@stat.math.ethz.ch
Cc: Tuszynski, Jaroslaw W.
Subject: baseline fitters
I am pretty pleased with baselines I fit to chromatograms using the
runquantile() function in caTools(v1.6) when its probs parameter is
set to 0.2 and its k parameter to ~1/20th of n (e.g., k ~ 225 for n ~
4500, where n is time series length
On 5/19/06, J Dougherty [EMAIL PROTECTED] wrote:
While there is no
charge for R, it IS properly licensed properly licensed under the GPL.
At one company I was working for, I had to run all the licenses of all
the software I had on my machine, through the legal department.
When they read GNU
See
Function promptPackage() and
http://cran.r-project.org/doc/manuals/R-exts.html#Rd-format section
2.1.4 fpr writing Rd files for packages. I just did it first time for my
package caMassClass, so you can see the results in its pdf file.
Jarek Tuszynski
-Original Message-
From: [EMAIL
http://cran.r-project.org/Rlogo.jpg
In the future all you have to do (on PC) is to right click on image you
want and press properties to get the exact link.
Jarek Tuszynski
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Erin Hodgess
Sent: Wednesday,
I might be missing something but I thought that AUC was a measure for
comparing ROC curves, so there is nothing else needed to compare them. The
larger AUC is the higher correlation of 2 variables compared. No other
measures or calculations are needed.
Jarek Tuszynski
-Original Message-
You use tune function to find optimal parameters needed for particular
classification algorithm. I had more experience with tune.svm but, I
would try first to put parameters covering the whole possible range of
each variable (in which algorithm do not crash), for example c(4^-2,
4^-1, 4^0, 4^1,
The simplest way to add C (C++) code in R, that I know is by creating a
package ( even if you are not planning on distributing it). See 'Writing
R Extensions' manual (http://cran.r-project.org/manuals.html) for
details. Download source codes of packages for more examples, many of
them will have .c
I will second Roger's suggestion, colorRampPalette is a great function for
creating your own palettes. For example, Matlab's jet palette (also
available in fields package under peculiar name 'tim.colors') can be defined
by:
jet.colors = colorRampPalette(c(#7F, blue, #007FFF, cyan,
#7FFF7F,
Hi,
You should also check my msc.features.select from caMassClass package. It
has feature selection algorithm that I found useful in case of mass-spectra
data. It performs individual feature selection and/or removes highly
correlated neighbor features.
Jarek
-Original Message-
From:
Does anybody know what is relation between 'T' value calculated by
'wilcox_test' function (coin package) and more common 'W' value?
Jarek Tuszynski
library(coin)
### Tritiated Water Diffusion Across Human Chorioamnion
### Hollander Wolfe (1999), Table 4.1, page 110
water_transfer -
The name conflicts in Epi and ROC packages (2 'ROC' functions are the
problem) cause the following code
to work once, but not twice:
library(MASS); data(cats);
x = cats[,2]
y = ifelse(cats[,1]=='F',0,1)
library(Epi); ROC(x,y,grid=0)$AUC
library(ROC); AUC(rocdemo.sca(y, x, dxrule.sca))
See Also
http://finzi.psych.upenn.edu/R/library/caTools/html/combs.html
Jarek Tuszynski
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
Sent: Thursday, December 08, 2005 11:19 AM
To: Ales Ziberna
Cc: R-help
Subject: Re: [R] Finding all possible partitions of N
See Wilcox.test and Wilcox_test functions.
Jarek Tuszynski
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of John Sorkin
Sent: Friday, December 02, 2005 7:13 AM
To: r-help@stat.math.ethz.ch
Subject: [R] sign and sign rank tests
R 2.1.1 on Windows 2K
I
It is a bug, I will have to fix. I assumed that data will have column names
I can use for legend. So temporary fix is to provide column names:
library(caTools)
a-matrix(rnorm(100), 100,1)
b-rbinom(100,1,0.7)
colnames(a) = test;
colAUC(a,b,plotROC=TRUE)
Thanks for reporting it.
