s for seasonal time
> series
>
> I would like to see lists corresponding to other
> categories of IMSL. Another classification system is
> GAMS at http://gams.nist.gov/Classes.plain . Section
> L, "Statistics, probability", would be relevant.
I don't see a Task Vie
lt;- try( some calculation )
if (inherits(value, "try-error")) handle the error
else handle a correct calculation
Duncan Murdoch
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PLEASE do read the postin
nts however can be obtained fairly easily.
R can calculate the incomplete gamma function (see ?pgamma), so that's
not necessarily a stumbling block.
Duncan Murdoch
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How do you suggest reading in this file??
>
.gct is not a standard filename extension. You need to know what is in
that file. Where did you get it? What program created it?
Chances are the easiest thing to do is to get the program that created
it to export in a we
t; the 3rd line in this gct file. I would just delete them, but I do not
> know how to open a gct. file
Use skip=2. See ?read.table.
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PLEASE do read t
en the derivative 2ax + b, has 2a = f(1) - f(0) +
f(-1), and b = (f(1) - f(-1))/2.
You should be able to generalize this to the case where the spline is
quadratic between knots k1 and k2 pretty easily.
Duncan Murdoch
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he derivatives.
I don't know COBS, but doesn't predict just evaluate the B-spline? The
point of what I posted is that the particular basis doesn't matter if
you can evaluate the quadratic at 3 points.
Duncan Murdoch
>
> Jim McDermott
>
> On 7/19/05, Duncan Murdoch
reporting all of the
knots correctly. Watch out for coincident knots (zero length
intervals); you don't care about the derivative on those, but they might
cause overflows in some calculations.
Duncan Murdoch
>
> Jim
>
> On 7/19/05, Duncan Murdoch <[EMAIL PROTECTED]> wr
s
complicated, and I think the procedure is quite different in Unix and
Windows. You want to give the process a chance at a clean shutdown if
possible.
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test PREFIX.test
[1,] NA NA NA NA
[2,] NA NA NA NA
[3,] NA NA NA NA
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On 7/20/2005 10:41 AM, Omar Lakkis wrote:
> Is there a way to test if a variable is a date?
Yes, but there are several different things people might call dates.
Which do you mean?
For example,
> today <- Sys.Date()
> today
[1] "2005-07-20"
> inherits(today, "D
er function to work in log
probabilities instead of probabilities, so that you can handle a larger
dynamic range before you run into underflow problems, and you don't need
to use convolve at all. Convert them back to probabilities at the very
end.
Duncan Murdoch
_
gt; the net (google for 'making creating R package') since I would
> guess that just about everyone has significant problems in creating
> their first package on Windows.
As far as I can tell, those all predate the release of 2.1.0. I think
your complaints are out of date.
lease?
Another thing you could do which would be valuable: get a student or
someone else who is reasonably computer literate, but unfamiliar with R
details, to do this while you sit watching and recording their mistakes.
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ciding where it fits and what to replace,
2. correcting the errors,
3. writing it in texinfo format.
I'd be happy to talk with someone who volunteers to do that. (I'd
suggest the volunteer should do number 1 first, so as not to waste a lot
of time on versions that don't fit.)
der directly. It also suggests paper="special", and horizontal=FALSE.
If that doesn't work, you'll have to ask whoever wrote the quality
checking program what they're looking for.
Duncan Murdoch
>
> Neither approach brought the favoured result. The error message I g
bits that are missing from the R-Admin
manual (and perhaps supply them)? It won't get better unless someone
improves it.
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PLEASE do read the pos
ules’. In
this case the Help Workshop will not be needed."
You can also do it on a case-by-case basis, as Uwe says, but I think
editing MkRules makes more sense if you don't want to install HHC.
Uwe's option is documented in ?INSTALL.
Duncan Murdoch
> [EMAIL PROTECTED]:~/src
J. Hosking wrote:
> Duncan Murdoch wrote:
>
>
>>Could you point out the specific bits that are missing from the R-Admin
>>manual (and perhaps supply them)? It won't get better unless someone
>>improves it.
