[Rd] cmdscale problem

2005-01-08 Thread Christian Kleiber
Dear R developers, there appears to be a small problem with function cmdscale: for non-Euclidean distance matrices, using option add=FALSE (the default), cmdscale misses the smallest eigenvalue. This affects GOF statistic g.1 (See Mardia, Kent + Bibby (1979): Multivariate Analysis, eq.

[Rd] p.adjust(NAs), was Re: [BioC] limma and p-values

2005-01-08 Thread Martin Maechler
GS == Gordon K Smyth [EMAIL PROTECTED] on Sat, 8 Jan 2005 01:11:30 +1100 (EST) writes: . GS p.adjust() unfortunately gives incorrect results when GS 'p' includes NAs. The results from topTable are GS correct. topTable() takes care to remove NAs before

[Rd] Documentation bug (PR#7483)

2005-01-08 Thread tac
Full_Name: Terry A. Cox Version: 2.0.1 OS: Mac OS X Submission from: (NULL) (138.88.250.18) In the file, http://cran.r-project.org/doc/manuals/R-exts.html, several of the headers have incorrect closing tags, e.g., h3 class=subsectionThe codeDESCRIPTION/code file/h4 This creates a problem in

Re: [Rd] Documentation bug (PR#7483)

2005-01-08 Thread ripley
http://cran.r-project.org is not part of R per se and has its own bug reporting address, [EMAIL PROTECTED] That file was made with makeinfo 4.6, and it is a bug in that version of makeinfo. It is not a problem in the version distributed with R for Windows, for example, made with the current

Re: [Rd] Standalone Mathlib, C++ and ISNAN()

2005-01-08 Thread Thomas Lumley
A review: The C++ math header undefines isnan, so if isnan is a macro, ISNAN() will not work in C++ code. C99 specifies that isnan is a macro, but in C90 compilers, where it is an extension, isnan is often a function (explaining why the issue didn't come up earlier). For example, isnan is a