Jarek Tuszynski
of those solutions works for you.
Good Luck.
Jarek Tuszynski
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Sent: Wednesday, November 23, 2005 5:47 PM
To: r-help@stat.math.ethz.ch
Cc: Tuszynski, Jaroslaw W.
Subject: Re: [R] finding peaks in a simple dataset with R
See, my old post at
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/61879.html
to see a list of ROC related packages and functions. One of them should
work well for your application. All of them take data in the form:
- x - real number value returned by the classifier
- y - true labels /
I was looking once for all supported image formats, here is what I found:
Format | read file to matrix | write matrix to file | write plot to file
---|-|--|---
PNG| | | png, bitmap, GDD
JPEG
Hi,
While installing precompiled packages I often get warnings like the one in
the subject. I usually ignore them, but I still do not understand why
windows packages are build with unreleased versions of R.
Is there some way to get packages build under R-2.2.0?
What are potential problems that
]
[mailto:[EMAIL PROTECTED]
Sent: Wednesday, November 16, 2005 11:27 AM
To: Tuszynski, Jaroslaw W.
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Warning message: package '...' was built under R version
2.3.0
Tuszynski, Jaroslaw W. wrote:
Hi,
While installing precompiled packages I often get
downloaded from PA1 does not give me any warnings or
errors.
Jarek Tuszynski
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
Sent: Wednesday, November 16, 2005 1:04 PM
To: Tuszynski, Jaroslaw W.
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Warning message: package
Yes. The Statlib mirror (which I suppose is what you call PA2) appears to
be badly messed up.
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark
Thanks for a great suggestions. I guess the code you suggested would look
something like this:
fregexpr = function(pattern, filename)
{ # same as gregexpr but operating on files not strings
# Only single string 'pattern's allowed
buf.size=1024
n = file.info(filename)$size
How about 'fft' function. It is a little higher level than Fortran function
you mention, since array can be any length and you do not need to pack
complex numbers into a vector of floats.
Jarek Tuszynski
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
Hi,
I am looking for a way to search a file for position of some expression,
from within R. My current code:
sha1Pos = gregexpr(sha1, readChar(filename,
file.info(filename)$size))[[1]]
Works fine for small files, but text files I will be working with might get
up to Gb range, so I was trying
Hi,
Recently I was told by users of some of the function I wrote that they
experience crashes in places where logical vector was passed to sum
function. However on my computer those functions work just fine. After
closer look at documentation of function 'sum', I realized that it is
defined only
Try:
sd (x,na.rm=TRUE)
[1] 1.707825
Jarek
\
Jarek Tuszynski, PhD. o / \
Science Applications International Corporation \__,|
(703) 676-4192 \
[EMAIL PROTECTED]
Try Breslow OR Breslowday filetype:R -robol search in Google.
Jarek
\
Jarek Tuszynski, PhD. o / \
Science Applications International Corporation \__,|
(703) 676-4192 \
Pretty neat.
Jarek
\
Jarek Tuszynski, PhD. o / \
Science Applications International Corporation \__,|
(703) 676-4192 \
[EMAIL PROTECTED] ` \
Hi,
The latest version of R had some changes to functions readbin() and
writeBin() [which] now support raw vectors as well as filenames and
connections.. As a result I am working on retiring raw2bin and bin2raw
functions from caTools package which do exactly the same. Thanks to Prof.
Ripley for
A few suggestions:
- read.fwf function sounds like what you need, but I have never used it so I
am not sure
- use readLines and manually extract needed positions and convert them to
numbers
Jarek
\
Jarek Tuszynski, PhD.
There a re a few ways to do it without loop. Here is one:
dat = matrix(runif(100), 50,2)
dat[,1] = dat[,1] = dat[,2]
Jarek
\
Jarek Tuszynski, PhD. o / \
Science Applications International Corporation
I agree with Martin R Graph Gallery has a lot of neat stuff.