>
>
> R-admin is fine. The problem is
7;ll get this error.
You might want to look at this page
http://www.stats.uwo.ca/faculty/murdoch/software/compilingDLLs/index.html#badname
or this one
http://www.stats.uwo.ca/faculty/murdoch/software/compilingDLLs/fortran.html
for more help.
Duncan Murdoch
__
) %% 4 - 2
The %% is the mod operator, so (x + 2) %% 4 adds 2 then maps all values
into the range 0 to 4. You'll need a different formula for a different
periodic function.
Use plot(f, from=-7, to=7) to see that this works.
Duncan Murdoch
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R-he
variance matrix.
The ellipse package can draw ellipses.
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's solve(t(Y), x). If x is stored as a 1xn
matrix, you'd use t(solve(t(Y), t(x)).
If you're trying to do multiple operations at once, you probably need to
use the second form.
Duncan Murdoch
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o it.
The logic is that being active means being the target of plot output,
and essentially all plot output comes from executed commands, not from
mouse clicks. Since you're executing commands already, why not put in
one more?
Duncan Murdoch
ere are command line options to tell it to skip these; in
particular, --vanilla tells it to skip all of them.
I'd guess your problem is with Rconsole, because that's where the
console settings are normally saved. Rename it to something else and
your problems should go away.
Duncan Murdo
he best way to do this in R?
Sys.sleep(10) should give you a 10 second pause with very little impact
on the system.
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ecific. In Windows, CPU usage measures in at 0% while
in a Sys.sleep loop. (It's not really zero, because R checks for events
to update the display, but it's very low).
Duncan Murdoch
>
> If I use instead
> system('sleep N')
> cpu usage does not go up.
>
iler, but with others it is sufficient to
ask R to set the FPU control word. Instructions are here:
<http://www.stats.uwo.ca/faculty/murdoch/software/compilingDLLs/index.html#fpu>
Duncan Murdoch
>
> On Tue, 2 Aug 2005, Tony Gill wrote:
>
>
>>Hi all,
>>
>>I just
it will actually improve
efficiency: that depends on whether optim evaluates the gradient and
function values at the same points or at different points.
You would use this as follows, assuming your function is called f:
f2 <- splitfn(f)
optim(par, f2$fn, f2$gr, ...)
Duncan Murdoch
___
rror when you did your
edits. The line number information is fairly useless: R has
concatenated all of the files together, you don't see the original line
number. Your best strategy is to look at where you made changes.
I'm hoping to improve the error reporting on parse errors
or here if
it's base code. Be sure to give enough details that others can see
things freeze.
And if it really is frozen, you can use Ctrl-Alt-Del to open the Windows
Task Manager, select the Rgui application, and "End task". Assuming
you have permission, etc.
Duncan Murdoch
&g
r
> "graphics.off()".
There are no exposed functions to do that. You're going to have to look
at the R source code, and add something.
Duncan Murdoch
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.
>
> spencer graves
Yes, I was talking about Rgui.exe. ESC doesn't stop Rterm.exe, which is
what XEmacs is running.
Duncan Murdoch
>
> Duncan Murdoch wrote:
>
>> On 8/4/2005 11:39 AM, Shengzhe Wu wrote:
>>
>>>and how about R on win
t very common. Or...
>
> How to differentiating myValue:
>
> varOne = 100
> varTwo = 50
> myValue = varOne-varTwo
>
> from codes-deprecated, or ns-alt, for example.
...you could do it by context. codes-deprecated will only show up in
*.Rd files as a possible search t
ive that error.
>
>
>>A solution - again given by the error message you quote! - is:
>>
>>./configure --enable-R-shlib --without-recommended-packages
>> ^
>>
>>That should clear things up.
>
>
sv: system is exactly
> singular
You will have to find a different solution to the problem. To machine
precision, that matrix looks singular. This usually indicates that it's
not the right matrix to try to invert.
