Displaying 20 results from an estimated 2000 matches similar to: "R package "kernlab" can not be properly loaded"
2011 Mar 07
2
use "caret" to rank predictors by random forest model
Hi,
I'm using package "caret" to rank predictors using random forest model and draw predictors importance plot. I used below commands:
rf.fit<-randomForest(x,y,ntree=500,importance=TRUE)
## "x" is matrix whose columns are predictors, "y" is a binary resonse vector
## Then I got the ranked predictors by ranking
2010 Nov 12
1
can not produce graph using "splom"
Hi,
I wrote a function basically to first read an input data file, then open an pdf file and draw graph using "splom". When testing, I ran the function line by line, it can produce nice plot, but with like 50 warnings. However, whenever I ran this function as a whole, it can not produce any plot, the pdf file has nothing in it. It seems the "splom" function even hasn't
2010 Nov 09
1
library(kernlab) --- unable to load shared library
Dear R users,
I have recently encountered a problem with using the function `library` in
order to load the package `kernlab`.
My output of sessionInfo() is as follows:
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
I have installed the package by
2013 Nov 03
1
Failed to install kernlab package
Hi everyone,
I am trying to install kernlab package, but failed many times by now on
CentOS 6 operating system. FYI, I have no problem with this package
installation on windows platform.
Here is the error message:
trying URL 'http://cran.wustl.edu/src/contrib/kernlab_0.9-18.tar.gz'
Content type 'application/x-gzip' length 1069148 bytes (1.0 Mb)
opened URL
2009 Apr 28
1
kernlab - custom kernel
hi,
I am using R's "kernlab" package, exactly i am doing classification using
ksvm(.) and predict.ksvm(.).I want use of custom kernel. I am getting some
error.
# Following R code works (with promotergene dataset):
library("kernlab")
s <- function(x, y) {
sum((x*y)^1.25)
}
class(s) <- "kernel"
data("promotergene")
gene <- ksvm(Class ~ .,
2006 Nov 24
1
How to find AUC in SVM (kernlab package)
Dear all,
I was wondering if someone can help me. I am learning SVM for
classification in my research with kernlab package. I want to know about
classification performance using Area Under Curve (AUC). I know ROCR
package can do this job but I found all example in ROCR package have
include prediction, for example, ROCR.hiv {ROCR}. My problem is how to
produce prediction in SVM and to find
2008 Aug 27
1
R 2.7.2 kernlab issues
Hello,
After upgrading to 2.7.2 this morning via the cran repository, I get the
following error when calling R via the command line:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/home/jstumpf/R/i486-pc-linux-gnu-library/2.7/kernlab/libs/kernlab.so':
libRlapack.so: cannot open shared object file: No such file or directory
Fatal error: unable to
2012 Nov 29
1
Help with this error "kernlab class probability calculations failed; returning NAs"
I have never been able to get class probabilities to work and I am relatively new to using these tools, and I am looking for some insight as to what may be wrong.
I am using caret with kernlab/ksvm. I will simplify my problem to a basic data set which produces the same problem. I have read the caret vignettes as well as documentation for ?train. I appreciate any direction you can give. I
2013 Apr 03
1
kernlab::kkmeans initial centers
Hi,
I am trying to pass initial cluster assignments to the kkmeans
method<http://rss.acs.unt.edu/Rdoc/library/kernlab/html/kkmeans.html>of
kernlab. It is not clear to me how I can set the parameter
*centers* with "initial cluster centers" as stated in the documentation?
thanks,
--ahmed
[[alternative HTML version deleted]]
2005 Mar 17
1
kernlab sigest
hello,
I have the following problem setting parameter 'frac' in the sigest
function of the kernlab package.
## executing the ?sigest example:
library(kernlab)
data(spam)
srange <- sigest(type~.,data = spam)
## works fine...
## setting 'frac' explicitly
## (in this case even to the default of .25)
options(error=recover)
srange <- sigest(type~.,data = spam, frac = .25)
##
2012 Jul 31
1
kernlab kpca predict
Hi!
