masked from package:base?

I am confused by the following description in
http://www.maths.lth.se/help/R/.R/library/systemfit/html/hausman.systemfit.
html

what does the "Not run" mean? 

if we do not load systemfit, how can we run 
the following code?

## Not run: library( systemfit )

data( kmenta )
attach( kmenta )
...

I install the package of systemfit, and run the code.

I got the warning:

library( systemfit )
data( kmenta )
attach( kmenta )

        The following object(s) are masked from package:base :

         q

	[[alternative HTML version deleted]]

On 12/1/05, Arne Henningsen <ahenningsen at email.uni-kiel.de> wrote:

On Friday 02 December 2005 02:50, August Berg wrote:

I am confused by the following description in

http://www.maths.lth.se/help/R/.R/library/systemfit/html/hausman.systemfi
t .

html

what does the "Not run" mean?

This means that the command "library( systemfit )" is not executed when
the
package is checked by "R CMD check".

@Jeff: I think we should remove "library( systemfit )" from the example
section, because everybody should know this.

if we do not load systemfit, how can we run
the following code?

## Not run: library( systemfit )

data( kmenta )
attach( kmenta )
...

I install the package of systemfit, and run the code.

I got the warning:

library( systemfit )
data( kmenta )
attach( kmenta )

        The following object(s) are masked from package:base :

         q

The data set "kmenta" has a (column) name called "q"
R> names(kmenta)
[1] "q" "p" "d" "f" "a"

If you attach these data to the search path, there are two objects with
the
name "q": the quantity from Kmenta's data set and the function to quit R.
Hence, attaching this data set masks the function "q" (quit) from the
package
called "base". However, you don't have to worry, because "q()" and "?q"
still
work as expected.

@Jeff: Since using "attach" is often troublesome, I suggest that we
remove "attach( kmenta )" from the example section and use "systemfit(
..., data =
kmenta )" instead.

Best wishes,
Arne

Thanks. But still report such an error:

pval <- 1 - pchisq( h, dim( fit3sls$bcov )[1] )

Error in pchisq(q, df, lower.tail, log.p) :
        Non-numeric argument to mathematical function

On 12/2/05, Arne Henningsen <ahenningsen at email.uni-kiel.de> wrote:

On Friday 02 December 2005 09:00, you wrote:

On 12/1/05, Arne Henningsen <ahenningsen at email.uni-kiel.de> wrote:

On Friday 02 December 2005 02:50, August Berg wrote:

I am confused by the following description in

http://www.maths.lth.se/help/R/.R/library/systemfit/html/hausman.systemfi

t .

html

what does the "Not run" mean?

This means that the command "library( systemfit )" is not executed

when

the
package is checked by "R CMD check".

@Jeff: I think we should remove "library( systemfit )" from the

example

section, because everybody should know this.

if we do not load systemfit, how can we run
the following code?

## Not run: library( systemfit )

data( kmenta )
attach( kmenta )
...

I install the package of systemfit, and run the code.

I got the warning:

library( systemfit )
data( kmenta )
attach( kmenta )

        The following object(s) are masked from package:base :

         q

The data set "kmenta" has a (column) name called "q"
R> names(kmenta)
[1] "q" "p" "d" "f" "a"

If you attach these data to the search path, there are two objects

with

the
name "q": the quantity from Kmenta's data set and the function to
quit

R.

Hence, attaching this data set masks the function "q" (quit) from the
package
called "base". However, you don't have to worry, because "q()" and

"?q"

still
work as expected.

@Jeff: Since using "attach" is often troublesome, I suggest that we
remove "attach( kmenta )" from the example section and use
"systemfit( ..., data =
kmenta )" instead.

Best wishes,
Arne

Thanks. But still report such an error:

pval <- 1 - pchisq( h, dim( fit3sls$bcov )[1] )

Error in pchisq(q, df, lower.tail, log.p) :
        Non-numeric argument to mathematical function

The object "h" is not numeric, but a list:
R> class(h)
[1] "hausman.systemfit"
R> names(h)
[1] "q"    "qVar" "m"    "df"   "pval"

You probably want this:
R> pval <- 1 - pchisq( h$m, dim( fit3sls$bcov )[1] )

Or you can just type
R> h
2.53565 (P-value: 0.924389)

This is documented in the systemfit manual, please type
R> ?hausman.systemfit

Best wishes,
Arne

--
Arne Henningsen
Department of Agricultural Economics
University of Kiel
Olshausenstr. 40
D-24098 Kiel (Germany)
Tel: +49-431-880 4445
Fax: +49-431-880 1397
ahenningsen at agric-econ.uni-kiel.de
http://www.uni-kiel.de/agrarpol/ahenningsen/

I see. I guess there is a typo in
http://www.maths.lth.se/help/R/.R/library/systemfit/html/hausman.systemfit
on that webpage, pval <- 1 - pchisq( h, dim( fit3sls$bcov )[1] )

Also, is there any way to open the data in atable(I apologize this is not a
question spefific for the Hausman test).

Best Regards,
August

On 12/1/05, Arne Henningsen <ahenningsen at email.uni-kiel.de> wrote:

On Friday 02 December 2005 02:50, August Berg wrote:

I am confused by the following description in

http://www.maths.lth.se/help/R/.R/library/systemfit/html/hausman.systemfi
t .

html

what does the "Not run" mean?

This means that the command "library( systemfit )" is not executed when
the
package is checked by "R CMD check".

@Jeff: I think we should remove "library( systemfit )" from the example
section, because everybody should know this.

I am new to R and what does [checked by "R CMD check"] mean?

On Friday 02 December 2005 10:21, August Berg wrote:

On 12/1/05, Arne Henningsen <ahenningsen at email.uni-kiel.de> wrote:

On Friday 02 December 2005 02:50, August Berg wrote:

I am confused by the following description in

http://www.maths.lth.se/help/R/.R/library/systemfit/html/hausman.systemfi
t .

html

what does the "Not run" mean?

This means that the command "library( systemfit )" is not executed when
the
package is checked by "R CMD check".

@Jeff: I think we should remove "library( systemfit )" from the example
section, because everybody should know this.

I am new to R and what does [checked by "R CMD check"] mean?

The source of an R package can be checked by the command 
   "R CMD check <package_name>" 
(on a  Unix/Linux machines; on Windows machines this is slightly different).

Further information is available in the manual "Writing R Extensions".

The source of an R package can be checked by the command
  "R CMD check <package_name>"
(on a  Unix/Linux machines; on Windows machines this is slightly

different).

In fact, it is exactly the same command on Windows.

Uwe Ligges

Why it did not work for me?

library( systemfit )
R CMD check systemfit

Error: syntax error in "R CMD"

R CMD check <systemfit>

Error: syntax error in "R CMD"