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Peter Dalgaard wrote:
> Duncan Murdoch <[EMAIL PROTECTED]> writes:
>
>
>>You will have to find a different solution to the problem. To machine
>>precision, that matrix looks singular. This usually indicates that it's
>>not the right matrix to try to
any complicated steps in my computation.
>
> Is there a faster way?
You'd probably do better with matrix multiplication:
rep(1, nrow(A)) %*% A
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On 8/5/2005 12:43 PM, Uwe Ligges wrote:
> Duncan Murdoch wrote:
>
>> On 8/5/2005 12:16 PM, Martin C. Martin wrote:
>>
>>>Hi,
>>>
>>>I have a 5x731 array A, and I want to compute the sums of the columns.
>>>Currently I do:
>>>
>&
uff yet.
My web page
http://www.murdoch-sutherland.com/Rtools/miktex.html
is getting kind of old, but it does tell you how to avoid using e-TeX.
Duncan Murdoch
>
> This is e-TeX, Version 3.141592-2.2 (MiKTeX 2.4) (preloaded format=latex
> 2005.8.5) 6 AUG 2005 09:28
> entering e
9.305764753298 * x1 * x3, where those
coefficients come from some other calculation, just do it like this:
makefn <- function(coeffs) {
function(x1, x2, x3) coeffs[1] +
coeffs[2]*x1 +
coeffs[3]*x2 +
coeffs[4]*x1*x3
}
Then use it like this:
f
ction lets a function do cleanup, and there
are various hooks available (see ?setHook), and finalizers (see
?reg.finalizer) for some kinds of objects.
Duncan Murdoch
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PL
/Desktop/Downloads/biomaRt/R/biomaRt.R')
>
> Error: bad restore file magic number (file may be corrupted) -- no data
> loaded
load() is for binary workspaces. Use source() to read source code.
Duncan Murdoch
__
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e the window; a new one will be created the next time you
draw something.
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wait<-function()
> {
> cat("press return to continue")
> unix("read stuff")
> }
You can also use par(ask=TRUE) to get R to pause the script whenever it
is about to erase the graphics window.
Duncan Murdoch
>
> and this worked nicely because I then
> did
function(expr, data) {
+ x <- eval(substitute(expr), envir=data)
+ return(mean(x))
+ }
> eg.function(a, data.test)
[1] 5.5
The "substitute" says to give back the unevaluated expression used for
the argument.
Duncan Murdoch
>
> Manuel
>
>> Thanks! Just to be sur
> accomplish this.
>
I think you need to do the separation into two parts as you did (or
using %/%), but it can all be one sprintf:
sprintf("%03d-%03d", Number %/% 1000, Number %% 1000)
Duncan Murdoch
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f
> world would that be?! :-)
Now, if you were to suggest that the stem() function is a bizarre
simulation of a stone-age tool on a modern computer, I might agree.
Duncan Murdoch
>
> -- Bert Gunter
>
>
>
>> -Original Message-
>> From: [EMAIL PROTEC
on win2K, MySQL version 5.0.21-community-nt
I don't know why you're using DBI; perhaps it interferes with RODBC somehow.
If that's not it, then you might want to try lower level methods than
sqlSave: perhaps use sqlQuery to send an INSERT command to the
database. Build up from
uot;('", id, "','", col1, "','", col2, "')",
sep="", collapse=",")
query <- paste("INSERT INTO example(id, col1, col2) VALUES", inserts)
sqlQuery(chan, query)
(This isn't even tested to see if I got
of vectors, so you could iterate through the list, using one of the
apply functions (or even a for loop):
apply(x, 2, function(col) {col[is.na(col)] <- 1000; col} )
which is essentially a short form for
for (i in 1:ncol(x)) {
col <- x[,i]
col[is.na(col)] <- 1000
x[,i] <- c
ave it as PNG, for instance.
>
You can type the extension when you save it, if you're typing the
filename. The default
names generally include the extension.
> Previous R versions work without problems.
>
Could you give a detailed description to reproduce the problem?
