Displaying 20 results from an estimated 2000 matches similar to: "step in Sweave"
2007 May 09
1
step() in sink() and Sweave()
Dear developers,
I just noticed that step() function currently prints the current model
using message(), but the resulting model using print(). The relevant
commands within the step() body are:
if (trace) message("Start: AIC=", format(round(bAIC, 2)), "\n",
cut.string(deparse(as.vector(formula(fit)))), "\n")
(with example() output:)
Start: AIC=190.69
2005 Apr 20
0
I: results from sammon()
Thanks for the attention paid to my rpoblem. Please find enclosed
the matrix with my dissimilarities. This is the only case in
which sammon(), from the MASS package, gives me this kind of problems.
Domenico
>
> > -----Messaggio originale-----
> > Da: Jari Oksanen [mailto:jarioksa at sun3.oulu.fi]
> > Inviato: mercoled?? 20 aprile 2005 11.53
> > A: Domenico Cozzetto
>
2005 May 04
1
MacOS X: update.packages(type="mac.binary") fails (PR#7834)
Dear Mr Moderator, please let me through. I want to reply to my own
thread. I once subscribed to this list, but then my subscription was not
accepted.
Now to the business:
The final failure came from missing .install.macbinary() function. I
grepped R-patched sourcesand the only instance of .install.macbinary()
was the call to the function in R-
patched/src/library/utils/R/packages2.R (stupid
2009 May 05
0
stepAICc function (based on MASS:::stepAIC.default)
Dear all,
I have tried to modify the code of MASS:::stepAIC.default(), dropterm() and addterm() to use AICc instead of AIC for model selection.
The code is appended below. Somehow the calculations are still not correct and I would be grateful if anyone could have a look at what might be wrong
with this code...
Here is a working example:
##
require(nlme)
model1=lme(distance ~ age + Sex, data =
2005 Sep 20
1
Shy Suggestion?
The R-exts manual says about 'Suggests' field in package DESCRIPTION:
"The optional `Suggests' field uses the same syntax as `Depends' and
lists packages that are not necessarily needed."
However, this seems to be a suggestion you cannot refuse. If you suggest
packages:
(a line from DESCRIPTION):
Suggests: MASS, ellipse, rgl, mgcv, akima, lattice
This is what happens:
2005 Aug 31
1
Why should package.skeleton() fail R CMD check?
I find it a bit peculiar that a package skeleton created with a utils
function package.skeleton() fails subsequent R CMD check. I do
understand that the function is intended to produce only a skeleton that
should be edited by the package author. I think that it would be
justified to say that the skeleton *should* fail the test. However, I
have two arguments against intentional failure:
* When you
2005 May 04
1
MacOS X: update.packages(type="mac.binary") fails (PR#7836)
Message 2 of today: it works now.
After re-installing R.app from the same R-2.1.0.dmg file, and
fixInNamespace'ing(*) install.packages(), I managed to update 23
outdated packages from CRAN binaries for MacOS X. What I did was to:
1. change call to .install.macbinaries() into call to install.binaries()
in install.packages(). install.binaries() is a function defined
utils/R/aqua/GUI.R.
2. I
2001 Mar 05
1
Canberra dist and double zeros
Canberra distance is defined in function `dist' (standard library `mva') as
sum(|x_i - y_i| / |x_i + y_i|)
Obviously this is undefined for cases where both x_i and y_i are zeros. Since
double zeros are common in many data sets, this is a nuisance. In our field
(from which the distance is coming), it is customary to remove double zeros:
contribution to distance is zero when both x_i
2001 Mar 05
1
Canberra dist and double zeros
Canberra distance is defined in function `dist' (standard library `mva') as
sum(|x_i - y_i| / |x_i + y_i|)
Obviously this is undefined for cases where both x_i and y_i are zeros. Since
double zeros are common in many data sets, this is a nuisance. In our field
(from which the distance is coming), it is customary to remove double zeros:
contribution to distance is zero when both x_i
2001 Oct 02
1
Graceful exit from fortran. (fwd)
rolf at math.unb.ca said:
> If I say something like
> if(x .gt. 42.d0) stop
> then indeed everything stops, i.e. R falls over. I'd ***like*** to be
> able to print out an informative error message (which I guess could be
> done -
In Fortran:
subroutine foo(..., ier)
integer ier
ier=0
...