I also think there should be a on CRAN website a list of R websites. And
in a perfect world one of the search engines scope would get extended to
search them all.
Jarek
\
I suspect that loop would be the fastest since it would have the least
memory overhead. You do not want to have too many internal copies of
7000x7000 matrices.
Jarek
\
Jarek Tuszynski, PhD. o / \
Science
See write.gif function in caTools.
Jarek
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of klebyn
Sent: Wednesday, October 05, 2005 8:05 PM
To: r-help@stat.math.ethz.ch
Subject: [R] playing with R: make a animated GIF file...
Hello all
I am playing
\__,|
(703) 676-4192 \
[EMAIL PROTECTED] ` \
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Sent: Thursday, October 06, 2005 8:19 AM
To: roger bos; Tuszynski, Jaroslaw W.
Cc: ([EMAIL PROTECTED])
Subject: Re
Hi,
I was playing with Mandelbrot sets and come up with the following code, I
thought I would share:
library(fields) # for tim.colors
library(caTools) # for write.gif
m = 400 # grid size
C = complex( real=rep(seq(-1.8,0.6, length.out=m), each=m ),
imag=rep(seq(-1.2,1.2,
It is unclear what you are trying to do, but check bin2raw in caTools
package:
print(x - (1:5)*pi)
[1] 3.141593 6.283185 9.424778 12.566371
[5] 15.707963
print(y - bin2raw(x))
[1] 18 2d 44 54 fb 21 09 40 18 2d 44 54 fb 21 19
[16] 40 d2 21 33 7f 7c d9 22 40 18 2d 44 54 fb 21
\
[EMAIL PROTECTED] ` \
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Sent: Monday, October 03, 2005 11:49 AM
To: Tuszynski, Jaroslaw W.
Cc: Haiyong Xu; Help R
Subject: Re: [R] dec2bin?
On Mon, 3 Oct 2005, Tuszynski
Maybe you forgot to list the name of dependent package in 'Depends' section
of 'DESCRIPTION' file. I think that would have effect you describe. See
http://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file for
details.
Jarek
-Original Message-
From: [EMAIL PROTECTED]
See http://www.stats.uwo.ca/faculty/murdoch/software/compilingDLLs/ and R
Installation and Administration manual for details that will have to be
followed very precisely.
My own 2 cents below should be taken as fuzzy recollections, compared to
detailed directions in 2 sources above. I do not know
See colAUC in caTools (there is a problem with 1.3 version, 1.4 is on the
way). See examples for other functions calculating AUC. An alternative
approach is:
x1 = x[y==1]; n1 = length(x1);
x2 = x[y==0]; n2 = length(x2);
r = rank(c(x1,x2))
auc =
R can hold very small numbers. It is the round-off error during addition
(and other basic operations) that causes the problem. For example:
x=1e-300
x
[1] 1e-300
(x+1)-1
[1] 0
If you need a code that can be immune to round-off problems - you need to
write it yourself (please correct me if I
Hi,
I was lately debugging parts of my 'colAUC' function in caTools package, and
in a process looked into other packages for calculating Areas Under ROC
Curves (AUC). To my surprise I found at least 6 other functions:
* wilcox.test
* AUC from ROC package,
* performance
ROC package can be found in BioConductor repository.
Jarek
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Sent: Thursday, September 22, 2005 3:28 PM
To: Tuszynski, Jaroslaw W.
Cc: ([EMAIL PROTECTED]); [EMAIL PROTECTED]; [EMAIL PROTECTED]
Subject: Re: Survey of ROC
Hi,
I need to split a string into 2 strings, with the split point defined by the
last occurrence of some substring. I come up with some convoluted code to do
so:
str = Chance favors the prepared mind
sub = e
y = unlist(strsplit(str,sub))
z = cbind(paste(y[-length(y)], sub, sep=, collapse = ),
Thanks for suggestions. I suspect the regexpr version will be better than
my version, since I use it to find an string towards the end of a large (up
to ~30Mb) test/XML file.
Thanks again.
