Displaying 20 results from an estimated 9000 matches similar to: "R 2.12.1 is released"
2013 Sep 16
1
Patch: fix segfault from empty raster
Hi,
A colleague recently came across an R crash, which I can boil down to
the following, running under Rgui on Windows 7:
library(ggplot2)
ggplot(data.frame(x=1, y=1, z=4.7), aes(x, y, z=z)) + stat_summary2d()
This reliably causes a segmentation fault. sessionInfo() below.
What's happening is that (for reasons which I'll discuss with the
ggplot2 developers) the 'colorbar'
2004 Dec 09
1
more clustering questions
Sorry to bother you kind folks again with my questions. I am trying to
learn as much as I can about all this, and I will admit that I don't
have the proper background, but I hope that someone can at least point
me in the correct direction.
I have created a test matrix for what I want to do:
s1 s2 s3 s4 s5
s1 10 5 0 8 7
s2 5 10 0 0 5
s3 0 0 10 0 0
s4 8 0 0 10 0
s5 7
2011 Oct 31
1
Question about copying reference objects using the initialize method
Dears,
I have a question about copying reference objects using the initialize method.
1) If the latter has no arguments, there is no problem to copy an object.
myClass = setRefClass("myClass", fields = list(value = "numeric") )
myClass$methods(initialize = function(...){
? value <<- 1
? callSuper(...)
})
newObject = myClass$new()
newObject$value = 2
copyObject =
2010 Jul 02
2
S4 classes and debugging - Is there a summary?
Dear all,
I'm getting more and more frustrated with the whole S4 thing and I'm
looking for a more advanced summary on how to deal with them. Often I
get error messages that don't make sense at all, or the code is not
doing what I think it would do. Far too often inspecting the code
requires me to go to the source, which doesn't really help in easily
finding the bit of code
2005 Jan 08
0
cmdscale problem
Dear R developers,
there appears to be a small problem with function cmdscale: for
non-Euclidean distance matrices, using option add=FALSE (the default),
cmdscale misses the smallest eigenvalue. This affects GOF statistic g.1
(See Mardia, Kent + Bibby (1979): Multivariate Analysis, eq. (14.4.7).
The corresponding formula in Cox + Cox (2001): Multidimensional Scaling,
2nd ed., p 38, would
2011 Feb 18
1
segfault during example(svm)
If do:
> library("e1071")
> example(svm)
I get:
svm> data(iris)
svm> attach(iris)
svm> ## classification mode
svm> # default with factor response:
svm> model <- svm(Species ~ ., data = iris)
svm> # alternatively the traditional interface:
svm> x <- subset(iris, select = -Species)
svm> y <- Species
svm> model <- svm(x, y)
svm>
2003 Oct 07
0
NaN values returned by cmdscale
Hello all,
I'm using R1.7.1 on Linux, generating sammon-optimized MDS plots from
distance matrices. This is a calculation I run routinely, often on
sample sets of up to 100 samples. This time, with three samples, the
sammon function returned an error (shown below), which I tracked down to
the cmdscale function it uses to find a starting configuration. In
short, cmdscale is returning NaN
2002 Feb 15
1
cmdscale k=1
In applying multidimensional scaling, it seems to me that sometimes the
underlying dimensionality of the matrix is 1. However I found a case
where cmdscale failed when I tried k=1. Here it is:
m<-matrix(
c(.5,.81,.23,.47,.61,
.19,.5,.06,.17,.28,
.77,.94,.5,.74,.85,
.53,.83,.26,.5,.64,
.39,.72,.15,.36,.5),
nrow=5)
# BTW I think cmdscale uses only the lower triangle--how to enter only
# that
2001 Dec 18
0
cmdscale: labels missing (PR#1220)
The function cmdscale tries to copy names from the source to the
result. This only works if the source is a matrix.
If m is a matrix with labels (rownames) and d is an object of
class "dist" with labels, this works:
cmdscale(m)
...but with this, there are no labels in the results:
cmdscale(d)
However, this works:
cmdscale(as.matrix(d))
My suggestion is to change, in
2013 Apr 09
0
How does clusplot exactly make use of cmdscale?