if (x .gt. 42.d0) then
ier=1
return
endif
2002 Nov 12
2
Wandering usr values in par(no.readonly=TRUW) (PR#2283)
--==_Exmh_1801894504P
Content-Type: text/plain; charset=us-ascii
Dear R folks,
Initially I had a plotting routine using logarithmic y-axes that failed after
repeated calls if I tried to restore the graphical parameters (which I wanted to
do because I used `layout' within the routine. I tried to isolate the problem
and found out that the following code with logarithmic axis is sufficient for
2002 Oct 30
4
Sweave in packages
Dear R folks,
One of the fantastic new tools in R is `Sweave'. I have tested it so much that I
know it works and produces fine documentation, and with (GNU) Emacs/ESS it is
nice to work with, too. I started to have a look at including some Swoven (is
that a strong verb?) documentation with my R package, but it seems that there is
no model to copy among those packages that I have installed in
2005 May 03
1
MacOS X: update.packages(type="mac.binary") fails (PR#7831)
Full_Name: Jari Oksanen
Version: R 2.1.0
OS: MacOS 10.3.9
Submission from: (NULL) (130.231.102.145)
For various reasons (which need not be expanded here) I have tried to update my
long neglected R in MacOS X using handy command line tool update.packages()
using readily available binaries of contributed packages at CRAN. However, this
fails with message saying that packages xxxx_*_tar.gz is not
2008 Feb 08
0
xspline(..., draw=FALSE) fails if there is no open device (PR#10728)
jari.oksanen at oulu.fi wrote:
> Full_Name: Jari Oksanen
> Version: 2.6.2 RC (2008-02-07 r44369)
> OS: Linux
> Submission from: (NULL) (130.231.102.145)
>
>
> Even if function xspline() is called with argument draw=3DFALSE, it req=
uires a
> graphics device (that it won't use since it was draw=3DFALSE). I run in=
to this
> because I intended to use xspline within a
2004 Feb 17
0
New package -- mvpart
The package mvpart is now available.
mvpart includes partitioning based on (1) multivariate numeric responses and
(2) dissimilarity matrices.
The package mvpart is a modification of rpart --
-- authors of original: Terry M Therneau and Beth Atkinson
<atkinson at mayo.edu>, and
R port of rpart Brian Ripley <ripley at stats.ox.ac.uk>.
Includes some modified routines from vegan --
2004 Feb 17
0
New package -- mvpart
The package mvpart is now available.
mvpart includes partitioning based on (1) multivariate numeric responses and
(2) dissimilarity matrices.
The package mvpart is a modification of rpart --
-- authors of original: Terry M Therneau and Beth Atkinson
<atkinson at mayo.edu>, and
R port of rpart Brian Ripley <ripley at stats.ox.ac.uk>.
Includes some modified routines from vegan --
2016 Mar 25
0
summary( prcomp(*, tol = .) ) -- and 'rank.'
> On 25 Mar 2016, at 10:08 , Jari Oksanen <jari.oksanen at oulu.fi> wrote:
>
>>
>> On 25 Mar 2016, at 10:41 am, peter dalgaard <pdalgd at gmail.com> wrote:
>>
>> As I see it, the display showing the first p << n PCs adding up to 100% of the variance is plainly wrong.
>>
>> I suspect it comes about via a mental short-circuit: If we
2017 Aug 25
0
Are r2dtable and C_r2dtable behaving correctly?
> On 25 Aug 2017, at 11:23 , Jari Oksanen <jari.oksanen at oulu.fi> wrote:
>
> It is not about "really arge total number of observations", but:
>
> set.seed(4711);tabs <- r2dtable(1e6, c(2, 2), c(2, 2)); A11 <- vapply(tabs, function(x) x[1, 1], numeric(1));table(A11)
>
> A11
> 0 1 2
> 166483 666853 166664
>
> There are
2000 Mar 21
1
summary.negbin broken in R-1.0.0, VR_6.1-7
Dear R people,
I am not sure if this is the correct place to tell about problems in evolving
programmes, but it seems that the `summary.negbin' function of the excellent
`MASS' library is now broken, and gives the following error message:
> summary(hm)
Error in summary.negbin(hm) : subscript out of bounds
`summary.negbin' calls `summary.glm' which seems to work and give the
2004 Dec 01
3
can't install r package on debian due to linker problem
hi,
my attempt to install the package Hmisc v3.0-1 fails with the message:
/usr/bin/ld: cannot find -lfrtbegin
collect2: ld returned 1 exit status
make: *** [Hmisc.so] Error 1
ERROR: compilation failed for package 'Hmisc'
i'm at a loss here. any hints will be very much appreciated.
i'm running:
debian stable
R version 2.0.1
gcc 2.95.4-14
g77 2.95.4-14
binutils 2.12.90.0.1-4