Jarek
\
Jarek Tuszynski, PhD.
I belive R, which is platform independent, does not work with any platform
specific software or languages, like Visual Basic. Can you write your code
by passing information through input/output files (CSV HML might be good
formats)?
Jarek Tuszynski
SAIC
-Original Message-
From: [EMAIL
See Writing R Extensions / Creating R package / Description file /
depends field (section 1.1.1).
Jarek
\===
Jarek Tuszynski, PhD. o / \
Science Applications International Corporation \__,|
(703) 676-4192
Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Sent: Tuesday, August 09, 2005 2:57 PM
To: Tuszynski, Jaroslaw W.
Subject: Re: [R] how to use the function from another package
Thanks very much for your help. Do I still have to write library( ) to load
the library in my code after I
Try:
n = 100;
x = matrix(seq(-10, 30, length.out=500), ncol=1)
col = colorRampPalette( c(green, white, red), space=rgb)(n) breaks =
c(seq(-10, 0, length.out=n/2)-0.5, 0, seq(0, 30, length.out=n/2)+0.5)
image(x, col=col, breaks=breaks)
See also today's discussion on R-Help about
If you have a code that takes 2 weeks to run, than it might be a case of
inefficient algorithm design. I was able to go from overnight runs (SELDI
data analysis) to 20 minute runs by identifying single inefficient function
that took most of the time, and writing it in C.
Jarek
How about:
trapz = function(x, y)
{ # computes the integral of y with respect to x using trapezoidal
integration.
idx = 2:length(x)
return (as.double( (x[idx] - x[idx-1]) %*% (y[idx] + y[idx-1])) / 2)
}
Jarek
\===
Jarek Tuszynski,
I always thought that ability to see and study the code of every package,
was a great thing about R and other open source environments. So I hope
there are no good ways of hiding the code of packages.
Jarek
\===
Jarek Tuszynski, PhD.
-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Martin Maechler
Sent: Tuesday, July 19, 2005 2:53 AM
To: Tuszynski, Jaroslaw W.
Cc: ([EMAIL PROTECTED])
Subject: Re: [R] New functions supporting GIF file format in R
JarekT == Tuszynski, Jaroslaw W [EMAIL PROTECTED]
on Mon, 18 Jul
Hi,
A minor announcement. I just added two functions for reading and writing GIF
files to my caTools package. Input and output is in the form of standard R
matrices or arrays, and standard R color-maps (palettes). The functions can
read and write both regular GIF images, as well as,
Hi,
I have a C code which produces array of integers and potentially a string,
and I have problems passing the string out. Here is the relevant part of the
code:
1 PROTECT(Ret = allocVector(INTSXP, n));
2 ret = (int*) INTEGER(Ret); /* get pointer to R's Ret */
3 for(i=0; in; i++)
I do not know if current XML package suppose to work for windows R Version
2.0.1; however, current version of XML works fine for current version of R
(2.1.1). Also, version of XML available when R Version 2.0.1 was current,
worked just fine as well. So the answer might be to update your R version.
I do not know the solution to your problem, but I had the similar problems
with image() function and most of derived functions. It seems that 'image'
function was really not meant for displaying image data, instead it was
designed to display matrices in the image format. Matlab had the same
Hi,
I was trying to figure out if there is a function in R that tests if R
object contains only integers. I though is.integer would be it, but this
function only checks whether its argument is of integer type or not. As a
result
x = (1:5)^2
is.integer(x)
Returns false. Of course
I tried your code and got different results:
system.time(ignore - f1(a))
[1] 0.83 0.09 1.08 NA NA
system.time(ignore - f2(a))
[1] 0.38 0.01 0.41 NA NA
system.time(ignore - f3(a))
[1] 0.32 0.04 0.43 NA NA
So I tried it again but with a
Hi,
I suddenly started getting strange errors while working on my caTools
package:
RCMD install C:/programs/R/rw2011/src/library/caTools
..
preparing package caTools for lazy loading
Error in file(file, r, encoding = encoding) :
all connections are
PROTECTED] `\
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Sent: Wednesday, June 29, 2005 10:07 AM
To: Tuszynski, Jaroslaw W.