The kernlab function kpca() mentions that new observations can be transformed by using predict. Theres also an example in the documentation, but as you can see i am getting an error there (As i do with my own data). I'm not sure whats wrong at the moment. I haven't any predict functions written by myself in the workspace either. I've tested it with using the matrix version and the
2009 Oct 04
3
error installing/compiling kernlab
Hi everybody,
I''m using R on a 64-bit Ubuntu 9.04 (Jaunty). I prefer to install R
packages from source, even if they are available in Synaptic. The
problem is that I can''t install/compile kernlab. Everything works fine
until it gets to the lazy loading part:
** preparing package for lazy loading
Creating a new generic function for "terms" in "kernlab"
2009 Dec 25
2
Help with SVM package Kernlab
Hi useR's,
I am resending this request since I got no response for my last post and I
am new to the list so pardon me if I am violating the protocol.
I am trying to use the "Kernlab" package for training and prediction using
SVM's. I am getting the following error when I am trying to use the predict
function:
> predictSvm = predict(modelforSVM, testSeq);
Error in
2009 Nov 29
2
kernlab's ksvm method freeze
Hello,
I am using kernlab to do some binary classification on aminoacid
strings.
I am using a custom kernel, so i use the kernel="matrix" option of the
ksvm method.
My (normalized) kernel matrix is of size 1309*1309, my results vector
has the same length.
I am using C-svc.
My kernlab call is something similiar to this:
ksvm(kernel="matrix", kernelMatrix, trainingDataYs,
2010 Nov 11
1
change axis labels and text size in "splom"
Hi everyone:
I'm using "splom" to draw scatterplot matrix. I'm wondering how can I change the axis labels to c(1,10,100,1000,...)
instead of c(1,2,3,...), and also how can I change the text size (for labels)?
Thanks a lot!
xcui
2012 Aug 19
1
kernlab | ksvm error
Dear list,
I am using the ksvm function from kernlab as follows:
(1) learning
> svm.pol4 <- ksvm(class.labs ~ ., data = train.data, prob.model = T, scale
= T, kernel = "polydot")
(2) prediction
> svm.pol.prd4 <- predict(svm.pol4, train.data, type = "probabilities")[,2]
But unfortunately, when calling the prediction, once in every 10s of times
(using the exact
2011 Aug 26
1
kernlab: ksvm() bug?
Hello all,
I'm trying to run a gird parameter search for a svm.
Therefore I'M using the ksvm function from the kernlab package.
----
svp <- ksvm(Ktrain,ytrain,type="nu-svc",nu=C)
----
The problem is that the optimization algorithm does not return
for certain parameters.
I tried to use setTimeLimit() but that doesn't seem to help.
I suspect that ksvm() calls c code that
2012 Feb 14
1
cross validation in rvm not working? (kernlab package)
Hi,
according to ?rvm the relevance vector machine function as implemented in the kernlab-package
has an argument 'cross' with which you can perform k-fold cross validation.
However, when I try to add a 10-fold cross validation I get the following error message:
Error in match.arg(type, c("C-svc", "nu-svc", "kbb-svc", "spoc-svc",
2005 Jul 07
1
Kernlab: problem with small datasets
Hi,
I found a small problem with kernlab. The problem, I think, is that the
3-fold cross-validation performed to estimate probabilities is not
class-balanced, so the classifier could find empty classes.
The following example (maybe a little forced) show the error:
data(glass)
set.seed(1)
2007 Dec 17
0
kernlab and gram matrix
Hi, this is a question about the R package kernlab.
I use kernlab as a library in a C++ program. The host application
defines a graph kernel (defined by me), generates a gram matrix and
trains kernlab directly on this gram matrix, like this:
regm<-ksvm(K,y,kernel="matrix"),
where K is the n x n gram kernelMatrix of my kernel, and y is the
R-vector of quantitative target values.