as Jeff mentioned.
As to David and his large bundles; those would definitely be appreciated.
Duncan Murdoch
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PLEASE do read the postin
ng failed. You could look at
plot(profile(fit.nls.s)) to see an indication of what's going on. If
your tau values don't exceed 2 on one side of the estimate, you can't
get a confidence limit on that side. Your data may not rule out any phi
values, or may not rule out a lower limit on
l options reset, dev()
> closed, environments detached and deleted, ...?
>
Not with the standard front-ends. I would guess you could write your
own front end that did that, but it would probably be easier to just
run R in a separate process, and close and restart it. I think that's
x27;s hard to read your message (I think it was posted in HTML), but I
think those are all valid errors in building those packages. You appear
to be missing some of their dependencies. This is not likely related to
permissions.
Duncan Murdoch
__
R-h
; confint(g1, level = 0.94)
Waiting for profiling to be done...
2.5% 97.5%
a0 1.257512 1.330881
KP 125.814709 163.862802
That's very strange. It would be nice to see a reproducible example.
Duncan Murdoch
__
R-help@r-pr
have roughly a N(0,1) distribution
if the parameter is
correct, so the confidence region corresponds to the set of parameters
where tau is in the
central 95% of that distribution, i.e. +/- 1.96. If tau never goes
outside that range, then you can't limit the parameter.
Duncan Murdoch
T
anding how to do this?
Can't you just call g(...)? I don't understand what the problem is.
Duncan Murdoch
Thanks a lot for your help!
Cheers,
Luca
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with names on them. I'd still advise
against using c(...), but it will give you the output you want with that
input; the problem is if your users do something like
g(1:2, 3:4) (which would give c(x1=1, x2=2, y1=3, y2=4)).
Duncan Murdoch
__
R-help
n 64 bit precision when the 32 bit compiler does them in
80 bit precision. Of course, individual calculations being more
accurate doesn't mean the final answer is, but small numeric differences
in floating point calculations are to be expected.
Duncan Murdoch
on
> that side of the continent.
>
It's possible that the mirror manager is unaware of this, and might like
to be informed. I know him, and will send an email.
Duncan Murdoch
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source = getOption("keep.source.pkgs"), which
defaults to FALSE. Normal evaluation uses getOption("keep.source"),
which defaults to TRUE.
You can see the difference if you save the functions, and use str(), e.g.
f <- function(x)1
g <- function(x)1
str(f)
str(g)
Duncan
, because they tend to use more 80 bit extended precision
intermediate values, but that is not guaranteed.
Rounding before comparing makes sense, but I would use signif() instead
of round(), I would choose a relatively small number of significant
digits, and I would expect to see a few false positive
> 32-bit and 64-bit. Note that coef()$fRow is a 1266 x 6 data.frame. Is it
> correct to infer that tiny difference between 32-bit and 64-bit are
> possible but have a low probability of occurring?
Differences are rare, but it's hard to assign a probability to them.
Duncan Murdoch
&g
But if you tried that, you'd get a different error:
> help.search(“linear algebra”)
Error: unexpected input in "help.search(“"
Assuming what you really typed was using plain ASCII quotes, please try
a recent R-patched version. The search
help.search("linear algebra")
wor
actually not really in the package source;
it's in the main part of the R sources, in file
https://svn.r-project.org/R/trunk/src/nmath/dbeta.c
(though it takes a few steps to get there, starting in the stats package
function do_dbeta).
Duncan Murdoch
>
> See the following.
>>
epend on which database system you're using, and I
think for all of them the question would be off topic here. You need to
ask on their help forum.
Duncan Murdoch
>
> Thanks once again, I'm very grateful.
>
>
> On Mon, Jun 8, 2015 at 2:06 AM, Duncan Murdoch <mailto:
arning in my opinion.
It is a common idiom in R programming to treat non-zero values as TRUE,
and zero as FALSE. If every use of a number where a logical is needed
generated a warning, you'd be swamped with them.
Duncan Murdoch
>
> mean(c(1,NA,10),10,200)
>
>
>
> On 08/
ub() or gsub() to replace the spaces with underscores.