Duncan Murd
ction(s,n) {
> sig2 <- n*s*s/(n-1)
> 2*(n/(2*sig2))^((n-1)/2) / gamma((n-1)/2) * exp(-n*s*s/(2*sig2)) * s^(n-2)
> }
>
>
Your initial factor looks a lot different from theirs. I think you
believed your variable name (i.e. sig2 is sigma^2), but didn't
define it that
the beginning.
You can also use a file named .Rprofile to contain commands to run; it
is searched for in the current directory, then the user's home
directory. So you could put your source("blahblah.R") into .Rprofile if
you want these functions to always be available.
Duncan
; I have put these in my ".Rprofile". But this is loaded from
> my home directory, not from the directory where I was when I
> started R, so it is the same every time.
Which version of R are you using? This is not the current documented
behaviour. It looks in the current directory
t; for (i in fl) {cat(paste('source("',i,'")\n',sep="")); source(i)}
> rm(i,fl)
>
> in this way you at least don't need a separate `.Rprofile' in each
> project dir.
Another alternative if you want something special in the project is
On 6/19/2006 10:19 AM, Joerg van den Hoff wrote:
> Duncan Murdoch wrote:
>> Just a few comments below on alternative ways to do the same things:
>>
>> On 6/19/2006 8:19 AM, Joerg van den Hoff wrote:
>>
>>> for short term usage of some specialized functions
ons that you don't use every day, or when using
functions written by someone else.
Duncan Murdoch
>
> I find that procedure simpler than learning the package mechanism. It
> is easy to add new functions periodically.
>
> Not long ago, I posted the R code I used to automa
Search("keyword", restrict="functions") (or even
without the "restrict" part).
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ou to fix this.
It needs to be done in the internals of R (function ArrayAssign, in
src/main/subassign.c, if you're interested). I'll try to take a look
and see if it looks reasonable to add.
Duncan Murdoch
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>> b <- array(as.raw(1:6),c(1,2,3))
>> b[1,,]
> [,1] [,2] [,3]
> [1,] 01 03 05
> [2,] 02 04 06
>> b[1,1,] <- raw(3)
> Error: incompatible types (from raw to raw) in array subset assignment
>
> I can work around this with computed i
input. Is there a simple way to get what I want?
E.g.
> x <- c(1,2,3,4,1,2,3,4)
> y <- c(1,2,3,1,2,3,1,2)
> rank(x+y/10)
[1] 1 3 6 7 2 4 5 8
gives me the answer I want, but only because I know the range of y and
the size of gaps in the x values. What do I do in
Peter Dalgaard wrote:
> Duncan Murdoch <[EMAIL PROTECTED]> writes:
>
>
>> Suppose I have two columns, x,y. I can use order(x,y) to calculate a
>> permutation that puts them into increasing order of x,
>> with ties broken by y.
>>
>> I'd lik
missed that
> explains this, I would be grateful.
>
I think the "organized in a certain way" part is actually important.
Using R CMD install --build is the documented way to achieve this. It's
not trivial to do this on Windows, because you need to set up a build
env
Gabor Grothendieck wrote:
> On 6/21/06, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>
>> Peter Dalgaard wrote:
>>
>>> Duncan Murdoch <[EMAIL PROTECTED]> writes:
>>>
>>>
>>>
>>>> Suppose I have two columns,
neccessarily, I know) to
> Sun/Solaris). so the strategy is not restricted to transfer from Linux
> -> Windows.
>
> and it is useful (if it is not 'accidental' that it works at all): in
> this way one can keep very easily in sync several local incarnations of
.
Duncan Murdoch
On 6/26/2006 9:08 AM, Balaji S. Srinivasan wrote:
> Hi,
>
> I recently had a problem installing the rgl package on OS X and put together
> a simple patch. The patched package is available here:
>
> http://jinome.stanford.edu/files/rgl_0.66-patched_for_gcc4.tar
ient to do something like this:
zmat <- matrix(NA, 3, 19)
zmat[cbind(20*x + 1, y/10 - 1)] <- z
x <- (0:2)/20
y <- (2:20)*10
contour(x,y,zmat)
Duncan Murdoch
>
> x y z
> [1,] 0.00 20 1.000
> [2,] 0.00 30 1.000
> [3,] 0.00 40 1.0
On 6/26/2006 10:39 AM, Gabor Grothendieck wrote:
> I think it would be helpful if this were added to the contour help file.