Cc: r help
Subject: Re: [R] all connections are in use error during lazyload stage of
packa ge installation
On 6/29
I do not know about details of numerical accuracy of R, it is probable
related to numerical accuracy of C compiler that was used to compile it (gcc
?).
However I would like to mention that I run into some problems with accuracy
of sum and cumsum functions. See:
x = c(1, 1e20, 1e40, -1e40,
I am not sure if you can make this code shorter through R specific
programming, but You can through simple programming technique of using
functions:
pFunc = function (S, d, N, p01, p11)
{
c1-N+1/2-abs(2*S-N-1/2+d); c-1:c1;
a-ceiling((c-1+d)/2); b-ceiling((c-d)/2);
Check suppressWarnings function.
Jarek
\===
Jarek Tuszynski, PhD. o / \
Science Applications International Corporation \__,|
(703) 676-4192 \
[EMAIL PROTECTED]
Hi,
A new version of caMassClass package was released today. The package
contain pipeline for processing and classification of protein mass spectra
data.
The main change is off-spinning from the library collection of generic
functions into a new package caTools. This package, which might be
If you need work-around, than you can always save excel file in csv format
and than read that. See 'read.csv' or 'read.csv2'.
Jarek
\===
Jarek Tuszynski, PhD. o / \
Science Applications International
Hi,
Today, I performed automatic updates of packages and somehow lost class
package. I loaded a library that depended on it and got:
Error: package 'class' could not be loaded
In addition: Warning message: there is no package called 'class' in:
library(pkg, character.only = TRUE,
AM
To: Tuszynski, Jaroslaw W.
Cc: ([EMAIL PROTECTED]); '[EMAIL PROTECTED]'
Subject: Re: [R] FYI: Problems while loading package class (VR)
Tuszynski, Jaroslaw W. wrote:
Hi,
Today, I performed automatic updates of packages and somehow lost class
package. I loaded a library that depended
as attribute but its name got truncated from xsi:schemaLocation to
schemaLocation.
Jarek
-Original Message-
From: Duncan Temple Lang [mailto:[EMAIL PROTECTED]
Sent: Tuesday, May 31, 2005 11:38 AM
To: Tuszynski, Jaroslaw W.
Cc: ([EMAIL PROTECTED]); '[EMAIL PROTECTED]'
Subject: Re: [R
Hi,
Consider the following code:
require(XML)
xmlFile = paste( ?xml version=\1.0\
encoding=\ISO-8859-1\?\n,
mzXML xmlns=\a\ xmlns:xsi=\b\
xsi:schemaLocation=\c\\n,
parentFile a=\a\ b=\b\ /\n,
/mzXML\n)
Great tip. Thanks.
One problem: a lot of hits are in REBOL language (whatever it is) that also
uses R extension.
Jarek
\===
Jarek Tuszynski, PhD. o / \
Science Applications International Corporation \__,|
Hi,
I am trying to write a function to read in a whole text file as a single
string ( so I can calculate its sha1 hash function using package
digest). I need a single string containing the whole file, and so far I
was using paste(readLines(fileName), collapse = ). Unfortunately this
function
Colors predefined in R follow closely colors predefined in in HTML language.
See:
http://users.rcn.com/giant.interport/COLOR/1ColorSpecifier.html
http://www.brobstsystems.com/colors1.htm
http://www.geocities.com/html4kids/colors.htm
And probably countless other websites defining them.
Jarek
Hi,
Is there a way to perform Big-endian / Little-endian byte swap in R?