Dear people,
I used clusplot to plot a partition result. The partition result was from
pamk with a distance object as input. Then I applied cmdscale on the same
distance object for coordinates to make another scatterplot.
My problem is this: the coordinates from the cmdscale calculation, though
with the same shape, were different in scale and rotation from the scatter
plot yielded by clusplot.
2014 Nov 06
1
limit of cmdscale function
Hi
We have a few questions regarding the use of the "isoMDS" function.
When we run "isoMDS" function using 60,000 x 60,000 data matrix,
we get the following error message:
------------------------------------
cmdscale(d, k) : invalid value of 'n'
Calls: isoMDS -> cmdscale
------------------------------------
We checked the source code of "cmdscale" and
2013 Feb 14
1
mapply error with Math (S4 group generic)
I get an error when using self-defined (not standard) functions with mapply
with S4 objects from the raster package that I develop: "Error in
as.character(sys.call(sys.parent())[[1]]) : cannot coerce type 'closure'
to vector of type 'character'". Does anyone understand why? The problem is
illustrated below. Thanks, Robert
> # First a general example that works
2008 Dec 10
2
exporting rast from R to GRASS
Hi, everybody!
i created a imagem by kriging using geoR package. I imported points
from GRASS("zn", after converted to geodata "zn_geo"), the border
"zn_border" and a raster mask. Then i interpolated the points by
kriging and created a raster image. Now, i need export this image back
to GRASS to use it in the module r.mapcalc. I can't do it. I tried use
2002 Nov 23
0
Intermittant hang in cmdscale (PR#2323)
Full_Name: Cam Webb
Version: 1.6.0 (fink X11 compile)
OS: Mac OS X (Jaguar)
Submission from: (NULL) (64.168.28.87)
This is an unpredictable, intermittant hang during cmdscale of the mva library.
Some data never cause a problem, other data always do, abut I can't track down
the difference in the structure of the data. Sometimes the function will work
for `difficult' data after it has
2013 Feb 14
0
How write raster files after manipulation?
I have 12 binary (raster) files
https://echange-fichiers.inra.fr/get?k=k3M2jatJyHy65Cs99G4 .
I would like to calculate the moving average for the 12 values for each
pixel in the 12 files.
For a simple vector we can get a moving average by using this :
x <- c(1,2,3,NA,NA,4,6,5,6,4,2,5)
movingmean <- rollapply(x, 3, FUN = mean, na.rm = T)
now I want
2002 Dec 19
1
newbie question on dist
hi,
i have just begun using R, so please bear with me.
i am trying to use cmdscale and display the result. i read the data
using read.table(), calculate the proximity matrix using dist() and
the display the result using the cmdscale(). this is very fine.
in addition, i want the display to distinguish between two classes
of records in my data. i have my data records marked as "1" or
2002 Jan 10
1
Size of type double in object type dist (PR#1255)
The following problem occurs in R 1.4.0 and 1.3.1 for Windows95,
but not in R 1.2.0 for Windows95.
The problem does not occur in R 1.4.0 for Linux PC, Linux Alpha
and HP-UX.
Sometimes, the type of 'Size' of an object of type 'dist'
changes from integer into double. Running cmdscale on such a
'dist' object gives invalid results.
I don't know what should be considered
2007 Jun 14
2
Difference between prcomp and cmdscale
I'm looking for someone to explain the difference between these
procedures. The function prcomp() does principal components anaylsis,
and the function cmdscale() does classical multi-dimensional scaling
(also called principal coordinates analysis).
My confusion stems from the fact that they give very similar results:
my.d <- matrix(rnorm(50), ncol=5)
rownames(my.d) <-
2013 Apr 26
1
prcomp( and cmdscale( not equivalent?
Hello,
I have a dilemma that I'm hoping the R gurus will be able to help resolve.
For background:
My data is in the form of a (dis)similarity matrix created from taking the
inverse of normalized reaction times. That is, each cell of the matrix
represents how long it took to distinguish two stimuli from one another-- a
square matrix of 45X45 where the diagonal values are all zero (since this
2010 Oct 15
0
R 2.12.0 is released
I've rolled up R-2.12.0.tar.gz a short while ago. This is a development
release which contains a number of new features.
Also, a number of mostly minor bugs have been fixed. See the full list
of changes below.
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.12.0.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in