Duncan Murdoch
> Sarah
>
> On Mon, Jun 8, 2015 at 10:15 AM, John Sorkin
> wrote:
>> I am reading a csv file. The column headers have spaces in them. The spaces
>> are replaced by a period. I want to replace the spac
uld you put together a tarball of the
package that I could actually run?
Duncan Murdoch
>
> ### BEGIN EXAMPLE ##
>
> #' Fake package to show nlme error
> #' @export
>
> main_function <- function(x){
> library(nlme)
> result <
On 16/06/2015 10:34 AM, Greg Hather wrote:
> Hi Duncan,
>
> I checked the global environment, and it was empty, so I think that
> rules out the second possibility. I posted a tarball at
>
> https://drive.google.com/file/d/0B8hBX90jtuLcaGtOUktqV2V4UUU/view?usp=sharing
>
> Thank you for your help
ult library? Perhaps you should try installing to
a personal library instead.
Duncan Murdoch
>
> Best,
> Uwe Ligges
>
>
>>
>> Thanks,
>> Axel
>>
>>
>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>> &
author didn't find
it very easy to use, but it might be worth investigating again.
The author put together a web page
http://r-resources.massey.ac.nz/StatSoftware/
that you might find useful as well.
Duncan Murdoch
__
R-help@r-project.or
ANextra"])
>options(repos=r)
> })
>
> -> packages are taken from cran.rstudio.com
>
> None of the solutions worked under RStudio, the packages are always
> installed from the public servers. Any ideas?
Your options seem to be trying to put a length two vect
;
> Thus if I output my plot with pdf(width=5, height=5) or pdf(width=15,
> height=15), the font-size / symbol-size remains the same.
>
>
> Is that possible in R?
That's the default, isn't it?
You need to give some reproducible code and explain what you
ibly, what actually
> *is* required.
There's often a difference between a requirement and the test for it.
If you meet the requirement, you should pass the test, but you can often
pass the test without meeting the requirement, and then you may find
that the test is improved in a later versi
modify the
expression than the text representation of it. For example, I think
your code would modify strings containing "pi", or variables with those
letters in them, etc. If you used substitute(expr) without the
deparse(), you could replace the symbol "pi" with the call to
On 04/07/2015 8:21 AM, David Winsemius wrote:
>
>> On Jul 3, 2015, at 11:05 PM, Duncan Murdoch wrote:
>>
>> On 04/07/2015 3:45 AM, David Winsemius wrote:
>>>
>>>> On Jul 3, 2015, at 5:08 PM, David Winsemius wrote:
>>>>
>>>>
>&
ingly un-
smart (it would not be the first time).
That's strange: the URL works for me. Perhaps you were unlucky and
tried while it was being replaced?
Duncan Murdoch
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do with what it
> *really* wants.
That's false. If you haven't given a complete sentence, you might still
pass, but if you have, you will pass. That's not "nothing to do" with
what it really wants, it's just an imperfec
f you want it displayed using native OpenGL code, it's likely a lot
more work. On Windows it's probably easiest; I don't know how hard it
would be to do on other platforms. I would not personally spend any
time on it.
Duncan Murdoch
> My code:
> library(rgl)
> library(
to give your object a class, and define a print method for that
class. It's pretty simple:
functionReturningTwoValues <- function() {return(structure(list(first=1,
second=2), class="MyClass"))}
print.MyClass <- function(x, ...) {
print(x$first, ...)
}
This is usin
> mh1823 POD package successfully from local zip file
It looks as though R couldn't make any connection. Perhaps you are
using a proxy? It looks as though you are on Windows; if so, you could
try running
setInternet2(TRUE)
before the install; that will use the proxy settings for Interne
to write a function f of x and y that produces the fitted
values. I haven't checked, but I'd assume it needs to take vector
inputs and produce a vector of responses. Then
persp3d(f)
will draw the surface. See ?persp3d.function for details on setting the
x and y ranges, etc.
Dunc
ifferent cores?
If you run your scripts in R (not under RStudio) it's certainly possible
to have multiple R processes running at the same time. Just do it.
Duncan Murdoch
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https:/
E -Iext/ftgl
-I/opt/X11/include/freetype2 -Iext -I/usr/local/include
-I/usr/local/include/freetype2 -I/opt/X11/include -Wall -mtune=core2
-g -O2 -fPIC -Wall -mtune=core2 -g -O2 -c ABCLineSet.cpp -o ABCLineSet.o
and so on.
