[Rd] Detecting bad lexical scoping

2011-03-17 Thread Ryan King
I've recently hunted down a troublesome bug in my own code, and am looking for an easy mechanism to detect this kind of error in other R code. The problem was an undefined variable inside of a function. Unfortunately, R looked for that variable in the global environment and found it since there wa

Re: [Rd] Detecting bad lexical scoping

2011-03-17 Thread Duncan Murdoch
On 16/03/2011 4:14 PM, Ryan King wrote: I've recently hunted down a troublesome bug in my own code, and am looking for an easy mechanism to detect this kind of error in other R code. The problem was an undefined variable inside of a function. Unfortunately, R looked for that variable in the glob

Re: [Rd] Feature request: display file name in R CMD check warning

2011-03-17 Thread Duncan Murdoch
On 16/03/2011 7:55 PM, Dan Tenenbaum wrote: Hi, I came across the following warning in R CMD check (it only occurred on Windows): The \usage entries for S3 methods should use the \method markup and not their full name. See the chapter 'Writing R documentation files' in manual 'Writing R Extens

Re: [Rd] Feature request: display file name in R CMD check warning

2011-03-17 Thread Duncan Murdoch
On 16/03/2011 7:55 PM, Dan Tenenbaum wrote: Hi, I came across the following warning in R CMD check (it only occurred on Windows): The \usage entries for S3 methods should use the \method markup and not their full name. See the chapter 'Writing R documentation files' in manual 'Writing R Extens

Re: [Rd] Detecting bad lexical scoping

2011-03-17 Thread Gabor Grothendieck
On Wed, Mar 16, 2011 at 4:14 PM, Ryan King wrote: > I've recently hunted down a troublesome bug in my own code, and am > looking for an easy mechanism to detect this kind of error in other R > code.  The problem was an undefined variable inside of a function. > Unfortunately, R looked for that var

Re: [Rd] Standardized Pearson residuals (and score tests)

2011-03-17 Thread peter dalgaard
On Mar 16, 2011, at 23:29 , Gordon K Smyth wrote: > Hi Peter and others, > > If it helps, I wrote a small function glm.scoretest() for the statmod package > on CRAN to compute score tests from glm fits. The score test for adding a > covariate, or any set of covariates, can be extracted very n

[Rd] New feature for download.packages(): optional resolution of package dependencies

2011-03-17 Thread Dr. Peter Ruckdeschel
Hi r-devels, may I ask for an enhancement for download.packages() to optionally resolve package dependencies similarly to the respective functionality in install.packages() ? This would be a major help in compiling a large number of packages (e.g. by means of download.view() from pkg ctv) for lat

Re: [Rd] Standardized Pearson residuals

2011-03-17 Thread peter dalgaard
On Mar 16, 2011, at 23:34 , John Maindonald wrote: > One can easily test for the binary case and not give the statistic in that > case. Warning if expected cell counts < 5 would be another possibility. > > A general point is that if one gave no output that was not open to abuse, > there'd be

Re: [Rd] Standardized Pearson residuals

2011-03-17 Thread Martin Maechler
> peter dalgaard > on Thu, 17 Mar 2011 15:45:01 +0100 writes: > On Mar 16, 2011, at 23:34 , John Maindonald wrote: >> One can easily test for the binary case and not give the >> statistic in that case. > Warning if expected cell counts < 5 would be another > poss

Re: [Rd] New feature for download.packages(): optional resolution of package dependencies

2011-03-17 Thread Simon Urbanek
On Mar 17, 2011, at 10:26 AM, Dr. Peter Ruckdeschel wrote: > Hi r-devels, > > may I ask for an enhancement for download.packages() > to optionally resolve package dependencies similarly to > the respective functionality in install.packages() ? > > This would be a major help in compiling a large

Re: [Rd] Feature request: display file name in R CMD check warning

2011-03-17 Thread Dan Tenenbaum
On Thu, Mar 17, 2011 at 2:36 AM, Duncan Murdoch wrote: > On 16/03/2011 7:55 PM, Dan Tenenbaum wrote: >> >> Hi, >> >> I came across the following warning in R CMD check (it only occurred on >> Windows): >> >> The \usage entries for S3 methods should use the \method markup and not >>> >>> their full

Re: [Rd] Feature request: display file name in R CMD check warning

2011-03-17 Thread Dan Tenenbaum
On Thu, Mar 17, 2011 at 9:33 AM, Dan Tenenbaum wrote: > On Thu, Mar 17, 2011 at 2:36 AM, Duncan Murdoch > wrote: >> On 16/03/2011 7:55 PM, Dan Tenenbaum wrote: >>> >>> Hi, >>> >>> I came across the following warning in R CMD check (it only occurred on >>> Windows): >>> >>> The \usage entries for

Re: [Rd] Standardized Pearson residuals

2011-03-17 Thread peter dalgaard
On Mar 17, 2011, at 16:14 , Martin Maechler wrote: >> peter dalgaard >>on Thu, 17 Mar 2011 15:45:01 +0100 writes: >> > >> Back to the original question: > >> The current rstandard() code reads > > ## FIXME ! -- make sure we are following "the literature": > rstandard.glm <- funct

Re: [Rd] Standardized Pearson residuals

2011-03-17 Thread John Fox
Dear Peter and Martin, On Thu, 17 Mar 2011 18:08:18 +0100 peter dalgaard wrote: > > On Mar 17, 2011, at 16:14 , Martin Maechler wrote: > > >> peter dalgaard > >>on Thu, 17 Mar 2011 15:45:01 +0100 writes: > >> > > > >> Back to the original question: > > > >> The current rstandar

Re: [Rd] Standardized Pearson residuals

2011-03-17 Thread Brett Presnell
John Maindonald writes: > One can easily test for the binary case and not give the statistic in > that case. > > A general point is that if one gave no output that was not open to > abuse, there'd be nothing given at all! Thanks John. I've been reluctant to push too hard for this on r-devel, b

Re: [Rd] Standardized Pearson residuals (and score tests)

2011-03-17 Thread Gordon K Smyth
On Thu, 17 Mar 2011, peter dalgaard wrote: On Mar 16, 2011, at 23:29 , Gordon K Smyth wrote: Hi Peter and others, If it helps, I wrote a small function glm.scoretest() for the statmod package on CRAN to compute score tests from glm fits. The score test for adding a covariate, or any set of

Re: [Rd] Feature request: display file name in R CMD check warning

2011-03-17 Thread Duncan Murdoch
On 11-03-17 12:33 PM, Dan Tenenbaum wrote: On Thu, Mar 17, 2011 at 2:36 AM, Duncan Murdoch wrote: On 16/03/2011 7:55 PM, Dan Tenenbaum wrote: Hi, I came across the following warning in R CMD check (it only occurred on Windows): The \usage entries for S3 methods should use the \method marku

Re: [Rd] avoid copying big object passed into optimize()

2011-03-17 Thread Zepu Zhang
Thanks! I found, say, exp(x) causes 2 duplications whereas sum(x) 0 duplication. Is there any document to learn from about this? (first time list user. sorry if anything about the posting procedure is wrong) On Wed, Mar 9, 2011 at 6:16 PM, Matt Shotwell wrote: > On Wed, 2011-03-09 at 17:15 -090