific?depth value to each as fmax changed depth depending on location. If fmax was very shallow then "deep" and "shallow" was dropped from the?predetermined sampling depths.

Hope this helps explain what I'm trying to do with the?ordering?of the data.

Thanks for all your help. Been a steep learning curve this last week with R

Shot
Tinus



On Tue, Sep 11, 2012 at 8:16 PM, arun <smartpink111 at yahoo.com> wrote:

Hi,
>The order you mentioned is confusing.? The given data shows depth to be increasing from Below,Surface,Fmax.
>
>This might help you in ordering.
>Coral1<-read.table(text="
>
>Seamount Station? Depth? Pico? Nano Micro Total_Ch
>
>Coral??? 1401 Surface 0.216 3.270 4.240??? 7.726
>
>Coral??? 1401??? Fmax 0.359 3.890 4.900??? 9.149
>
>Coral??? 1401? Below 0.178 1.360 1.210??? 2.748
>
>Coral??? 1402 Surface 0.231 4.140 3.670??? 8.041
>
>Coral??? 1402??? Fmax 0.863 4.340 3.750??? 8.953
>
>Coral??? 1402? Below 0.176 0.386 0.214??? 0.776
>",sep="",header=TRUE,stringsAsFactors=TRUE)
>
>?Coral2<-with(Coral1 , aggregate(cbind(Pico, Nano, Micro), list(Depth),FUN=mean))
>?Coral2[order(Coral2$Pico,Coral2$Nano,Coral2$Micro),]
>?# Group.1?? Pico? Nano Micro
>#1?? Below 0.1770 0.873 0.712
>#3 Surface 0.2235 3.705 3.955
>#2??? Fmax 0.6110 4.115 4.325
>
>#reverse order
>
>?Coral2[rev(order(Coral2$Pico,Coral2$Nano,Coral2$Micro)),]
>?# Group.1?? Pico? Nano Micro
>#2??? Fmax 0.6110 4.115 4.325
>#3 Surface 0.2235 3.705 3.955
>#1?? Below 0.1770 0.873 0.712
>
>
>A.K.
>
>
>
>
>
>----- Original Message -----
>From: Tinus Sonnekus <tsonnekus at gmail.com>
>To: r-help at r-project.org
>Cc:
>Sent: Tuesday, September 11, 2012 1:52 PM
>Subject: [R] Maintaining specific order when using aggregate or change order on axis
>
>Hi All,
>
>I'm using the following code to produce some stacked bar graphs.
>
>*setwd("C:\\Users\\Tinus\\Documents\\NMMU\\R\\Seamounts")*
>*SChla <- read.csv("SM_Chla_data.csv")*
>*
>*
>*#Extract mean values from data file*
>*
>*
>*Coral <- SChla[185:223,] #Reduce SChla to Coral only*
>*coral <- with(Coral , aggregate(cbind(Pico, Nano, Micro),
>list(Depth),FUN=mean))*
>*rownames(coral) <- coral[,1] *
>*coral <- t(coral[,-1]) # Remove Station col and transpose*
>
>*barplot(coral, main="Size fractionated Chl a for Coral", *
>* ylab = "Coral", xlim = c(0,8), horiz = TRUE,*
>* xlab = expression ("Chlorophyll a " ~~ (mu*g ~ l^{-1})), *
>* col =c("light green", "green", "dark green"),*
>* legend = rownames(coral))*
>
>Here is the *head(Coral) *before station col removal and t()
>
>? ? Seamount Station? ?Depth? Pico? Nano Micro Total_Ch
>185? ? Coral? ? 1401 Surface 0.216 3.270 4.240? ? 7.726
>186? ? Coral? ? 1401? ? Fmax 0.359 3.890 4.900? ? 9.149
>187? ? Coral? ? 1401? ?Below 0.178 1.360 1.210? ? 2.748
>188? ? Coral? ? 1402 Surface 0.231 4.140 3.670? ? 8.041
>189? ? Coral? ? 1402? ? Fmax 0.863 4.340 3.750? ? 8.953
>190? ? Coral? ? 1402? ?Below 0.176 0.386 0.214? ? 0.776
>
>So I use the same code for the six other seamounts. The depth has
>the following values? surface, shallow, deep, fmax and below . These are in
>order as you go down the water column. The problem is when I use the *coral
><- with(Coral , aggregate(cbind(Pico, Nano, Micro), list(Depth),FUN=mean)) *the
>
>depth values gets stored in ascending values.
>
>head(coral)
>? Group.1? ? ? Pico? ? ? Nano? ? ?Micro
>1? ?Below 0.1652727 0.8610909 0.7227273
>2? ? Deep 0.1480000 1.1700000 1.1000000
>3? ? Fmax 0.3067273 3.1845455 3.2245455
>4 Shallow 0.2617500 1.8242500 1.8637500
>5 Surface 0.1693333 2.7083333 2.7858333
>
>I would like to maintain the order surface, shallow, deep, fmax and below. *Or
>*if there is a way I can rearrange the yaxis in the order surface, shallow,
>
>deep, fmax and below.
>
>Any suggestions?
>
>Thank you
>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 at gmail.com
>
>??? [[alternative HTML version deleted]]
>
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