Duncan Murdoch
__
R-help@r-proj
rom_swirl" is doing, so it's hard to say.
You should ask its author.
If it is using the "wininet" method to download from an https site, then
it is Windows that is issuing the error: you may be able to configure
Internet Explorer to avoid it. Ask Microsoft how.
Dunc
On 19/07/2015 4:58 PM, Preetam Pal wrote:
> Hi,
> If i have a quadratic objective function with a system of linear constraints
> for multiple variables, is there any inbuilt function that i can use?
Google says the quadprog package should help.
Dunca
#x27;
>
> What could be a way out of this maze?
>
You should build (to a *.tar.gz tarball) first. That will probably succeed.
Then try to install the tarball. That will probably fail with the same
error as above. If so, make it available to someone else to try.
Duncan Murdoch
_
ed with it, but setting a "plot.new" hook (or
"before.plot.new") might do it for you. See ?plot.new.
It might be tricky, because some par() parameters (e.g. "mfrow")
shouldn't be called before every plot. You'd have to look at
par("mfrow") to d
ackage
doesn't have one, it sounds as though it hasn't been actively
maintained. Will definitely be a case of "some assembly required", not
to mention the usual "use at your own risk".
Duncan Murdoch
>
> (I also tried type = “
u use
setInternet2(TRUE)
This will be the default in R 3.2.2 (and is the default already in
R-patched).
Duncan Murdoch
>
> Warning: unable to access index for repository
> https://cran.r-project.org/bin/windows/contrib/3.2
>
> Warning message:
>
> package �MTS� is not availa
On 26/07/2015 9:10 PM, Steven Yen wrote:
> How do I judge if a matrix contain any NA or otherwise non-missing,
> non-numerical?
David told you about any(). You may also want to use !is.finite()
instead of is.na().
Duncan Murdoch
> In the following, I would like to deliver ONE logica
the
problem to them. This list is just for R.
The likely cause of that error in R is a corrupted file. That might be
.Rdata, or whatever file you're trying to load or read.
Duncan Murdoch
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s far slower than I'd
expect. I just used the code below to set up a database of 1
documents of 2000 letters each, and searching those documents for "abc"
takes about 70 milliseconds:
database <- replicate(10000, paste(sample(letters, 2000, rep=TRUE),
collapse="")
a good
> R hack to do this?
On Windows, shell.exec(dir) will open Explorer at that directory.
(It'll do something else if dir isn't a directory name, or has spaces in
it without quotes, so you need to be a little careful.)
On OSX, system2("open", di
dle changes (e.g. 1 changed to 2 in the 3.2.0 release). It's a patch
release when only the patchlevel changes.
Duncan Murdoch
> ---
> Jeff NewmillerThe . . Go
On 05/08/2015 4:36 PM, peter dalgaard wrote:
>
>> On 05 Aug 2015, at 20:32 , Duncan Murdoch wrote:
>>
>> On 05/08/2015 2:15 PM, Jeff Newmiller wrote:
>>> So 3.1.3 to 3.2.0 was a major release?
>>
>> Yes. We do have the oddity (see ?version) that 3 is
On 08/08/2015 1:32 PM, Waichler, Scott R wrote:
> Hi, I can't install package rgl. The last lines from the install process
> talking about the error are:
I'd guess you have an OpenGL problem. Does glxgears run?
Duncan Murdoch
>
> ** testing if installed package can
> 24839 frames in 6.0 seconds = 4153.389 FPS
> 7152 frames in 6.0 seconds = 1192.594 FPS
> . . .
>
So it looks as though OpenGL is working. I really have no idea what is
causing the error you're seeing. rgl works for me, but I don't have a
64 bit Linux to try it on. (
in ?path.expand and the R for Windows FAQ. Thierry
should set the R_USER environment variable to whatever home dir he
wants. RStudio is probably doing that for him.
Duncan Murdoch
>
> Sarah
>
> On Tue, Aug 11, 2015 at 10:41 AM, Thierry Onkelinx > wrote:
>
>> Dear all,
s.
And the docs do recommend using system2() rather than shell(). But I
don't think either of those things should have caused that error.
