Dear R developer,
I am an R user and am currently having a problem with versions of R 3.0.0. We
build larger correlation matrices of 3 with pairwise correlations made. We
have been using a line of code
simMat=bicor(datExpr1,use=p)
To build the similarity matrix with datExpr1 being a
On Aug 19, 2013, at 20:53 , Shelton, Samuel wrote:
Dear R developer,
I am an R user and am currently having a problem with versions of R 3.0.0.
We build larger correlation matrices of 3 with pairwise correlations
made. We have been using a line of code
simMat=bicor(datExpr1,use=p)
Hi Sam,
I assume you mean that correlation for _genes_ (not samples)
11262:3 is 0? I am the maintainer of the WGCNA package but
unfortunately I don't have access to a Mac big enough to try
3x3 correlation matrix, but I would be thankful if you could
try reproducing the problem with
On Tue, Aug 20, 2013 at 9:23 AM, peter dalgaard pda...@gmail.com wrote:
What is bicor()? From the WGCNA package? Perhaps the package is doing
something incompatible with the long vector support in R 3.0.0. You need to
report such queries to the maintainer.
The maintainer is reporting for
Hi Samuel,
WGCNA currently does not support calculations with matrices larger
than the old R limit, and it will take some time to update it to
support the large matrices. Furthermore, WGCNA relies on other
functions (most notably hclust) that would have to be updated as well
to support long
I am using a variant of stopifnot a lot. can I suggest that base R
extends its functionality? I know how to do this for myself. this is
a suggestion for beginners and students. I don't think it would break
anything.
first, I think it would be more useful if it had an optional character
On Wed, Aug 21, 2013 at 12:11 AM, ivo welch ivo.we...@anderson.ucla.edu wrote:
I am using a variant of stopifnot a lot. can I suggest that base R
extends its functionality? I know how to do this for myself. this is
a suggestion for beginners and students. I don't think it would break
Thank you, it does work now indeed. My platform is 32 bit.
-- Txikiak
On 08/20/2013 12:00 PM, r-devel-requ...@r-project.org wrote:
Date: Mon, 19 Aug 2013 14:08:33 +0100
From: Prof Brian Ripley rip...@stats.ox.ac.uk
To: r-devel@r-project.org
Subject: Re: [Rd] Issues in installing R-devel
On Aug 20, 2013, at 14:41, ivo welch ivo.we...@anderson.ucla.edu wrote:
A second enhancement would be a smart string, which knows that
everything inside {{...}} should be evaluated.
I think one the HTML templating libraries (whisker or mustache or some such)
provides something not unlike
On Tue, Aug 20, 2013 at 11:41 AM, ivo welch ivo.we...@anderson.ucla.edu wrote:
I am using a variant of stopifnot a lot. can I suggest that base R
extends its functionality? I know how to do this for myself. this is
a suggestion for beginners and students. I don't think it would break
If all you care about is emulating static type checking, then you can also
accomplish the same thing with lambda.r using type constraints on function
definitions.
e.g.
f(m) %::% matrix : matrix
f(m) %as% { m }
f(as.data.frame(matrix(rnorm(12),nrow=3)))
Error in UseFunction(f, ...) : No
thx, deepayan: how is stopifnot better than
if (!all(...)) stop()
given that we have stopifnot() and I have seen it used often, I think
my two suggestions would make it better.
thx, michael: the %and% and %or% constructs are indeed relics of my
perl background. my own definition is
On Tue, Aug 20, 2013 at 6:00 PM, ivo welch ivo.we...@gmail.com wrote:
character string at the end of an existing function, stopifnot(). (2)
I think estrings (that behave like characters but are interpolated
before printout) are useful in the same way perl interpolated strings
are useful.
The
functionality is nice. syntax is weird. I think I would have
preferred an interpolate function call.
stop( i(class is `class(pi)` and $pi) )
three typing letters, too, and more logical. most importantly, I wish
we had some form of this in base R from the outset--whatever it is--so
that my
first, I think it would be more useful if it had an optional character
string, so users could write
stopifnot( is.matrix(m), m is not a matrix )
Another option is to just generate better error messages automatically, e.g.:
library(assertthat)
x - 1:10
assert_that(is.matrix(x))
Error: x
On 08/20/2013 11:41 AM, ivo welch wrote:
A second enhancement would be a smart string, which knows that
everything inside {{...}} should be evaluated.
stopifnot( is.matrix(m), m is not a matrix, but a {{class(m)}} )
a variant with more traditional syntax might be
if (!is.matrix(m))
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