R help - Oct 2012 - Newly installed version; can't run lm function

New installation seems to have behavior I cannot figure out.  Here is
illustrative sequence where I load a small data set (test) from Crawley's
files and try to run a simple linear model and get an error message.  Oddly, R
reports that the variable 'test$ozone' is numeric while, after attaching
test, the variable ozone is not numeric.  Can someone please help?  This
behavior is occurring with multiple data sets loaded from outside R.  Thank you
in advance.
Michael Grant


Example:
> test
   ozone garden
1      3      A
2      5      B
3      4      A
4      5      B
5      4      A
6      6      B
7      3      A
8      7      B
9      2      A
10     4      B
11     3      A
12     4      B
13     1      A
14     3      B
15     3      A
16     5      B
17     5      A
18     6      B
19     2      A
20     5      B
> is.data.frame(test)
[1] TRUE
> is.numeric(test$ozone)
[1] TRUE
> is.factor(test$garden)
[1] TRUE
> lm(ozone~garden)
Error in model.frame.default(formula = ozone ~ garden, drop.unused.levels =
TRUE) :
  invalid type (list) for variable 'ozone'
> attach(test)
> is.numeric(ozone)
[1] FALSE
> is.numeric(test$ozone)
[1] TRUE

	[[alternative HTML version deleted]]

Hi Michael,

Try

fit <- lm(ozone~garden, data = test)
summary(fit)

See ?lm for more details.

HTH,
Jorge.-


On Sat, Oct 20, 2012 at 8:26 AM, Michael Grant <> wrote:
> New installation seems to have behavior I cannot figure out.  Here is
> illustrative sequence where I load a small data set (test) from
Crawley's
> files and try to run a simple linear model and get an error message.
>  Oddly, R reports that the variable 'test$ozone' is numeric while,
after
> attaching test, the variable ozone is not numeric.  Can someone please
> help?  This behavior is occurring with multiple data sets loaded from
> outside R.  Thank you in advance.
> Michael Grant
>
>
> Example:
> > test
>    ozone garden
> 1      3      A
> 2      5      B
> 3      4      A
> 4      5      B
> 5      4      A
> 6      6      B
> 7      3      A
> 8      7      B
> 9      2      A
> 10     4      B
> 11     3      A
> 12     4      B
> 13     1      A
> 14     3      B
> 15     3      A
> 16     5      B
> 17     5      A
> 18     6      B
> 19     2      A
> 20     5      B
> > is.data.frame(test)
> [1] TRUE
> > is.numeric(test$ozone)
> [1] TRUE
> > is.factor(test$garden)
> [1] TRUE
> > lm(ozone~garden)
> Error in model.frame.default(formula = ozone ~ garden, drop.unused.levels
> = TRUE) :
>   invalid type (list) for variable 'ozone'
>
> > attach(test)
> > is.numeric(ozone)
> [1] FALSE
> > is.numeric(test$ozone)
> [1] TRUE
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
	[[alternative HTML version deleted]]

On Oct 19, 2012, at 2:26 PM, Michael Grant wrote:
> New installation seems to have behavior I cannot figure out.  Here is
illustrative sequence where I load a small data set (test) from Crawley's
files and try to run a simple linear model and get an error message.  Oddly, R
reports that the variable 'test$ozone' is numeric while, after attaching
test, the variable ozone is not numeric.  Can someone please help?  This
behavior is occurring with multiple data sets loaded from outside R.  Thank you
in advance.
> Michael Grant
> 
> 
> Example:
>> test
>   ozone garden
> 1      3      A
> 2      5      B
> 3      4      A
> 4      5      B
> 5      4      A
> 6      6      B
> 7      3      A
> 8      7      B
> 9      2      A
> 10     4      B
> 11     3      A
> 12     4      B
> 13     1      A
> 14     3      B
> 15     3      A
> 16     5      B
> 17     5      A
> 18     6      B
> 19     2      A
> 20     5      B
>> is.data.frame(test)
> [1] TRUE
>> is.numeric(test$ozone)
> [1] TRUE
>> is.factor(test$garden)
> [1] TRUE
>> lm(ozone~garden)
> Error in model.frame.default(formula = ozone ~ garden, drop.unused.levels =
TRUE) :
>  invalid type (list) for variable 'ozone'
This is not surprising for two reasons. Crawley's presumptuously named text
"The R Book" teaches students to use `attach`, leaving them unprepared
to deal with the rather predictable confusion that unfortunate practice leads
to. (The second reason is that you have not yet used `attach`.)
> 
>> attach(test)
>> is.numeric(ozone)
And when I do that, I do not get the same result:

test <- read.table(text="  ozone garden
1      3      A
2      5      B
3      4      A
4      5      B
5      4      A
6      6      B
7      3      A
8      7      B
9      2      A
10     4      B
11     3      A
12     4      B
13     1      A
14     3      B
15     3      A
16     5      B
17     5      A
18     6      B
19     2      A
20     5      B", header=TRUE)
is.data.frame(test)
#[1] TRUE
is.numeric(test$ozone)
#[1] TRUE
is.factor(test$garden)
#[1] TRUE
lm(ozone~garden)

# Error which seems perfectly expected without a 'data' argument.
attach(test)
is.numeric(ozone)
####-------

# I get 
> is.numeric(ozone)
[1] TRUE

So you have done something else. What it is we cannot tell. Why not send a
letter to Crawley? He's the one you paid money for that fat book, and whose
dataset you are importing in some unspecified manner. Or perhaps use:

str(test)


> [1] FALSE
>> is.numeric(test$ozone)
> [1] TRUE
> 
> 	[[alternative HTML version deleted]]
> 
-- 

David Winsemius, MD
Alameda, CA, USA
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

You have an object named "ozone" kicking around in your
workspace/global
environment.  This is apparently not of mode "numeric" and it is
masking
the "ozone" object (column) from the attached data frame
"test".

Simply doing ls() would have told you this.

Presumably you also got a warning about this when you attached test.
Heed the warning!

As others have advised you ***don't use attach()***!!!

Instead, use "data= ..." in your call to lm().

     cheers,

         Rolf Turner

On 20/10/12 10:26, Michael Grant wrote:
> New installation seems to have behavior I cannot figure out.  Here is
illustrative sequence where I load a small data set (test) from Crawley's
files and try to run a simple linear model and get an error message.  Oddly, R
reports that the variable 'test$ozone' is numeric while, after attaching
test, the variable ozone is not numeric.  Can someone please help?  This
behavior is occurring with multiple data sets loaded from outside R.  Thank you
in advance.
> Michael Grant
>
>
> Example:
>> test
>     ozone garden
> 1      3      A
> 2      5      B
> 3      4      A
> 4      5      B
> 5      4      A
> 6      6      B
> 7      3      A
> 8      7      B
> 9      2      A
> 10     4      B
> 11     3      A
> 12     4      B
> 13     1      A
> 14     3      B
> 15     3      A
> 16     5      B
> 17     5      A
> 18     6      B
> 19     2      A
> 20     5      B
>> is.data.frame(test)
> [1] TRUE
>> is.numeric(test$ozone)
> [1] TRUE
>> is.factor(test$garden)
> [1] TRUE
>> lm(ozone~garden)
> Error in model.frame.default(formula = ozone ~ garden, drop.unused.levels =
TRUE) :
>    invalid type (list) for variable 'ozone'
>
>> attach(test)
>> is.numeric(ozone)
> [1] FALSE
>> is.numeric(test$ozone)
> [1] TRUE
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>