gt;
> > On 4 May 2017, at 20:13, Murat Tasan <mmu...@gmail.com> wrote:
> >
> > The only semi-efficient method I've found around this is to `apply`
> across
> > rows (more accurately through blocks of rows coerced into dense
> > sub-matrices of P), but I'
Hi all ---
I have a large sparse matrix, call it P:
```
> str(P)
Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
..@ i : int [1:7868093] 4221 6098 8780 10313 11102 14243 20570
22145 24468 24977 ...
..@ p : int [1:7357] 0 0 269 388 692 2434 3662 4179 4205 4256 ...
Using PostgreSQL's parameterized query form, this works:
R> dbSendQuery(CONN, "SELECT * FROM foo WHERE val = $1 OR val = $2",
list("bar", "baz"))
... and becomes: SELECT * FROM foo WHERE val = 'bar' OR val = 'baz';
I cannot figure out, however, if something like this is possible with
ter it is installed, a character object
> called ".packageName" containing its name. It is not exported from
> the package. Functions in your package can refer to it as just
> .packageName.
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Thu, Dec
In a package I'm writing, I'm placing all SQL code here:
/inst/sql/
And so when referring to these blocks of code from the package's R
code, I do something like so:
system.file("sql", "my_example_file.sql", package = "ThisPackage",
mustWork = TRUE)
But, referring to the package itself with the
The hash package implements hashmaps which must be cleared prior to
removal to free memory, e.g.:
x - hash(some_long_list_of_keys_and_values_here)
clear(x)
rm(x)
I first assumed this held for re-assignment, too... e.g. one should:
x - hash(some_long_list_of_keys_and_values_here)
clear(x)
Hi all --- I've stumbled upon some pretty annoying behavior, and I'm
curious how others may have gotten around it.
When using subset(...) on a data frame that contains a custom S3
field, the class is dropped in the result:
MyClass - function(x) structure(x, class = MyClass)
df - data.frame(x =
:02 PM, Murat Tasan mmu...@gmail.com wrote:
Hi all --- I've stumbled upon some pretty annoying behavior, and I'm
curious how others may have gotten around it.
When using subset(...) on a data frame that contains a custom S3
field, the class is dropped in the result:
MyClass - function(x
... nd nevermind, figured it out (from the final example on the
Extract.data.frame page):
`[.MyClass` - function(x, i, ...) {
NextMethod([)
mostattributes(RV) - attribute(x)
RV
}
cheers,
-m
On Wed, Nov 12, 2014 at 11:02 PM, Murat Tasan mmu...@gmail.com wrote:
And as a follow
for the flexible creation of multiple regions, depending on what
you want to draw in each of those regions.
Paul
On 10/07/14 15:33, Murat Tasan wrote:
6. iteratively downgrade to earlier versions of R until it's working
again... then try to diff out the offending source code change.
i can try
coordinates) to manually
set the clipping region
6 other?
On Mon, Oct 6, 2014 at 12:00 PM, Murat Tasan mmu...@gmail.com wrote:
Hi all -- I just encountered a behavior that I believe has changed
from previous versions, though I haven't chased back the last version
that behaves as my existing code
Hi all -- I just encountered a behavior that I believe has changed
from previous versions, though I haven't chased back the last version
that behaves as my existing code expects quite yet.
Perhaps this is a bug, though perhaps I'm missing a subtle detail
somewhere in the documentation...
Here's
Another (easier) kludge is augmenting a call to each par(plt = ...) call:
par(plt = some_plt_coordinates); box(lty = 0)
The box(lty = 0) addition makes downstream calls work as expected, but
yeah... this is a kuldge.