Duncan Murdoch
>
> On August 12, 2015 10:05:19 PM PDT, Anshuk Pal Chaudhuri
> wrote:
>> Hi All,
>>
>> I have been trying
oo long to execute,
and some timer ticks get lost; I'm not sure if the underlying code takes
account of that.)
Duncan Murdoch
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PLEASE d
mula on the very first line; that's already a formula.)
Duncan Murdoch
Regards,
Philippe
[[alternative HTML version deleted]]
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h
y the maintainer of the
package. Have you tried writing there? (You might already know the
answer if you've reported the "issues" to them.)
Duncan Murdoch
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https://
On 05/12/2014 3:11 PM, Ranjan Maitra wrote:
On Fri, 5 Dec 2014 12:54:17 -0500 Duncan Murdoch
wrote:
> On 05/12/2014 12:34 PM, Ranjan Maitra wrote:
> > Hi,
> >
> > I have been using Deducer for the past year for my very basic 100-level
introductory statistics classes fo
iterartions.
I'm not sure what you mean by the last part, but you can generate binary
data using rbinom:
firstgroup <- rbinom(9, size=1, prob=0.999)
second <- rbinom(13, size=1, prob=0.001)
third <- rbinom(14, size=1, prob=0.5)
Duncan Murdoch
Frederic Ntirenganya
Maseno Unive
could not provide an answer to my problem.
But it refers to demo(plotmath), and that's where you could find the
answer to your question: use bar(). For example,
mtext(text=expression(Winter(DJF)~mean~daily~precipitation~bar(italic(P))), side=3,
line=1, cex=1.3, col="bla
ks.
The test you want is based on is.null(), and you definitely don't want
quotes there. For example,
if (!is.null(obj$spec) && !is.null(obj$spec$Fisher))
Fisher <- obj$spec$Fisher
Duncan Murdoch
__
R-help@r-project.org mailing li
env1, ...) # use the first one again
On the other hand, maybe it only makes sense for one of these to ever
exist. Then you should create one for the package,
and just use that. For example,
env <- new.env(parent = emptyenv())
fn1 <- function(...) { # get stuff f
lt is added to
functions you load via source(), but not to functions in a package,
because it makes the image noticeably bigger. You can add it to package
code by setting an environment variable during the INSTALL: the
variable is "R_KEEP_PKG_SOURCE=yes". Presumably RStudio is telling yo
http://www.infoworld.com/article/2688074/big-data/big-data-164727-bossie-awards-2014-the-best-open-source-big-data-tools.html
Turns out R won an award (on September 29!), and we didn't even notice.
The RCloud project also won one.
Duncan Murdoch
_
in special
conditions at all. The only way you'll get a different value is if the
argument to is.na() does tricky stuff like looking at the evaluation stack.
Duncan Murdoch
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https://stat.
to 404s. There are no NEWS files in here
> either: http://cran.r-project.org/doc/html/ So there are a bunch of
> broken links here.
If you read these from within the HTML help system in R, the links
aren't broken. CRAN copied some of the files from there, but not all.
You can also
ength 2."
>
> I do think I get what is going on with this, but why should I buy into
> this conceptualization? Why is it better to say that a matrix *is* a
> vector than to say that a matrix *contains* a vector? The latter seems to
> be the more common way of thinking bu
On 25/12/2014 3:59 PM, Bert Gunter wrote:
> On Thu, Dec 25, 2014 at 12:41 PM, Duncan Murdoch
> wrote:
>> Would you say a cube contains a polygon, or a cube is a polygon?
>
> Neither, actually. I'd say a cube is a polyhedron or a square is a polygon.
>
> :-)
>
ed mode having no attributes other
than names". The page also points out a third meaning for the word,
i.e. "the formal class "vector" in the methods package".
So all your confusion is somewhat understandable, but it's still tiresome.
Duncan Murdoch
>
>
>
not writable by
you. There are two solutions: use "Run as administrator" when you run
the installer, or install it somewhere else.
Duncan Murdoch
>
>
>
> Would you please help me to successfully complete download process so that I
> can start improing my R ski
t;- sum((x-a)^2)
> attr(res, "gradient") <- 2*(x-a)
> res
> }
> ---
> I get the gradient with
> attr(f(3,2),"gradient")
> but how do I get the function value it self?
value <- f(3,2)
gradient <- attr(value, &
RUE.
