R help - Jun 2014 - x,y scatterplots, with averaging by a column

Hallo!

I have this matrix:

SampleID, Day, Species1, Species2,Species3,...,Speciesn
1,Monday,abundance values
2,Monday,abundance values
11,Tuesday,abundance values
12,Tuesday,abundance values
21,Wednesday,abundance values
22,Wednesday,abundance values

I would like to plot the Days on the x-axis, and the species abundance 
data on the y-axis. Each pair of values (i just have two measurements 
for each day) should be represented by their mean with absolute error 
bars (so we have basically a vertical min,max-range) and whiskers. The 
means for each Species observation should be connected with lines.
Also of interest would be annotating the whispers with their sample ID 
(because the whiskers basically represent the values for y1,2 (11,12; 
21,22)).
Any help is welcome! I am new to R, so please bear with me. Thank you!

-- 
Tim Richter-Heitmann (M.Sc.)
PhD Candidate



International Max-Planck Research School for Marine Microbiology
University of Bremen
Microbial Ecophysiology Group (AG Friedrich)
FB02 - Biologie/Chemie
Leobener Stra?e (NW2 A2130)
D-28359 Bremen
Tel.: 0049(0)421 218-63062
Fax: 0049(0)421 218-63069

On Mon, 30 Jun 2014 10:42:28 AM Tim Richter-Heitmann
wrote:
> Hallo!
> 
> I have this matrix:
> 
> SampleID, Day, Species1, Species2,Species3,...,Speciesn
> 1,Monday,abundance values
> 2,Monday,abundance values
> 11,Tuesday,abundance values
> 12,Tuesday,abundance values
> 21,Wednesday,abundance values
> 22,Wednesday,abundance values
> 
> I would like to plot the Days on the x-axis, and the species 
abundance
> data on the y-axis. Each pair of values (i just have two 
measurements
> for each day) should be represented by their mean with absolute 
error
> bars (so we have basically a vertical min,max-range) and whiskers. 
The
> means for each Species observation should be connected with lines.
> Also of interest would be annotating the whispers with their sample 
ID
> (because the whiskers basically represent the values for y1,2 
(11,12;
> 21,22)).
Hi Tim,
I think this might get you started:

trhdf<-data.frame(SampleID=seq(0,50,by=10)+(1:2),
 Day=factor(rep( c("Monday","Tuesday","Wednesday",
  "Thursday","Friday","Saturday"),
 each=2),levels=c("Monday","Tuesday","Wednesday",
  "Thursday","Friday","Saturday")),
 Species1=sample(0:20,12),Species2=sample(0:20,12),
 Species3=sample(0:20,12),Species4=sample(0:20,12),
 Species5=sample(0:20,12))

rollfunc<-function(x,FUN="mean",roll=2) {
 lenx<-length(x)
 xmeans<-rep(NA,lenx/2)
 start<-1
 for(xm in 1:(lenx/2)) {
  xmeans[xm]<-do.call(FUN,list(x[start:(start+roll-1)]))
  start<-start+roll
 }
 return(xmeans)
}

xpos<-rep(1:6,5)+seq(-0.4,0.4,by=0.2)
ypos<-as.vector(sapply(trhdf[,3:7],rollfunc))
ymin<-as.vector(sapply(trhdf[,3:7],rollfunc,"min"))
ymax<-as.vector(sapply(trhdf[,3:7],rollfunc,"max"))

library(plotrix)

plot(xpos,ypos,pch=c("1","2","3","4","5"),ylim=c(0,20),
 xaxt="n",xlab="Day",ylab="Abundance")
dispersion(xpos,ypos,ymax,ymin,interval=FALSE)
staxlab(1,at=1:6,
 labels=c("Monday","Tuesday","Wednesday",
  "Thursday","Friday","Saturday"))

Jim