[R] help with predict and plotting confidence intervals

[Michael Denslow]

Dear R help,

This seems to be a commonly asked question and I am able to run examples that have been proposed, but I can't seems to get this to work with my own data. Reproducible code is below. Thank you in advance for any help you can provide.

The main problem is that I can not get the confidence lines to plot correctly.
The secondary problem is that predict is not able to find my object when 
I include a model object.

## THE DATA
wt.data <- data.frame(code = factor(LETTERS[1:24]),
	area = c(60865,480,656792,92298,1200,1490,8202,4000,220,245,4000,390,325,
	16,162911,20235,68800,3389,7,696,4050,1498,1214,99460),
	species = c(673,650,1353,1026,549,536,782,734,516,580,673,560,641,443,1105,
	871,789,575,216,407,942,655,582,1018))

# TRANSFORM AND ADD TO DATAFRAME
wt.data$logA <- log10(wt.data$area)
wt.data$logS <- log10(wt.data$species)

wt.mod <- lm(logS~logA, data = wt.data)

# PLOT THE DATA
with(wt.data,plot(logA,logS, ylim = c(2.3,3.2),xlim = c(0,6)))
abline(wt.mod, lwd = 2)


# create a prediction dataframe the same length as data
pred.frame <- data.frame(a = seq(0,6, length.out = 24))

# error ' object "logA" not found'
# I am not sure why object is not found, I assume this has to do with 
# the way I added the transformed variables to the dataframe
pp <- predict(wt.mod, int = "p", newdata=pred.frame)

# runs ok?
pp <- predict(lm(wt.data$logS~wt.data$logA), int = "p", newdata=pred.frame)

# lines are jagged??
# I am not sure how to get the lines to draw correctly here
matlines(pred.frame$a,pp, lty=c(1,2,2),col="black")


> sessionInfo()
R version 2.8.1 (2008-12-22) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_2.8.1

Michael Denslow

Graduate Student
I.W. Carpenter Jr. Herbarium [BOON]
Department of Biology
Appalachian State University
Boone, North Carolina U.S.A.

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Southeast Regional Network of Expertise and Collections
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