-m
On Mon, Oct 6, 2014 at 12:00 PM, Murat Tasan mmu...@gmail.com wrote:
Hi
have you looked at the ROCR package?
there are at least a few ways to plot multiple ROC curves with the
ROCR functions that come to mind.
e.g. if you pass lists of 'scores' and 'labels' in to the
prediction(...) method, the default plot(...) method will display all
of the ROC (or precision-recall,
hi all -- i'm running into a strange problem that i can't seem to
easily get around, but i'm probably just missing something obvious.
i have a model to which some data is fit using glm with no intercept
term (using my data variables x and y and a specific link function
mylink):
hi all -- let's say i have the following simplified plyr code:
factor_table - data.frame(dim1 = 1:10, dim2 = 1:4)
foo - maply(factor_table, function(dim1, dim2) list(a = foo, b =
runif(10)))
foo will now be a 10 x 4 x 2 array (of mode 'list'), and i'll have to
access a b element like so:
hi all -- i don't know if this is a bug or not, thought i would survey the
crowd before trying to submit a report...
if i specify a cut height for a dendrogram that is higher than the full
dendrogram itself, my expectation is that the $upper value would be NULL or
NA, and the $lower value would
hi all --
i've written a series of procedures to annotate nodes in a dendrogram
object.
i'd like to be able to easily pluck out some of these attributes and view
them in tree form.
in a regular list, i'd do something like:
sapply(my_list, function(x) x$my_entry)
and in a dendrogram, i can use
attributes(x) - temp
and there are a lot of wasted operations there.)
Duncan Murdoch
Hope this helps,
Rui Barradas
Em 09-05-2013 18:35, Murat Tasan escreveu:
hi all -- i looked through the R Language Definition document, but
couldn't
find any particular warning or example that would
-project.org]
On Behalf
Of Murat Tasan
Sent: Friday, May 10, 2013 8:16 AM
To: Duncan Murdoch
Cc: r-help@r-project.org
Subject: Re: [R] attr vs attributes
thanks, both.
the only real difference between the two approaches that i can see is
when
assigning _new_ attributes to an object
hi all -- i looked through the R Language Definition document, but couldn't
find any particular warning or example that would clarify the best use of
attribute setting for R objects.
let x be some R object, and i'd like to add attribute foo with value
bar.
case 1:
attr(x, foo) - bar
case 2:
, Murat Tasan wrote:
i'm somehow embarrassed to even ask this, but is there any built-in
method for doing this:
my_list - list()
my_list[[1]] - matrix(1:20, ncol = 5)
my_list[[2]] - matrix(20:1, ncol = 5)
now, knowing that these matrices are identical in dimension, i'd like
to unfold the list
i'm somehow embarrassed to even ask this, but is there any built-in
method for doing this:
my_list - list()
my_list[[1]] - matrix(1:20, ncol = 5)
my_list[[2]] - matrix(20:1, ncol = 5)
now, knowing that these matrices are identical in dimension, i'd like
to unfold the list to a 2x4x5 (or some
FYI - this is my current method, but somehow i just don't like it ;-)
foo - array(NA, dim = c(4,5,length(my_list)))
for(k in 1:length(my_list)) {
foo[,,k] - my_list[[k]]
}
-m
On Thu, Feb 14, 2013 at 1:03 AM, Murat Tasan mmu...@gmail.com wrote:
i'm somehow embarrassed to even ask
.
On Sun, Jan 20, 2013 at 2:59 PM, Murat Tasan mmu...@gmail.com wrote:
hi all - i'm having some difficulty figuring out how to convert
between user units (which i can't find a definition for in the
plotrix package) and either (a) device units (e.g. inches with PDFs)
or (b) user coordinates along any
hi all - i'm having some difficulty figuring out how to convert
between user units (which i can't find a definition for in the
plotrix package) and either (a) device units (e.g. inches with PDFs)
or (b) user coordinates along any particular axis.
