On 02/03/2015 22:48, Therneau, Terry M., Ph.D. wrote:
I've moved nlme from Depends to Imports in my coxme package. However, a
few of the examples for lmekin use one of the data sets from nlme. This
is on purpose, to show how the results are the same and how they differ.
If I use
Hervé Pagès hpa...@fredhutch.org
on Mon, 2 Mar 2015 13:00:47 -0800 writes:
Hi,
On 03/02/2015 12:18 PM, Dénes Tóth wrote:
On 03/02/2015 04:37 PM, Martin Maechler wrote:
On 2 March 2015 at 09:09, Duncan Murdoch wrote:
| I generally recommend that
As I expected: there was something simple and obvious, which I somehow could
not see.
Thanks for the pointer.
Terry T.
On 03/03/2015 03:12 AM, Prof Brian Ripley wrote:
On 02/03/2015 22:48, Therneau, Terry M., Ph.D. wrote:
I've moved nlme from Depends to Imports in my coxme package. However,
The `gzcon` function both modifies and copies a connection object:
# compressed text
con1 - url(http://www.stats.ox.ac.uk/pub/datasets/csb/ch12.dat.gz;)
con2 - gzcon(con1)
# almost indistinguishable
con1==con2
identical(summary(con2), summary(con1))
# both support gzip
On 03/03/2015 02:28 AM, Martin Maechler wrote:
Diverted from R-help :
as it gets into musing about new R language primitives
William Dunlap wdun...@tibco.com
on Fri, 27 Feb 2015 08:04:36 -0800 writes:
You could define functions like
is.true - function(x) !is.na(x) x
On 3/3/15 1:26 PM, Hervé Pagès wrote:
On 03/03/2015 02:28 AM, Martin Maechler wrote:
Diverted from R-help :
as it gets into musing about new R language primitives
William Dunlap wdun...@tibco.com
on Fri, 27 Feb 2015 08:04:36 -0800 writes:
You could define functions like
Stephanie,
Actually, it's as.logical that isn't preserving matrix dimensions, because
it coerces to a logical vector:
x - matrix(sample(c(NA_integer_, 1:100), 500, replace=TRUE), nrow=50)
dim(as.logical(x))
NULL
~G
On Tue, Mar 3, 2015 at 2:09 PM, Stephanie M. Gogarten
On 03/03/2015 02:17 PM, Gabriel Becker wrote:
Stephanie,
Actually, it's as.logical that isn't preserving matrix dimensions,
because it coerces to a logical vector:
x - matrix(sample(c(NA_integer_, 1:100), 500, replace=TRUE), nrow=50)
dim(as.logical(x))
It's true, as.logical() doesn't
I still think GRanges should be a subclass of DataFrame,
which would make this easy, but I don't seem to be winning that argument.
Just impossible. As Michael mentioned back in November, they have
conflicting APIs.
Maybe a new GRangesFrame that is a DataFrame and holds a GRanges
Seems like rowData could be made to work universallly through coercion.
rowRanges would not, however, and one would like a convenient mechanism to
condition on whether range information is available. One way is to
introduce a new class and rely on dispatch. But that adds complexity.
On Tue, Mar
This.
It would be damned near perfect as a return value for assays coming out of
an object that held several such assays at several time points in a
population, where there are both assay-wise and covariate-wise holes that
could nonetheless be usefully imputed across assays.
Statistics is the
Jim et al.,
Why have two accessors (rowRanges, rowData), each of which are less
flexible than the underlying structure and thus will fail (return NULL? or
GRanges()/DataFrame() ?) in some proportion of valid objects?
~G
On Tue, Mar 3, 2015 at 2:37 PM, Jim Hester james.f.hes...@gmail.com wrote:
On 03/03/2015 03:06 PM, Peter Haverty wrote:
I'd like to see a basic class that takes a DataFrame and a sub-class that
takes a GRanges.
Yes.
I still think GRanges should be a subclass of DataFrame,
which would make this easy, but I don't seem to be winning that argument.
Just impossible.
There are some nice similarities in these new imaginary types. A
GRangesFrame is a list of dimensionally identical things (columns) and
some row meta-data (the GRanges). The SE-like object is similarly a list
of dimensionally like things (matrices, RleDataFrames, BigMatrix objects,
HDF5-backed
After a bit more investigation, I think I've found the cause of the bug,
and I have a patch.
This bug happens with grep(), when:
* Running on Windows.
* The search uses fixed=TRUE.
* The search pattern is a single byte.
* The current locale has a multibyte encoding.
===
Diverted from R-help :
as it gets into musing about new R language primitives
William Dunlap wdun...@tibco.com
on Fri, 27 Feb 2015 08:04:36 -0800 writes:
You could define functions like
is.true - function(x) !is.na(x) x
is.false - function(x) !is.na(x) !x
and
Hey everyone:
I am a Master student from Saarland Unirversity, Germany with the major of
Bioinformatics. And I am interested in statistical learning which is also
my major work in the future with the implementation by R. So I 'd like join
the google summer code this year by doing tasks in your
Hi to All,
I am building a package in R and whenever I run command R CMD build OAR
in the terminal, I get the following error:
* checking for file ‘OAR/DESCRIPTION’ ... OK
* preparing ‘OAR’:
* checking DESCRIPTION meta-information ... ERROR
Malformed Depends or Suggests or Imports or Enhances
On 03/03/2015 5:47 AM, Evans Otieno Ochiaga wrote:
Hi to All,
I am building a package in R and whenever I run command R CMD build OAR
in the terminal, I get the following error:
* checking for file ‘OAR/DESCRIPTION’ ... OK
* preparing ‘OAR’:
* checking DESCRIPTION meta-information ...
Hi Evans,
* checking for file ‘OAR/DESCRIPTION’ ... OK
* preparing ‘OAR’:
* checking DESCRIPTION meta-information ... ERROR
Malformed Depends or Suggests or Imports or Enhances field.
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