[R] bargraph.CI and arrows

[Reid, Doug (MNRF)]

Hello R-Help folks.  I'm fairly new to R and particularly the graphing functions.  The figures I have made look great though and so I want to use it more.
I am using bargraph.CI and have made several charts successfully using raw data.  I have a figure, however that doesn't lend itself to the functions (calculations) in bargraph.CI because it does not present conventional  means and standard errors.  Still I would like the figure to have the same look as others I am presenting so I want to use the same plot function
Selection ratios and associated standard errors were calculated as per Manley et al (2002) to assess cover type preference for some critters.  Selection Ratios were calculated at two scales from a sample of individual animal locations from the population (used points), and an equal number of random locations (available points): 2nd order across the entire area of possible occurrence, and 3rd order within home ranges.
I want to make a grouped bar chart, using these results:

Cover

SR

Order

SE

Water

0.3309

2nd

0.027909

Open Low

0.22865

2nd

0.024847

Treed Low

1.083006

2nd

0.01808

Sparse

1.966667

2nd

0.254225

Deciduous

0.792079

2nd

0.087706

Mixedwood

0.972441

2nd

0.060019

Conifer

2.226475

2nd

0.048635

Disturbance

0.410596

2nd

0.025288

Other

0.125

2nd

0.124985

Water

0.221983

3rd

0.02152

Open Low

0.648352

3rd

0.08363

Treed Low

1.138462

3rd

0.021742

Sparse

0.976744

3rd

0.149728

Deciduous

0.928571

3rd

0.114005

Mixedwood

1.032432

3rd

0.072452

Conifer

1.880137

3rd

0.046046

Disturbance

0.376321

3rd

0.027415

Other

0

3rd

0


Selection Ratio (SR)  is calculated using
Proportion of used points (oi)/proportion of available points (ði)
Standard error for the selection ratio (SE)
s.e = (sqrt((ði*(1-ði)/ n*(oi^2)) where n is the total number of points
These equations do not lend themselves to making the calculations in R, so I am simply trying to plot the results.  Here is my code:
################################################
data <- read.csv("data.csv")
#Specify the order that factors appear in (alphabetical is default)
data$Cover <- ordered (data$Cover, levels = c("Disturbance", "Deciduous", "Mixedwood",
"Conifer", "Sparse", "Treed Low", "Open Low", "Water", "Other"))

#define errors
sem = function(SE) (SE*1)
errors = with(data, tapply(SE, Cover, sem))
errors

#define benchmark value
benchmark <- 1.0

library(sciplot)
library(graphics)

#make default barchart to determine x-coordinates for error bars#
bargraph.CI(Cover, SR, Order, data = data, lc=FALSE, uc=FALSE) ->bpN.out
bpN.out

#make barchart so it looks right#

par(mar = c(10,8,1,1), oma = c(1,1,1,1))
bargraph.CI(Cover, SR, Order, data = data, ylim=c(0,2.5), ylab = "Selection Ratio",
                     cex.names = 1, cex.axis = 1.5, cex.lab = 1.5, las=2, err.width = 0.03, legend=F,
                                axis.lty=1, cex=1.1,lc=FALSE, uc=FALSE)

#Plot benchmark line at SR = 1.0
abline(h=benchmark, lty = "dotdash", lwd=2)

#Plot error bars
for(i in 1:length(bpN.out)){
arrows(bpN.out$xvals[i],means[i],bpN.out$xvals[i],means[i]+errors[i], angle=90, length=.1)
arrows(bpN.out$xvals[i],means[i],bpN.out$xvals[i],means[i]-errors[i], angle=90, length=.1)
}
 ###
Two questions:

1.       Though I have specified lc=FALSE and uc=FALSE when I call for the plot I get a warning for each of the 18 bars produced, I believe because it cannot calculate a confidence interval.  How can I suppress the function within bargrapg.CI that wants to make the calculation? When I call bpN.out I also get the full list of N/A values for the $CI.  Wondering if I can prevent this from happening, or if I need to.

2.       Instead of plotting error bars I get, "Error in means[i] + errors[i] : non-numeric argument to binary operator".  Is there something else I should be doing to get the SE values I have calculated to define the width of the error bars I want to plot?




Thanks for your help!


Douglas E. B. Reid PhD
Boreal Silviculture Reasearch Program Lead
Centre for Northern Forest Ecosystem Research
(807) 343-4008



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