An ugly way is by using readBin/writeBin:
ByteSwap = function(X, size)
{
writeBin(X, tmp.dat)
readBin(tmp.dat, typeof(X), n = length(x), size=size,
endian=swap)
}
x =
Try:
A=matrix(c(1,3,4,5,7, -0.2, 0.8, 0.3, 0.2, 0.9 ),5,2)
A
[,1] [,2]
[1,]1 -0.2
[2,]3 0.8
[3,]4 0.3
[4,]5 0.2
[5,]7 0.9
A[order(A[,2]), ]
[,1] [,2]
[1,]1 -0.2
[2,]5 0.2
[3,]4 0.3
[4,]3 0.8
[5,]7 0.9
Jarek
On 9 Oct 2004, Brian D. Ripley wrote:
On Fri, 8 Oct 2004, Tuszynski, Jaroslaw W. wrote:
Finally a question: I still need to get moving windows mad function
faster my runmad function is not that much faster than apply/embed
combo, and that I used before, and this is where my code
Hi,
Lately my Latex engine used for checking packages stop working, and I can
not figure out how to fix it.
When creating my package (caMassClass) I get the
* checking caMassClass-manual.tex ... ERROR
LaTeX errors when creating DVI version.
This typically indicates Rd problems.
Hi,
I am trying to debug my code and looking for any tool to help me out with
it. My main problem is with the error messages I can not figure out where
they come from (what function produced them) and what do they mean. Is there
such a think as list of error messages produced by R and standard R
I think it is a problem with matrices in R and C being stored in different
row/column order
void gowsim ( double *mat, int *OBJ, int *MATDESC) {
double x [*MATDESC][*OBJ];
int i, j, nrow, ncol;
nrow = *OBJ;
ncol = *MATDESC;
/* Rebuild Matrix */
for (j=0; j ncol; j++)
Hi,
I am looking for functions that would allow me to access raw binary data of
R vectors. One way would be to use:
x = (1:10)*pi
writeBin(x, temp.bin)
r = readBin(temp.bin, raw, n=length(x)*8)
Other to write my own C code. Is there any other simpler way?
I this message
25, 2005 11:28 AM
To: 'Tuszynski, Jaroslaw W.'; r-help@stat.math.ethz.ch
Subject: RE: [R] Casting in R
Have you looked at the XML package on CRAN?
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
The business of the statistician is to catalyze the scientific learning
Hi,
I run into following problem. It seems to me that operation in the 3rd line
should be valid.
b = matrix(as.raw(0), 8,8)
q = as.raw(1:8)
b[1,] = q
Error: incompatible types in subset assignment
length(b[1,])
[1] 8
typeof(b[1,])
[1] raw
length(q)
[1] 8
typeof(q)
[1] raw
Is this a bug
Hello,
I am trying to implement function for reading/writing some XML file format.
One feature of that XML format is that a lot of binary data is stored in
Base64 format, and since R's XML package does not seem to support it, I just
wrote my own converter from raw format to Base64, and back.
Hi,
I run into a problem with R CMD Rd2dvi command: it gives me File `Rd.sty'
not found error (See the output message on the bottom). I get the same
error when running RCMD check. My system is: Windows 2000, R version
2.0.1, MiKTeX version 2.4. I do have a Rd.sty file in R_HOME/share/texm
Hi,
I run into the following problem:
data(iris)
as.array(iris[,-5])
Error in dimnames-.data.frame(`*tmp*`, value = list(c(Sepal.Length, :
invalid dimnames given for data frame
as.array(as.matrix(iris[,-5]))
When trying to convert numeric data frame to an array. Conversion to matrix
works
Hi,
Consider the following example:
sort(10:1, partial=3)
## 1 2 3 7 6 5 4 8 9 10
sort(10:1, index=T)
## $x: 1 2 3 4 5 6 7 8 9 10
## $ix: 10 9 8 7 6 5 4 3 2 1
sort(10:1, partial=3, index=T)
## 1 2 3 7 6 5 4 8 9 10
The first 2 calls gave expected returns;
Hi,
Lately I run into a problem that my code R code is spending hours performing
simple moving window statistical operations. As a result I did searched
archives for alternative (faster) ways of performing: mean, max, median and
mad operation over moving window (size 81) on a vector with about
88 matches
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