Duncan Murdoch
>
> I run a program whose global variables take up about 50 Megabytes of
> memory, but when I monitor the progress of the program it seems to
> allocating 150 Megabytes of memory, with peaks of up to 2 Gigabytes.
>
> I know that the global variables aren't
o a function that modified it could attach c(3,3,1) as
an attribute, and later functions that wanted to do more things to it
could start looking there.
I guess the tricky part would be getting rid of that attribute if you
didn't want to pass it along the chain, e.g. the final call shouldn&#
; Error in gzfile(file, "wb") : cannot open the connection
> In addition: Warning message:
> In gzfile(file, "wb") :
> cannot open compressed file 'c:/data', probable reason 'Permission
> denied'
Can you save to the file "c:\data" fr
what result is expected
for any real number x. Since R's numeric type only approximates the
real numbers we might not be able to get a perfect match, but at least
we could quantify how close we get. Or is the input really character
data? The original post mentioned reading numbers from a t
On 01/01/2015 1:21 PM, Mike Miller wrote:
> On Thu, 1 Jan 2015, Duncan Murdoch wrote:
>
>> On 31/12/2014 8:44 PM, David Winsemius wrote:
>>>
>>> On Dec 31, 2014, at 3:24 PM, Mike Miller wrote:
>>>
>>>> This is probably a FAQ, and I don'
On 01/01/2015 2:43 PM, Mike Miller wrote:
> On Thu, 1 Jan 2015, Duncan Murdoch wrote:
>
>> On 01/01/2015 1:21 PM, Mike Miller wrote:
>>> On Thu, 1 Jan 2015, Duncan Murdoch wrote:
>>>
>>>> On 31/12/2014 8:44 PM, David Winsemius wrote:
>>>>
On 01/01/2015 10:05 PM, Mike Miller wrote:
> On Thu, 1 Jan 2015, Duncan Murdoch wrote:
>
>> On 01/01/2015 1:21 PM, Mike Miller wrote:
>>
>>> I understand that it's all about the problem of representing digital
>>> numbers in binary, but I still find som
ectory `/home/Edoardo/r-3.1.2/src'
> make: *** [R] Error 1
>
>
> I am not an expert programmer and would appreciate some help. My final
> objective is to install R as shared library in order to use RHIPE.
> Thanks
>
This sounds more like an R-devel topic for discuss
irely using other types, that's the sort of thing that belongs in a
user-contributed package. I'm not aware of one that already has it, so
you may have to write this yourself.
Duncan Murdoch
>
> It isn't a big deal for me because unsigned 16-bit integers are working
>
the way GNU tr (Linux/UNIX) works. I'm looking around
> and not finding such a thing. I can use gsub() to translate on the fly
> and then coerce back to integer format:
It's really trivial to write a wrapper for readBin to do what you want:
myReadBin <- function(...) {
X
R-forge in the nls14 package.
With that package, you get the same error as in base, but you can do
newDeriv(`[`(x,y), stop("no derivative when indexing"))
and then fnDeriv() (the nls14 replacement for deriv()) works on your
example.
Duncan Murdoch
>
> Thanks again,
> Erin
>
that are really just
small-form-factor laptops should be okay.
But your old toshiba laptop is probably okay too --- as long as it is
running Windows XP or newer, it is probably fine for R.
Duncan Murdoch
__
R-help@r-project.org mailing list
t use packages that misbehave. The ideal R package
will run on all platforms where R runs. Some require effort from the
user to provide prerequisites, but no good R package runs only on one
platform.
Duncan Murdoch
__
R-help@r-project.org mailing
s them to LF.
This is really irritating when files get changed for no good reason.
Duncan Murdoch
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PLEASE do read the posting guide h
u can probably use quartz.options() to change the default size and
avoid the above problem.
Duncan Murdoch
> Thanks,
>
> Mike
>
> On Mon, Jan 12, 2015 at 1:46 PM, Fraser D. Neiman
> wrote:
>
>>
>> In my experience, another negative to RStudio is its performance
are set in a text file that
is loaded at startup, or when you call the loadRconsole() function. You
can also save or load it from the menu, using the Edit | GUI
preferences... dialog.