as an example, suppose i set up a PDF device with
hi all - i've seen versions of this question before, but none seem to get
directly at my solving my (probably very simple) issue:
i simply want to annotate the tick marks on an axis with (superscripted)
10^x notation, and tried this:
axis(1, at = axTicks(1), as.expression(substitute(10^foo,
-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf
Of Murat Tasan
Sent: Wednesday, November 14, 2012 9:06 AM
To: r-help@r-project.org
Subject: [R] vectorized plotmath expressions via substitute()
hi all - i've seen versions of this question before
hi all - i'm trying to 'R CMD build' a package, but i have what
appears to be a bootstrapping problem:
i've included a vignette in my package, with R code interwoven (and
built using Sweave), but in this documentation i have a code line:
library(MyPackage)
now, when trying to build a .tar.gz
hi all - i have a source package i'm writing that i'd like to be able
to install with a special library that my R src files rely on.
to be more precise, i have a normal R package directory structure
(i.e. src/ R/ man/ DESCRIPTION NAMESPACE etc.).
i also have another directory here called depPkg,
files).
am i completely off here in my usage of Makevars?
thanks!
-murat
On Oct 4, 4:52 pm, Murat Tasan mmu...@gmail.com wrote:
hi all - i have a source package i'm writing that i'd like to be able
to install with a special library that my R src files rely on.
to be more precise, i have a normal
so i've narrowed it down to a case that works, and one that doesn't
(but i think should?)
here's the working Makevars file (copied directly):
-- WORKING EXAMPLE
JANSSON_DIR = $(PWD)/jansson-1.3
JANSSON_LIB_DIR = $(PWD)/jansson-1.3/lib
JANSSON_INCLUDE_DIR
hi all - i'm having trouble using lme to specify a mixed effects
model.
i'm pretty sure this is quite easy for the experienced anova-er, which
i unfortunately am not.
i have a data frame with the following columns:
col 1 : Score1 (this is a continuous numeric measure between 0 and
1)
col 2 :
to understand the concepts of mixed effects models, so just walking
you through a lme model specification is not likely to help.
Bert Gunter
On Tue, Jul 27, 2010 at 8:24 PM, Murat Tasan mmu...@gmail.com wrote:
hi all - i'm having trouble using lme to specify a mixed effects
model.
i'm
hi all - i'm just wondering what sort of code people write to
essentially performa an aggregate call, but with different functions
being applied to the various columns.
for example, if i have a data frame x and would like to marginalize by
a factor f for the rows, but apply mean() to col1 and
hi, i'm trying to prepend some plain (i.e. unevalutated) text to a
typographically evaluated R expression in a legend(...) call.
here's a working legend(...) call that is close to what i'd like
(where x and y are returned from an lm(...) call):
legend(topleft, legend = c(bquote(R^2 ==
), as bquote expects an R expression.
On Jul 10, 11:22 pm, David Winsemius dwinsem...@comcast.net wrote:
On Jul 10, 2010, at 10:45 PM, David Winsemius wrote:
On Jul 10, 2010, at 8:58 PM, Murat Tasan wrote:
hi, i'm trying to prepend some plain (i.e. unevalutated) text
, David Winsemius dwinsem...@comcast.net wrote:
On Jul 10, 2010, at 11:22 PM, David Winsemius wrote:
On Jul 10, 2010, at 10:45 PM, David Winsemius wrote:
On Jul 10, 2010, at 8:58 PM, Murat Tasan wrote:
hi, i'm trying to prepend some plain (i.e. unevalutated) text
hi all - i'm working on an R package that makes use of my own shared
library written in C.
but i also am making use of another C-written library.
(my package is for facilitating biological namespace translations via
online (i.e. up-to-date) biological databases.)
problem is, the library i'm using
hi folks, i use ESS mode in emacs often to interact with R, and while
i know how to save a session transcript, i'm wondering how to save
just the history of the commands (i.e. identically to how R gives the
history save option from its native CLI).
if you use ESS with an R process, commands
row names are not the same as line numbers or indices.
you've likely done some row-based selection on an original matrix or
data frame.
observe from the example below.
