Gavin,
I agree w.r.t. documenting all arguments.  However, it is quite natural to expect that something as basic as `na.action’ would work for more generally than with only one particular type of usage.  Why should the behavior of princomp(x, …), where x is a data matrix or dataframe be any different than when a formula is provided, with regards to the NA action?  It should be easy enough to remove the rows of `x’ with NAs.  This is my main point.

Ravi

From: Gavin Simpson [mailto:ucfagls@gmail.com]
Sent: Friday, May 30, 2014 10:46 AM
To: Ravi Varadhan
Cc: peter dalgaard; r-devel@r-project.org
Subject: Re: [Rd] A bug in princomp(), perhaps?

Ravi,

You mean something /more/ explicit than the Usage section, wherein `na.action` only exists in the formula method?

I doubt we'd want RCore to go down the road of documenting all the arguments that do/don't work with particular methods included in an Rd file, beyond the Usage section.

G

On 30 May 2014 06:33, Ravi Varadhan <ravi.varadhan@jhu.edu<mailto:ravi.varadhan@jhu.edu>> wrote:
Thank you, Peter.  Now I see that.

I still think the documentation of `na.action' can be made more explicit to state that this option is only used for princomp.formula.

Best regards,
Ravi

-----Original Message-----
From: peter dalgaard [mailto:pdalgd@gmail.com<mailto:pdalgd@gmail.com>]
Sent: Friday, May 30, 2014 5:15 AM
To: Ravi Varadhan
Cc: r-devel@r-project.org<mailto:r-devel@r-project.org>
Subject: Re: [Rd] A bug in princomp(), perhaps?

It's only documented to work for princomp.formula; other methods do not know about na.action.

-pd

On 29 May 2014, at 22:10 , Ravi Varadhan <ravi.varadhan@jhu.edu<mailto:ravi.varadhan@jhu.edu>> wrote:

> Hi,
> It may be my misunderstanding, but it seems that the "na.action" in the princomp() function for principal components analysis does not work.  Please see this simple example:
>
> u <- matrix(rnorm(75), ncol=1)
> v <- matrix(rnorm(20), ncol=1)
> x <- u%*%t(v) + matrix(rnorm(20*75),ncol=20) x[1,1] <- NA pc.out <-
> princomp(x, na.action=na.exclude) Error in cov.wt(z) : 'x' must
> contain finite values only
>>
>
> Note, I have:
>> options("na.action")
> $na.action
> [1] "na.omit"
>
> Thanks,
> Ravi
>
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>
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--
Peter Dalgaard, Professor,
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Phone: (+45)38153501<tel:%28%2B45%2938153501>
Email: pd.mes@cbs.dk<mailto:pd.mes@cbs.dk>  Priv: PDalgd@gmail.com<mailto:PDalgd@gmail.com>

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