[R-sig-eco] error message when declaring a variable as factor

[Mike Marsh]

Dear R users,
I am using clustering (with hclust) and PERMANOVA (adonis) in R to 
compare richness and foliar cover data from two shrub-steppe landscapes 
separated by about 5 miles, one grazed (measured with eleven plots) and 
the other ungrazed (measured with ten plots) for the last 20 years.
I combined data from two years to increase degrees of freedom, giving me 
42 rows.
Environmental data consist of elevation, slope, aspect (as heatload), 
E.Site (=environmental "Site" from USGS soil surveys), and "group", 
which distinguishes the grazed landscape from the ungrazed one.
I wanted to declare the last two sites as factor, E.Site having 5 levels 
and group, of course, having two. Data for both were expressed as 
numbers, if that makes a difference.

When I ran the following script I received the error message shown for 
group (with levels "1" and "2", but no error for E.Site (with levels 1 
to 5).

Wd0709.q0809.richness.env<-as.data.frame(read.table(file.choose(),header=T))
Wd0709.q0809.richness.env$group <- 
as.factor(Wd0709.q0809.richness.env$group)
Error in as.vector(x, mode) : invalid 'mode' argument
Wd0709.q0809.richness.env$E.Site <- 
as.factor(Wd0709.q0809.richness.env$E.Site)

When I then added group to the adonis equation, the message returned was

"Error in eval(expr, envir, enclos) : object "group" not found".

I repeated the above steps using just the data for the most recent year 
(21 rows of data), and two levels, still, for group. No error message 
was returned.

Then I re-coded the full environmental data set of 42 rows, separating 
the plots into 4 distinct "groups" by year and by landscape treatment. 
Again, no error message was returned.

I would like to correct the above error so that I can treat the two 
landscapes as just two levels in adonis.

Thanks for any help you can offer.

Mike Marsh
member, Washington Native Plant Society