You mean an example of building up the z matrix from points, or just a
general discussion of the issue?
Duncan Murdoch
>
> On 6/26/06, Duncan Murdoch <[EMA
If it dies the same
way, you could perhaps try to diagnose what is going wrong and send a
patch if it's an rgl bug. Given the age of your video driver
(9/20/2000), you might be able to update it and fix a bug there.
Duncan Murdoch
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> If the customized distribution CD is OK, I also hope to get some technical
> help/advice from the core group members if any one is interested.
See the R Installation and Administration manual first. It tells how to
build R installers with non-standard included packages. Hopefully f
On 6/27/2006 8:05 AM, Liaw, Andy wrote:
>
> From: Duncan Murdoch
>>
>> On 6/26/2006 3:14 PM, Dongseok Choi wrote:
>> > Hello all!
>> >
>> > I hope this is the right place to post this question.
>> >
>> > The Oregon Chapter
implementations, so there isn't much motivation to spend
several hours doing the necessary work. But if you want to contribute
this, please do.
Be careful about where you get the code: the interp implementation in
akima is not licensed freely enough to be included in R ("
d DBI, presumably because one is newer than
the other.
I have always found it easier to use RODBC. Because it uses the more
general ODBC interface, it may be slower than a package that is tuned to
a particular database, but it works, which is a substantial advantage.
Duncan Murdoch
ovides different results in some cases, e.g.
> -5 %% 2
[1] 1
> mod(-5, 2)
[1] -1
so be careful about your definitions. I don't know a simple substitute
for instring().
Duncan Murdoch
I'm pretty sure that mod() and
> instring() are very basic and don't have any exoti
ize=4 )
> Xmin <- readBin( con, numeric(), n=1, size=4 )
> Ymin <- readBin( con, numeric(), n=1, size=4 )
>
> I think there is a problem if I read the character. Have you any ideas ???
>
> Thanks for help.
> Jörn Schulz.
I would also worry about the alignment of the
to draw them yourself. That is, draw the
plot with axes=FALSE, then draw the axes using the axis() function,
using pretty() to calculate the tick locations.
Duncan Murdoch
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is
>> what the "integrate" description refers to)?
>>
>
> Just put a "for"-loop in your function to iterate over t.
Or use Vectorize().
vlambdat <- Vectorize(lambdat)
should give a function that can be passed to integrate(), assuming that
lambdat wor
rame"
attribute. This means you can extract the columns as if they were just
lists.
So if your columns are named A, B, and C, and the dataframe is dataf,
you get them as vectors using
dataf$A, dataf$B, and dataf$C
Duncan Murdoch
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sed substitute twice: the inner call gets the unevaluated expression
that was passed as "dependent"; the outer one puts that in place of the
"dep" variable.
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backslashes ("\") as escape characters. It's easier just to
use forward slashes, i.e. c:/Documents..., and easiest of all is to use
the function file.choose() which pops up a file selection dialog.
Duncan Murdoch
> Warning message:
> file.show(): file 'C:Documents and Settin
above); you're probably better off working with .Rprofile.
Duncan Murdoch
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> pmin(table(tb))
V2
V1 A M O S
Apple 1 0 1 1
Mango 1 1 0 1
Orange 1 0 1 1
> pmin(table(tb[,2:1]))
V1
V2 Apple Mango Orange
A 1 1 1
M 0 1 0
O 1 0 1
S 1 1 1
Duncan Murdoch
>
>
>
see how the author would
like to be cited, or a default format if the author hasn't specified.
Duncan Murdoch
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On 7/8/2006 3:44 PM, justin rapp wrote:
> I apologize for my constant questions but I am new to R and trying to
> gain an appreciation for its capabilities. The following task is easy
> in Excel and I was hoping somebody could give me a quick explanation
> for how it can be acheived in R so I can
ad of var(x). Whether that makes sense depends on the context of
your problem.