(and in the future please don't expect people to sort through your
500+ line matrices by hand to find your problems.)
x -
The primary reason is for development.
I do install via the traditional R CMD INSTALL (or variant) method,
but I want to keep the C code external from the R package.
In particular, I want to be able to modify the C code (and thus the
compiled .so library functions) without having to constantly re-
identify that will allow for linking/loading of shared objects along
the LD_LIBRARY_PATH.
On Jan 30, 5:52 pm, Murat Tasan mmu...@gmail.com wrote:
The primary reason is for development.
I do install via the traditional R CMD INSTALL (or variant) method,
but I want to keep the C code external from
hi all, i posted a question before about this, but i may have been too
cryptic to understand.
in short, there exists an R package that someone is writing. this
package depends on a custom library (written in C,), compiled as a
shared, and called by the package's functions via the .Call(...)
hi, i'm having some trouble getting a package to load a shared library
object in .onLoad(...)
i have a shared object file, say mylib.so.
if i start an R session, and via the CLI specify the actual library
via:
dyn.load(mylib.so)
everything works quite well (i.e. i can then follow with some
, but is a
temporary requirement for my writing this package for some colleagues.
On Jan 26, 5:16 pm, Murat Tasan mmu...@gmail.com wrote:
hi, i'm having some trouble getting a package to load a shared library
object in .onLoad(...)
i have a shared object file, say mylib.so.
if i start an R
hi all - quick question:
i have a matrix 'y' of response values, with two explanatory variables
'x1' and 'x2'.
tested values of 'x1' and 'x2' are sitting in two vectors 'x1' and
'x2'.
i want to learn model parameters without unrolling the matrix of
response values.
example below:
# some fake
i've written a function to coerce a matrix (e.g. from numeric to
logical), but i'd like to know if someone has a more elegant method
for this:
m - matrix(c(0, 1, 1, 0), ncol = 2)
m - as.logical(m)
m
[1] FALSE TRUE TRUE FALSE
i'd like 'm' to still be a matrix with the original dimensions. in
,] TRUE FALSE
On Sun, Sep 27, 2009 at 6:59 PM, Murat Tasan mmu...@gmail.com wrote:
i've written a function to coerce a matrix (e.g. from numeric to
logical), but i'd like to know if someone has a more elegant method
for this:
m - matrix(c(0, 1, 1, 0), ncol = 2)
m - as.logical(m)
m
more generally, if you want to test for some minimum threshold T on
the number of zeros, try:
if(length(which(dart[,1977] == 0)) T) { # some code to handle the
too-few-zeros-case }
On Sep 27, 4:54 pm, Marcio Resende mresende...@yahoo.com.br wrote:
I have a matrix 700x2000 which is
hi, folks,
how have you gone about reporting a p-value from a test when the
returned value from a test (in this case a rank-sum test) is
numerically equal to 0 according to the machine?
the next lowest value greater than zero that is distinct from zero on
the machine is likely
hi all - quick question:
i have a matrix m, say nrow=5, ncol=4.
in a function i'd like to retrieve certain rows or columns from m, but
which rows/cols are not known ahead of time.
the function should return a sub-matrix (i.e. still of class
'matrix').
when selecting a single column (or row), the
awesome! thanks much!
On Jul 24, 6:41 pm, Duncan Murdoch murd...@stats.uwo.ca wrote:
On 24/07/2009 6:34 PM, Murat Tasan wrote:
hi all - quick question:
i have a matrix m, say nrow=5, ncol=4.
in a function i'd like to retrieve certain rows or columns from m, but
which rows/cols
Hi - since Rgraphviz was officially moved over to Bioconductor, this might
be a misguided post, but it's worth a shot:
I'm plotting a graph using Rgraphviz and in an attempt to force the edges to
be behind the nodes (on a fairly complex graph), I set the outputorder
graph attribute to edgesfirst
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