Duncan Murdoch
>
> PS. Neither setOutputColors, nor require(colorout) work in the interactive
> session
hat many people has seen something
> similar, before. However, somehow, I can't find an answer string on
> stackexchange or analogous pages.
>
> Thanks in advance!
>
Is that just daylight savings time ending? 3 AM standard time is two
hours later than 2 AM daylight savings
I don't know the answer to your question. If nobody else answers it,
I'd suggest asking in R-devel instead, and include some simple code that
illustrates the problem, e.g. using "echo" to pipe something into an R
process and explaining what part of the output you want to suppr
On 16/01/2015 3:55 AM, PRAMEET LAHIRI wrote:
> find_rtools() is a function of the 'devtools' package. Maybe it's an
> issue with that package and not R, and I'm pretty sure Duncan Murdoch
> put great efforts in asserting Rtools is working well with R (that's
>
x <- c(-30,30)
>> y <- c(-5,5)
>> plot.window(x , y)
>
> or any other form of "plot" function, it doesn't show anything. I used
What are you expecting to see? As the help says, plot.window() doesn't
plot anything, it just sets up the coordinates. Use plot
llion entries. If your computer has a couple GB of
memory, that should be no problem (though it's not hard to think of
models where it really would be a problem, e.g. y ~ .^2).
You should post more details (and not in HTML) for more specific help.
Duncan Murdoch
I tried attaching the data
t call to be sure
they cover the full range of both datasets.
Duncan Murdoch
>
> thanks
> Alireza
>
>
> convertToRadius<-function(x){return(sqrt(x/pi))}
>
> myd=data.frame(x=c(84390255386 ,74390255386, 78028317380 ,53594648044,422)
>,y=c(9498
so every T gets converted.) The reason is that you didn't tell
read.table what type to expect, so it tried to work it out from the values.
If you know that all values are character, say so, and things will be fine:
read.table(, colClasses = "character")
(You might want
. You could try running your code under valgrind if
you know how to do that (or want to read the manual and learn).
Duncan Murdoch
>
> This is on Ubuntu 14.10 with R built from source.
>
> > sessionInfo()
> R version 3.1.2 Patched (2014-12-08 r67137)
> Platform: x86_64-unknown-
much appreciated.
You posted this question in R-devel yesterday. That's probably the
right location; reposting it here is not the solution.
More comments there.
Duncan Murdoch
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1111
> But, then I get this funny result !!!
> all(pcor[,1]==1)
> [1] FALSE
>> pcor[2,2]==1
> [1] TRUE
>> pcor[3,2]==1
> [1] FALSE
> Could anybody please comment on this?Many thanks.
> [[alternative HTML version deleted]]
Please just sen
ill
be displayed without decimals if they are close enough to whole numbers.
Duncan Murdoch
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On 30/01/2015 8:17 AM, Knut Krueger wrote:
Am 30.01.2015 um 12:51 schrieb Duncan Murdoch:
> You are mixing up formatting with storage. Floating point numbers will
> be displayed without decimals if they are close enough to whole numbers.
>
> Duncan Murdoch
>
Ok, I am talki
s not a base
R function.
Duncan Murdoch
>
> I thought I would need the x/y elements (as described in the help file
> at the end of the description of the use of the dpl argument) to
> describe ad hoc dummy points as way to define a polygon or two as a
> boundary. However, it gives
ed packages:
[1] knitr_1.8 animation_2.3 rgl_0.95.1158 CBRIutils_1.0
That's an old version of rgl; current on CRAN is 0.95.1201.
<http://cran.r-project.org/src/contrib/rgl_0.95.1201.tar.gz> (CRAN OSX
currently has an old binary; I don't recommend that you use it. I don
tically. You just
need to say that you want the WebGL driver, and it handles the details.
I've used it with Markdown (that's what the current rgl vignette uses),
but there are also other input formats that can produce .html output.
Duncan Murdoch
Keith J
On 03/02/2015 15:14, Dunc
On 03/02/2015 12:18 PM, David Winsemius wrote:
On Feb 3, 2015, at 7:14 AM, Duncan Murdoch wrote:
> On 03/02/2015 9:43 AM, keith.jew...@campdenbri.co.uk wrote:
>> Dear all,
>>
>> I am using writeWebGL to create an HTML page containing an interactive 3D plot. It works f
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