Duncan Murdoch
>
> When I use:
> by(data.logistic,data.logistic$Ydrafted,summary)
>
> I receive no errors. I cut and pasted your mysummary function directly
> into my r console. Should I have made
sults.
For example, in the case of FracSim, the error occurred when trying to
run the fracsim.1d example. Apparently the example gave no finite
values so plot() couldn't set up a coordinate system. (You can see this
if you click on the "ERROR" link in the summary.)
Since t
basename() works. If you're on a system that doesn't think \\ is a path
separator, you could do something like
x <- "C:\\Documents and Settings\\myName\\My
Documents\\RProjects\\Project1\\file.name.csv"
basename(gsub('\\\\','/',x))
Duncan Murdoch
1000)
> plot(vec,vec,log="xy", axes=F)
> axis(1, at=10^c(0,2,4,6), labels=expression(1, 10^2, 10^4, 10^6))
> axis(2, at=10^c(0,2,4,6), labels=expression(1, 10^2, 10^4, 10^6))
> box()
Duncan Murdoch
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ot;.
>
> I can't seem to find it!
>
> So where should I be looking?
The devices are in the grDevices package. Look in the src directory
there for the C code. XFig is in the devPS.c file.
Duncan Murdoch
>
> Also -- a more general question on this topic -- presumably
&g
On 7/10/2006 8:51 PM, Randy Zelick wrote:
> Hello there,
>
> This question is relative to WindowsXP, using R 2.2.1:
Time to upgrade. choose.dir (mentioned by Rich) was introduced in the
next release.
Duncan Murdoch
>
> I am looking for a function that allows a user to interac
The same question applies to "--no-restore-data",
> although this presumably would have to be decided in a .First()
> function or something like it.
>
This one can't currently be changed.
Duncan Murdoch
> on a similar note, I would love a CMD BATCH invokation to output jus
This looks to me like a good suggestion, but I generally don't make
modifications to platform-specific things on platforms I don't use, so
I'd suggest posting this to R-devel or on the bug list as a wishlist
item. Otherwise it might get lost.
Duncan Murdoch
_
gs into errors, so traceback will work.
A common situation where I've seen that error is with binary saves from
earlier versions of R being loaded into current versions. For example,
if you installed a package before, but didn't re-install it with 2.3.1,
or if you are reloading a works
On 7/11/2006 6:59 PM, Patrick Connolly wrote:
> On Tue, 11-Jul-2006 at 06:41PM -0400, Duncan Murdoch wrote:
>
> []
>
> |>
> |> options(warn=2) will convert warnings into errors, so traceback will work.
> |>
> |> A common situation where I've
hat.
If you prefer the newsgroup interface, you should also look at gmane.
Gabor G posted a list of the newsgroups here:
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/75239.html
recently.
Duncan Murdoch
>
> Best, Darren
>
> __
> R
way:
library(tripack)
y <- runif(100)
x <- runif(100)
vm <- voronoi.mosaic(x,y)
plot(vm)
points(x,y,col='blue')
and if you want the axes,
axis(1)
axis(2)
box()
Duncan Murdoch
> plot(x,y,col='blue')
>
> when you look at the plot of the mosaic overlayed with the raw d
> profiles, how do i put them in a single figure with labels identifying each
> one of them?
> This thing is getting me almost crazy...
See the corresp() function in MASS and the cca() function in vegan.
Both of these can produce biplots.
Duncan Murdoch
mistaken.
>
> I am running R 2.3.1 and have recently updated all packages.
I reproduced this once in R-patched, but since then have been unable to
do so. I can reproduce it reliably with "set.seed(1)" at the start in R
2.3.1. So it looks to me as though we've pro
n function that calls the one in zoo and modifies the result.
I don't think you should modify zoo without really careful thought: you
should assume that the package has been tested the way it was written,
and may give incorrect results if you go in and change one function
without considering
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